Updating workflows/variant-calling/generic-variant-calling-wgs-pe from 0.1.1 to 0.1.2 by gxydevbot · Pull Request #310 · galaxyproject/iwc

gxydevbot · 2023-11-28T01:46:46Z

Hello! This is an automated update of the following workflow: workflows/variant-calling/generic-variant-calling-wgs-pe. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6
toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.4
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1

The workflow release number has been updated from 0.1.1 to 0.1.2.

github-actions · 2024-03-05T21:41:42Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`false`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmpz4c4n4id/files/7/d/9/dataset_7d908bfb-60a4-4d5b-8cca-711b00fc6485.dat' 'ERR3485802.fastq.gz' && ln -sf '/tmp/tmpz4c4n4id/files/5/6/f/dataset_56feda9e-76e3-4092-83fc-7c3af0900fb1.dat' 'ERR3485802_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastq.gz'   -i 'ERR3485802.fastq.gz' -o first.fastq.gz  -I 'ERR3485802_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                                          &&  mv first.fastq.gz '/tmp/tmpz4c4n4id/job_working_directory/000/4/outputs/dataset_c5823120-23f5-4e3c-9a86-e323f6b92114.dat' && mv second.fastq.gz '/tmp/tmpz4c4n4id/job_working_directory/000/4/outputs/dataset_eedb4b3f-888a-4a9b-94be-53f2eb6e6182.dat'

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Traceback (most recent call last):
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1252, in prepare
    tool_evaluator.set_compute_environment(compute_environment, get_special=get_special)
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/evaluation.py", line 140, in set_compute_environment
    self._validate_incoming(incoming)
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/evaluation.py", line 283, in _validate_incoming
    visit_input_values(self.tool.inputs, incoming, validate_inputs)
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/parameters/__init__.py", line 208, in visit_input_values
    visit_input_values(
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/parameters/__init__.py", line 224, in visit_input_values
    callback_helper(
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/parameters/__init__.py", line 159, in callback_helper
    new_value = callback(**args)
                ^^^^^^^^^^^^^^^^
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/evaluation.py", line 280, in validate_inputs
    value = input.from_json(value, request_context, context)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpz4c4n4id/galaxy-dev/lib/galaxy/tools/parameters/basic.py", line 2125, in from_json
    raise ParameterValueError("specify a dataset of the required format / build for parameter", self.name)
galaxy.tools.parameters.basic.ParameterValueError: parameter 'input': specify a dataset of the required format / build for parameter

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a270df8fdb3011eeb98e8dba4e0e62ff"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpz4c4n4id/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 28042ee027c0dd35
- history_state
  - error
- invocation_id
  - 28042ee027c0dd35
- invocation_state
  - scheduled
- workflow_id
  - 28042ee027c0dd35

github-actions · 2024-06-28T12:34:58Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`false`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmpfssbqaga/files/5/d/7/dataset_5d7f8f65-aab6-43ee-ab13-5a3bb2db3f08.dat' 'ERR3485802.fastq.gz' && ln -sf '/tmp/tmpfssbqaga/files/4/7/8/dataset_478e2043-630b-4ce3-98f1-7ad29f5575c7.dat' 'ERR3485802_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastq.gz'   -i 'ERR3485802.fastq.gz' -o first.fastq.gz  -I 'ERR3485802_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                                          &&  mv first.fastq.gz '/tmp/tmpfssbqaga/job_working_directory/000/4/outputs/dataset_9672ad49-fdb6-41c3-9783-88ba91d60bb5.dat' && mv second.fastq.gz '/tmp/tmpfssbqaga/job_working_directory/000/4/outputs/dataset_6436c89c-73af-437a-8d25-e59d9f7491d6.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"74a8f1ca354111efb88e819919866c44"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpfssbqaga/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 6d1903d2a7697dff
- history_state
  - error
- invocation_id
  - 6d1903d2a7697dff
- invocation_state
  - scheduled
- workflow_id
  - 6d1903d2a7697dff

gxydevbot · 2024-09-23T14:55:43Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-09-23T15:18:06Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmpzlky_v4l/files/1/8/8/dataset_188e7349-c305-4172-8054-fdbd5e8cb3e3.dat' 'ERR3485802.fastq.gz' && ln -sf '/tmp/tmpzlky_v4l/files/4/8/a/dataset_48a90d04-02c1-4211-a892-4f753a5521c0.dat' 'ERR3485802_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastq.gz'   -i 'ERR3485802.fastq.gz' -o first.fastq.gz  -I 'ERR3485802_R2.fastq.gz' -O second.fastq.gz                                                 &&  mv first.fastq.gz '/tmp/tmpzlky_v4l/job_working_directory/000/4/outputs/dataset_464ccfaf-9e86-4d49-a2bb-7d08e2b66aee.dat' && mv second.fastq.gz '/tmp/tmpzlky_v4l/job_working_directory/000/4/outputs/dataset_4bd7be6f-be15-486a-a72d-0595b22f6498.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"baca149c79be11efa3826fbf8f5041b9"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpzlky_v4l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 8d215961e677b8ba
- history_state
  - error
- invocation_id
  - 8d215961e677b8ba
- invocation_state
  - scheduled
- workflow_id
  - 8d215961e677b8ba

gxydevbot · 2024-09-24T14:31:14Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-09-24T14:40:04Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmpv1gad90b/files/8/d/7/dataset_8d703642-fdfc-4d03-8fc3-7f112a5db3ad.dat' 'ERR3485802.fastq.gz' && ln -sf '/tmp/tmpv1gad90b/files/2/f/c/dataset_2fcc3bbb-84bf-4110-b851-27454cb22253.dat' 'ERR3485802_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastq.gz'   -i 'ERR3485802.fastq.gz' -o first.fastq.gz  -I 'ERR3485802_R2.fastq.gz' -O second.fastq.gz                                                 &&  mv first.fastq.gz '/tmp/tmpv1gad90b/job_working_directory/000/4/outputs/dataset_cfa7c789-6609-4254-b069-66ee469dccc3.dat' && mv second.fastq.gz '/tmp/tmpv1gad90b/job_working_directory/000/4/outputs/dataset_5e778c48-66e3-43a6-a1cf-6c57556f6aa1.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ad8d2ab67a8211ef975649c497eaf1d0"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpv1gad90b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - eaeec6be92929b42
- history_state
  - error
- invocation_id
  - eaeec6be92929b42
- invocation_state
  - scheduled
- workflow_id
  - eaeec6be92929b42

gxydevbot · 2024-10-07T05:31:16Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-10-07T05:39:57Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5f571730846e11efba2c6f3aee8507dd"`
chromInfo	`"/tmp/tmp5nlhwu17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5f571730846e11efba2c6f3aee8507dd"`
chromInfo	`"/tmp/tmp5nlhwu17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5f571730846e11efba2c6f3aee8507dd"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmp5nlhwu17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5f571730846e11efba2c6f3aee8507dd"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmp5nlhwu17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"5f571730846e11efba2c6f3aee8507dd"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmp5nlhwu17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmp5nlhwu17/files/b/f/f/dataset_bff48d4b-c7c1-4549-8881-3a6059bfa641.dat' 'ERR3485802.fastq.gz' && ln -sf '/tmp/tmp5nlhwu17/files/3/4/c/dataset_34cc3690-000f-417c-82cb-600a36adfc51.dat' 'ERR3485802_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastq.gz'   -i 'ERR3485802.fastq.gz' -o first.fastq.gz  -I 'ERR3485802_R2.fastq.gz' -O second.fastq.gz                                                 &&  mv first.fastq.gz '/tmp/tmp5nlhwu17/job_working_directory/000/4/outputs/dataset_dc4c8768-02a8-47d7-8515-d46a035d3d2a.dat' && mv second.fastq.gz '/tmp/tmp5nlhwu17/job_working_directory/000/4/outputs/dataset_68a00f76-c0c2-4e5f-aaa3-0fad65b62ab3.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5f571730846e11efba2c6f3aee8507dd"`
chromInfo	`"/tmp/tmp5nlhwu17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5f571730846e11efba2c6f3aee8507dd"`
chromInfo	`"/tmp/tmp5nlhwu17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5f571730846e11efba2c6f3aee8507dd"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmp5nlhwu17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5f571730846e11efba2c6f3aee8507dd"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp5nlhwu17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5f571730846e11efba2c6f3aee8507dd"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmp5nlhwu17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5f571730846e11efba2c6f3aee8507dd"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp5nlhwu17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5f571730846e11efba2c6f3aee8507dd"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmp5nlhwu17/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 4977f4417df6778e
- history_state
  - error
- invocation_id
  - 4977f4417df6778e
- invocation_state
  - scheduled
- workflow_id
  - 4977f4417df6778e

gxydevbot · 2024-10-21T05:20:06Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-10-21T05:30:29Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"633874168f6d11ef8d5edba4a076862a"`
chromInfo	`"/tmp/tmpo17czyl7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"633874168f6d11ef8d5edba4a076862a"`
chromInfo	`"/tmp/tmpo17czyl7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"633874168f6d11ef8d5edba4a076862a"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpo17czyl7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"633874168f6d11ef8d5edba4a076862a"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpo17czyl7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"vcf"`
__workflow_invocation_uuid__	`"633874168f6d11ef8d5edba4a076862a"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpo17czyl7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmpo17czyl7/files/7/f/e/dataset_7fef314f-9fe5-483f-a26a-2a75fd3995c2.dat' 'ERR3485802.fastqsanger.gz' && ln -sf '/tmp/tmpo17czyl7/files/d/a/6/dataset_da62e2f4-2b5a-4fb1-95f1-4a1fdbe5158b.dat' 'ERR3485802_R2.fastqsanger.gz' &&  cp '/tmp/tmpo17czyl7/job_working_directory/000/4/configs/tmpknp8ppy1' galaxy.json &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastqsanger.gz'   -i 'ERR3485802.fastqsanger.gz'   -I 'ERR3485802_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                                && mv first.fastqsanger.gz '/tmp/tmpo17czyl7/job_working_directory/000/4/outputs/dataset_4e5190b5-80e9-4f73-bf0d-5e7cb21b417a.dat' && mv second.fastqsanger.gz '/tmp/tmpo17czyl7/job_working_directory/000/4/outputs/dataset_6fff3634-8c52-46a2-951e-abe4e38bd661.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"633874168f6d11ef8d5edba4a076862a"`
chromInfo	`"/tmp/tmpo17czyl7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"633874168f6d11ef8d5edba4a076862a"`
chromInfo	`"/tmp/tmpo17czyl7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"633874168f6d11ef8d5edba4a076862a"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpo17czyl7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"633874168f6d11ef8d5edba4a076862a"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpo17czyl7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"633874168f6d11ef8d5edba4a076862a"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpo17czyl7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"633874168f6d11ef8d5edba4a076862a"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpo17czyl7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"633874168f6d11ef8d5edba4a076862a"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpo17czyl7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 336d113d4ce60f03
- history_state
  - error
- invocation_id
  - 336d113d4ce60f03
- invocation_state
  - scheduled
- workflow_id
  - 336d113d4ce60f03

gxydevbot · 2024-10-28T05:13:30Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-10-28T05:22:14Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"576bfe3094ec11ef9d29354a1d6173e9"`
chromInfo	`"/tmp/tmp2ab1q9r_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"576bfe3094ec11ef9d29354a1d6173e9"`
chromInfo	`"/tmp/tmp2ab1q9r_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"576bfe3094ec11ef9d29354a1d6173e9"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmp2ab1q9r_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"576bfe3094ec11ef9d29354a1d6173e9"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmp2ab1q9r_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"576bfe3094ec11ef9d29354a1d6173e9"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmp2ab1q9r_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmp2ab1q9r_/files/c/a/b/dataset_cabe3d8c-c09e-4ed3-a05e-3b37bc017d71.dat' 'ERR3485802.fastqsanger.gz' && ln -sf '/tmp/tmp2ab1q9r_/files/7/1/3/dataset_713fa8d2-08c4-4715-afa1-b30011260352.dat' 'ERR3485802_R2.fastqsanger.gz' &&  cp '/tmp/tmp2ab1q9r_/job_working_directory/000/4/configs/tmpip9ujeo9' galaxy.json &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastqsanger.gz'   -i 'ERR3485802.fastqsanger.gz'   -I 'ERR3485802_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                                && mv first.fastqsanger.gz '/tmp/tmp2ab1q9r_/job_working_directory/000/4/outputs/dataset_a7f9eb72-faad-4b69-9177-0c6701477ffe.dat' && mv second.fastqsanger.gz '/tmp/tmp2ab1q9r_/job_working_directory/000/4/outputs/dataset_1ad6cc85-99e4-4662-9768-746c5cfc4f8a.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"576bfe3094ec11ef9d29354a1d6173e9"`
chromInfo	`"/tmp/tmp2ab1q9r_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"576bfe3094ec11ef9d29354a1d6173e9"`
chromInfo	`"/tmp/tmp2ab1q9r_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"576bfe3094ec11ef9d29354a1d6173e9"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmp2ab1q9r_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"576bfe3094ec11ef9d29354a1d6173e9"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp2ab1q9r_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"576bfe3094ec11ef9d29354a1d6173e9"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmp2ab1q9r_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"576bfe3094ec11ef9d29354a1d6173e9"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp2ab1q9r_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"576bfe3094ec11ef9d29354a1d6173e9"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmp2ab1q9r_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 9149d93cc4f2cf5c
- history_state
  - error
- invocation_id
  - 9149d93cc4f2cf5c
- invocation_state
  - scheduled
- workflow_id
  - 9149d93cc4f2cf5c

gxydevbot · 2024-11-18T05:43:28Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-11-18T05:50:29Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d05fbda6a57011ef8bc8efeb99dce3a1"`
chromInfo	`"/tmp/tmp4aihula_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d05fbda6a57011ef8bc8efeb99dce3a1"`
chromInfo	`"/tmp/tmp4aihula_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d05fbda6a57011ef8bc8efeb99dce3a1"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmp4aihula_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d05fbda6a57011ef8bc8efeb99dce3a1"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmp4aihula_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d05fbda6a57011ef8bc8efeb99dce3a1"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmp4aihula_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmp4aihula_/files/3/2/b/dataset_32b9731f-43d9-4752-bab0-fa32896990e0.dat' 'ERR3485802.fastqsanger.gz' && ln -sf '/tmp/tmp4aihula_/files/f/1/a/dataset_f1a29417-c308-4837-a1db-730600500ace.dat' 'ERR3485802_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastqsanger.gz'  -i 'ERR3485802.fastqsanger.gz'   -I 'ERR3485802_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                                && mv first.fastqsanger.gz '/tmp/tmp4aihula_/job_working_directory/000/4/outputs/dataset_404e2ca5-6b1e-4e04-abc2-c9d8a5e40868.dat' && mv second.fastqsanger.gz '/tmp/tmp4aihula_/job_working_directory/000/4/outputs/dataset_598229da-e6aa-40e1-95b8-81a2ee9c7fb4.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d05fbda6a57011ef8bc8efeb99dce3a1"`
chromInfo	`"/tmp/tmp4aihula_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d05fbda6a57011ef8bc8efeb99dce3a1"`
chromInfo	`"/tmp/tmp4aihula_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d05fbda6a57011ef8bc8efeb99dce3a1"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmp4aihula_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d05fbda6a57011ef8bc8efeb99dce3a1"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp4aihula_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d05fbda6a57011ef8bc8efeb99dce3a1"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmp4aihula_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d05fbda6a57011ef8bc8efeb99dce3a1"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp4aihula_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d05fbda6a57011ef8bc8efeb99dce3a1"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmp4aihula_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 3c3978793f2a67ad
- history_state
  - error
- invocation_id
  - 3c3978793f2a67ad
- invocation_state
  - scheduled
- workflow_id
  - 3c3978793f2a67ad

gxydevbot · 2025-01-27T05:44:55Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2025-01-27T05:55:04Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"16302f1cdc7311ef96aa6045bd05d7a0"`
chromInfo	`"/tmp/tmpo7vpfmee/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"16302f1cdc7311ef96aa6045bd05d7a0"`
chromInfo	`"/tmp/tmpo7vpfmee/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"16302f1cdc7311ef96aa6045bd05d7a0"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpo7vpfmee/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"16302f1cdc7311ef96aa6045bd05d7a0"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpo7vpfmee/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"16302f1cdc7311ef96aa6045bd05d7a0"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpo7vpfmee/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmpo7vpfmee/files/8/0/6/dataset_80677181-d27d-467a-a6a1-cb6855305c16.dat' 'ERR3485802.fastqsanger.gz' && ln -sf '/tmp/tmpo7vpfmee/files/9/b/8/dataset_9b8c1418-a7be-4079-9de5-ae59241091ee.dat' 'ERR3485802_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastqsanger.gz'  -i 'ERR3485802.fastqsanger.gz'   -I 'ERR3485802_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                                && mv first.fastqsanger.gz '/tmp/tmpo7vpfmee/job_working_directory/000/4/outputs/dataset_8e2965cc-4dfb-4016-8b2e-453b0bb73aaf.dat' && mv second.fastqsanger.gz '/tmp/tmpo7vpfmee/job_working_directory/000/4/outputs/dataset_18c8acdc-8303-428c-8ad6-222783f564b3.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"16302f1cdc7311ef96aa6045bd05d7a0"`
chromInfo	`"/tmp/tmpo7vpfmee/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"16302f1cdc7311ef96aa6045bd05d7a0"`
chromInfo	`"/tmp/tmpo7vpfmee/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"16302f1cdc7311ef96aa6045bd05d7a0"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpo7vpfmee/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"16302f1cdc7311ef96aa6045bd05d7a0"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpo7vpfmee/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"16302f1cdc7311ef96aa6045bd05d7a0"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpo7vpfmee/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"16302f1cdc7311ef96aa6045bd05d7a0"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpo7vpfmee/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"16302f1cdc7311ef96aa6045bd05d7a0"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpo7vpfmee/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 157ca8954fc1ed77
- history_state
  - error
- invocation_id
  - 157ca8954fc1ed77
- invocation_state
  - scheduled
- workflow_id
  - 157ca8954fc1ed77

gxydevbot · 2025-02-10T05:52:53Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2025-02-10T06:05:24Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d8e70808e77411efb46f00224853aab3"`
chromInfo	`"/tmp/tmpifhyy9vr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d8e70808e77411efb46f00224853aab3"`
chromInfo	`"/tmp/tmpifhyy9vr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d8e70808e77411efb46f00224853aab3"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpifhyy9vr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d8e70808e77411efb46f00224853aab3"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpifhyy9vr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d8e70808e77411efb46f00224853aab3"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpifhyy9vr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmpifhyy9vr/files/4/a/f/dataset_4af32270-3701-442a-b22e-733428c27651.dat' 'ERR3485802.fastqsanger.gz' && ln -sf '/tmp/tmpifhyy9vr/files/5/3/4/dataset_53450e13-d31c-4ecf-b5d7-116cd9ffe256.dat' 'ERR3485802_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastqsanger.gz'  -i 'ERR3485802.fastqsanger.gz'   -I 'ERR3485802_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                                && mv first.fastqsanger.gz '/tmp/tmpifhyy9vr/job_working_directory/000/4/outputs/dataset_14746131-ace9-4c94-8d49-d93511ffcb54.dat' && mv second.fastqsanger.gz '/tmp/tmpifhyy9vr/job_working_directory/000/4/outputs/dataset_e8ec69ec-7f92-4196-af6c-285f1087c430.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d8e70808e77411efb46f00224853aab3"`
chromInfo	`"/tmp/tmpifhyy9vr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d8e70808e77411efb46f00224853aab3"`
chromInfo	`"/tmp/tmpifhyy9vr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d8e70808e77411efb46f00224853aab3"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpifhyy9vr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d8e70808e77411efb46f00224853aab3"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpifhyy9vr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d8e70808e77411efb46f00224853aab3"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpifhyy9vr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d8e70808e77411efb46f00224853aab3"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpifhyy9vr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d8e70808e77411efb46f00224853aab3"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpifhyy9vr/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 3e77761d0c910f2a
- history_state
  - error
- invocation_id
  - 3e77761d0c910f2a
- invocation_state
  - scheduled
- workflow_id
  - 3e77761d0c910f2a

gxydevbot · 2025-02-17T05:59:33Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2025-02-17T06:12:03Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d0584824ecf511ef82cc000d3a19435f"`
chromInfo	`"/tmp/tmp5jx2rtyb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d0584824ecf511ef82cc000d3a19435f"`
chromInfo	`"/tmp/tmp5jx2rtyb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d0584824ecf511ef82cc000d3a19435f"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmp5jx2rtyb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d0584824ecf511ef82cc000d3a19435f"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmp5jx2rtyb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d0584824ecf511ef82cc000d3a19435f"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmp5jx2rtyb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Step 3: Name for genome database:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -sf '/tmp/tmp5jx2rtyb/files/e/2/e/dataset_e2e295b3-dada-42e9-9833-b2b775a40351.dat' 'ERR3485802.fastqsanger.gz' && ln -sf '/tmp/tmp5jx2rtyb/files/f/f/3/dataset_ff3fb8ee-9472-4e1c-a4af-cbb85217c4e7.dat' 'ERR3485802_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastqsanger.gz'  -i 'ERR3485802.fastqsanger.gz'   -I 'ERR3485802_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                                && mv first.fastqsanger.gz '/tmp/tmp5jx2rtyb/job_working_directory/000/4/outputs/dataset_b6b318b2-351a-4409-a7ea-238378823795.dat' && mv second.fastqsanger.gz '/tmp/tmp5jx2rtyb/job_working_directory/000/4/outputs/dataset_4c88713f-c452-4832-a051-ec68272a49e5.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d0584824ecf511ef82cc000d3a19435f"`
chromInfo	`"/tmp/tmp5jx2rtyb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	`{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}`
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d0584824ecf511ef82cc000d3a19435f"`
chromInfo	`"/tmp/tmp5jx2rtyb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d0584824ecf511ef82cc000d3a19435f"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmp5jx2rtyb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d0584824ecf511ef82cc000d3a19435f"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp5jx2rtyb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d0584824ecf511ef82cc000d3a19435f"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmp5jx2rtyb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d0584824ecf511ef82cc000d3a19435f"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp5jx2rtyb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"d0584824ecf511ef82cc000d3a19435f"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmp5jx2rtyb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 25b2324ffaca25aa
- history_state
  - error
- invocation_id
  - 25b2324ffaca25aa
- invocation_state
  - scheduled
- workflow_id
  - 25b2324ffaca25aa

github-actions · 2026-09-07T12:53:17Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled
Step 3: Name for genome database:
- step_state: scheduled

Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.6+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/fastp:1.3.6--h43da1c4_0

Command Line:

ln -sf '/tmp/tmpsg9pqqon/files/0/d/a/dataset_0da11211-f8be-4d6b-996e-f0b4fc443836.dat' 'ERR3485802.fastqsanger.gz' && ln -sf '/tmp/tmpsg9pqqon/files/7/a/e/dataset_7ae88674-9c0a-436c-9dfc-32b4e60ea56f.dat' 'ERR3485802_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'ERR3485802.fastqsanger.gz'  -i 'ERR3485802.fastqsanger.gz'   -I 'ERR3485802_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                    --dont_eval_duplication                  && mv first.fastqsanger.gz '/tmp/tmpsg9pqqon/job_working_directory/000/4/outputs/dataset_11fecafb-5da7-43da-8971-75184c8780c4.dat' && mv second.fastqsanger.gz '/tmp/tmpsg9pqqon/job_working_directory/000/4/outputs/dataset_fe6f31c5-1683-4b16-88dd-48db5a06eabd.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 2500
total bases: 376657
Q20 bases: 371549(98.6439%)
Q30 bases: 370136(98.2687%)
Q40 bases: 1744(0.463021%)

Read2 before filtering:
total reads: 2500
total bases: 376700
Q20 bases: 355761(94.4415%)
Q30 bases: 351290(93.2546%)
Q40 bases: 131(0.0347757%)

Read1 after filtering:
total reads: 2492
total bases: 375257
Q20 bases: 370593(98.7571%)
Q30 bases: 369355(98.4272%)
Q40 bases: 1744(0.464748%)

Read2 after filtering:
total reads: 2492
total bases: 375297
Q20 bases: 355082(94.6136%)
Q30 bases: 350732(93.4545%)
Q40 bases: 131(0.0349057%)

Filtering result:
reads passed filter: 4984
reads failed due to low quality: 16
reads failed due to too many N: 0
reads failed due to too short: 0
reads failed due to adapter dimer: 0
reads with adapter trimmed: 30
bases trimmed due to adapters: 393

Insert size peak (evaluated by paired-end reads): 263

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title ERR3485802.fastqsanger.gz -i ERR3485802.fastqsanger.gz -I ERR3485802_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz --dont_eval_duplication 
fastp v1.3.6, time used: 0 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b6d3d5c4aaba11f1baa170a8a5aeedac"`
chromInfo	`"/tmp/tmpsg9pqqon/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
duplicated_reads	`{"handling_options": {"__current_case__": 0, "eval_dups": "--dont_eval_duplication"}}`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_front_select": {"__current_case__": 1, "cut_front": ""}, "cut_right_select": {"__current_case__": 1, "cut_right": ""}, "cut_tail_select": {"__current_case__": 1, "cut_tail": ""}}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b6d3d5c4aaba11f1baa170a8a5aeedac"`
chromInfo	`"/tmp/tmpsg9pqqon/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b6d3d5c4aaba11f1baa170a8a5aeedac"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpsg9pqqon/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b6d3d5c4aaba11f1baa170a8a5aeedac"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpsg9pqqon/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b6d3d5c4aaba11f1baa170a8a5aeedac"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpsg9pqqon/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b6d3d5c4aaba11f1baa170a8a5aeedac"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpsg9pqqon/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b6d3d5c4aaba11f1baa170a8a5aeedac"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpsg9pqqon/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy4):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b6d3d5c4aaba11f1baa170a8a5aeedac"`
chromInfo	`"/tmp/tmpsg9pqqon/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
image_content_input	`None`
png_plots	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 8, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 25, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 18, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b6d3d5c4aaba11f1baa170a8a5aeedac"`
chromInfo	`"/tmp/tmpsg9pqqon/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b6d3d5c4aaba11f1baa170a8a5aeedac"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpsg9pqqon/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b6d3d5c4aaba11f1baa170a8a5aeedac"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpsg9pqqon/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b6d3d5c4aaba11f1baa170a8a5aeedac"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpsg9pqqon/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_gene_stats	`false`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Other invocation details
- history_id
  - ea21b5fe2cb3356b
- history_state
  - error
- invocation_id
  - ea21b5fe2cb3356b
- invocation_state
  - scheduled
- workflow_id
  - ea21b5fe2cb3356b

…m 0.1.1 to 0.1.2

gxydevbot · 2026-09-21T13:20:52Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2026-09-21T13:35:14Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled
Step 3: Name for genome database:
- step_state: scheduled

Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.7+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/fastp:1.3.7
```

Command Line:

ln -sf '/tmp/tmp0i8v5xff/files/8/0/d/dataset_80d954f9-34e7-49b8-bd3d-290231883059.dat' 'ERR3485802.fastqsanger.gz' && ln -sf '/tmp/tmp0i8v5xff/files/1/0/c/dataset_10c6fc21-4ebe-4c53-80eb-94bf876167a7.dat' 'ERR3485802_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'ERR3485802.fastqsanger.gz'  -i 'ERR3485802.fastqsanger.gz'   -I 'ERR3485802_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                    --dont_eval_duplication                  && mv first.fastqsanger.gz '/tmp/tmp0i8v5xff/job_working_directory/000/4/outputs/dataset_11ec40c0-4f56-4372-a147-65f90d0b9e4c.dat' && mv second.fastqsanger.gz '/tmp/tmp0i8v5xff/job_working_directory/000/4/outputs/dataset_f81c0b86-9a4a-4cc8-ab31-79ea244d59e7.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 2500
total bases: 376657
Q20 bases: 371549(98.6439%)
Q30 bases: 370136(98.2687%)
Q40 bases: 1744(0.463021%)

Read2 before filtering:
total reads: 2500
total bases: 376700
Q20 bases: 355761(94.4415%)
Q30 bases: 351290(93.2546%)
Q40 bases: 131(0.0347757%)

Read1 after filtering:
total reads: 2492
total bases: 375257
Q20 bases: 370593(98.7571%)
Q30 bases: 369355(98.4272%)
Q40 bases: 1744(0.464748%)

Read2 after filtering:
total reads: 2492
total bases: 375297
Q20 bases: 355082(94.6136%)
Q30 bases: 350732(93.4545%)
Q40 bases: 131(0.0349057%)

Filtering result:
reads passed filter: 4984
reads failed due to low quality: 16
reads failed due to too many N: 0
reads failed due to too short: 0
reads failed due to adapter dimer: 0
reads with adapter trimmed: 30
bases trimmed due to adapters: 393

Insert size peak (evaluated by paired-end reads): 263

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title ERR3485802.fastqsanger.gz -i ERR3485802.fastqsanger.gz -I ERR3485802_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz --dont_eval_duplication 
fastp v1.3.7, time used: 0 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ed6b42d2b5c011f199ae7c1e52412a17"`
chromInfo	`"/tmp/tmp0i8v5xff/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
duplicated_reads	`{"handling_options": {"__current_case__": 0, "eval_dups": "--dont_eval_duplication"}}`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_front_select": {"__current_case__": 1, "cut_front": ""}, "cut_right_select": {"__current_case__": 1, "cut_right": ""}, "cut_tail_select": {"__current_case__": 1, "cut_tail": ""}}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ed6b42d2b5c011f199ae7c1e52412a17"`
chromInfo	`"/tmp/tmp0i8v5xff/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ed6b42d2b5c011f199ae7c1e52412a17"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmp0i8v5xff/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ed6b42d2b5c011f199ae7c1e52412a17"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp0i8v5xff/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ed6b42d2b5c011f199ae7c1e52412a17"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmp0i8v5xff/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ed6b42d2b5c011f199ae7c1e52412a17"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp0i8v5xff/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ed6b42d2b5c011f199ae7c1e52412a17"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmp0i8v5xff/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy4):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ed6b42d2b5c011f199ae7c1e52412a17"`
chromInfo	`"/tmp/tmp0i8v5xff/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
image_content_input	`None`
png_plots	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 8, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 25, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 18, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ed6b42d2b5c011f199ae7c1e52412a17"`
chromInfo	`"/tmp/tmp0i8v5xff/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ed6b42d2b5c011f199ae7c1e52412a17"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmp0i8v5xff/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ed6b42d2b5c011f199ae7c1e52412a17"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmp0i8v5xff/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ed6b42d2b5c011f199ae7c1e52412a17"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmp0i8v5xff/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_gene_stats	`false`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Other invocation details
- history_id
  - 07c5d6d1db2899c3
- history_state
  - error
- invocation_id
  - 07c5d6d1db2899c3
- invocation_state
  - scheduled
- workflow_id
  - 07c5d6d1db2899c3

…lling-wgs-pe

github-actions · 2026-10-16T08:50:06Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled
Step 3: Name for genome database:
- step_state: scheduled

Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.7+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/fastp:1.3.7
```

Command Line:

ln -sf '/tmp/tmp23vqzj4o/files/6/f/7/dataset_6f783542-bd21-4b43-8685-9b6eabcff229.dat' 'ERR3485802.fastqsanger.gz' && ln -sf '/tmp/tmp23vqzj4o/files/5/b/8/dataset_5b8bdd14-fd0a-4d23-9f38-889cdd849d7a.dat' 'ERR3485802_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'ERR3485802.fastqsanger.gz'  -i 'ERR3485802.fastqsanger.gz'   -I 'ERR3485802_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                    --dont_eval_duplication                  && mv first.fastqsanger.gz '/tmp/tmp23vqzj4o/job_working_directory/000/4/outputs/dataset_d408eebe-8c73-409b-8a23-e2d3b721efd4.dat' && mv second.fastqsanger.gz '/tmp/tmp23vqzj4o/job_working_directory/000/4/outputs/dataset_f5899758-e206-4d32-8a05-7da7ccbc6106.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 2500
total bases: 376657
Q20 bases: 371549(98.6439%)
Q30 bases: 370136(98.2687%)
Q40 bases: 1744(0.463021%)

Read2 before filtering:
total reads: 2500
total bases: 376700
Q20 bases: 355761(94.4415%)
Q30 bases: 351290(93.2546%)
Q40 bases: 131(0.0347757%)

Read1 after filtering:
total reads: 2492
total bases: 375257
Q20 bases: 370593(98.7571%)
Q30 bases: 369355(98.4272%)
Q40 bases: 1744(0.464748%)

Read2 after filtering:
total reads: 2492
total bases: 375297
Q20 bases: 355082(94.6136%)
Q30 bases: 350732(93.4545%)
Q40 bases: 131(0.0349057%)

Filtering result:
reads passed filter: 4984
reads failed due to low quality: 16
reads failed due to too many N: 0
reads failed due to too short: 0
reads failed due to adapter dimer: 0
reads with adapter trimmed: 30
bases trimmed due to adapters: 393

Insert size peak (evaluated by paired-end reads): 263

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title ERR3485802.fastqsanger.gz -i ERR3485802.fastqsanger.gz -I ERR3485802_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz --dont_eval_duplication 
fastp v1.3.7, time used: 0 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5692a524c93b11f1a9dd3833c5d8dabf"`
chromInfo	`"/tmp/tmp23vqzj4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
duplicated_reads	`{"handling_options": {"__current_case__": 0, "eval_dups": "--dont_eval_duplication"}}`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_front_select": {"__current_case__": 1, "cut_front": ""}, "cut_right_select": {"__current_case__": 1, "cut_right": ""}, "cut_tail_select": {"__current_case__": 1, "cut_tail": ""}}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5692a524c93b11f1a9dd3833c5d8dabf"`
chromInfo	`"/tmp/tmp23vqzj4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5692a524c93b11f1a9dd3833c5d8dabf"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmp23vqzj4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5692a524c93b11f1a9dd3833c5d8dabf"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp23vqzj4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5692a524c93b11f1a9dd3833c5d8dabf"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmp23vqzj4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5692a524c93b11f1a9dd3833c5d8dabf"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp23vqzj4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5692a524c93b11f1a9dd3833c5d8dabf"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmp23vqzj4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy4):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5692a524c93b11f1a9dd3833c5d8dabf"`
chromInfo	`"/tmp/tmp23vqzj4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
image_content_input	`None`
png_plots	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 8, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 25, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 18, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5692a524c93b11f1a9dd3833c5d8dabf"`
chromInfo	`"/tmp/tmp23vqzj4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5692a524c93b11f1a9dd3833c5d8dabf"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmp23vqzj4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5692a524c93b11f1a9dd3833c5d8dabf"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmp23vqzj4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"5692a524c93b11f1a9dd3833c5d8dabf"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmp23vqzj4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_gene_stats	`false`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Other invocation details
- history_id
  - 9a2a01057f2a4ec0
- history_state
  - error
- invocation_id
  - 9a2a01057f2a4ec0
- invocation_state
  - scheduled
- workflow_id
  - 9a2a01057f2a4ec0

iuc/lofreq_call/lofreq_call/2.1.5+galaxy3: b11e8e9c23bf -> 14af3b671440 iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0: 7dfca164d2e3 -> 3e0e44d971d5 iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1: 971e07ca4456 -> 4165b712b569 iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0: aa35ee7f3ab2 -> 3330ebe7c0c7

github-actions · 2026-10-16T12:55:08Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled
Step 3: Name for genome database:
- step_state: scheduled

Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.7+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/fastp:1.3.7
```

Command Line:

ln -sf '/tmp/tmp3ov999s3/files/5/7/5/dataset_575c3287-e736-4be1-8d60-26ffd16bb93f.dat' 'ERR3485802.fastqsanger.gz' && ln -sf '/tmp/tmp3ov999s3/files/4/f/6/dataset_4f614a9c-a410-408b-974f-0fc53ad82226.dat' 'ERR3485802_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'ERR3485802.fastqsanger.gz'  -i 'ERR3485802.fastqsanger.gz'   -I 'ERR3485802_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                    --dont_eval_duplication                  && mv first.fastqsanger.gz '/tmp/tmp3ov999s3/job_working_directory/000/4/outputs/dataset_76d26a2f-eddc-44c6-811e-7eacbcfad9c0.dat' && mv second.fastqsanger.gz '/tmp/tmp3ov999s3/job_working_directory/000/4/outputs/dataset_efae3b3b-1e9b-4813-98bc-2d66c3b3bbf0.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 2500
total bases: 376657
Q20 bases: 371549(98.6439%)
Q30 bases: 370136(98.2687%)
Q40 bases: 1744(0.463021%)

Read2 before filtering:
total reads: 2500
total bases: 376700
Q20 bases: 355761(94.4415%)
Q30 bases: 351290(93.2546%)
Q40 bases: 131(0.0347757%)

Read1 after filtering:
total reads: 2492
total bases: 375257
Q20 bases: 370593(98.7571%)
Q30 bases: 369355(98.4272%)
Q40 bases: 1744(0.464748%)

Read2 after filtering:
total reads: 2492
total bases: 375297
Q20 bases: 355082(94.6136%)
Q30 bases: 350732(93.4545%)
Q40 bases: 131(0.0349057%)

Filtering result:
reads passed filter: 4984
reads failed due to low quality: 16
reads failed due to too many N: 0
reads failed due to too short: 0
reads failed due to adapter dimer: 0
reads with adapter trimmed: 30
bases trimmed due to adapters: 393

Insert size peak (evaluated by paired-end reads): 263

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title ERR3485802.fastqsanger.gz -i ERR3485802.fastqsanger.gz -I ERR3485802_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz --dont_eval_duplication 
fastp v1.3.7, time used: 0 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8dddf298c96011f1a9dd000d3a96d7dc"`
chromInfo	`"/tmp/tmp3ov999s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
duplicated_reads	`{"handling_options": {"__current_case__": 0, "eval_dups": "--dont_eval_duplication"}}`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_front_select": {"__current_case__": 1, "cut_front": ""}, "cut_right_select": {"__current_case__": 1, "cut_right": ""}, "cut_tail_select": {"__current_case__": 1, "cut_tail": ""}}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8dddf298c96011f1a9dd000d3a96d7dc"`
chromInfo	`"/tmp/tmp3ov999s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": null, "input_type_selector": "gb", "remove_version": true}`

Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8dddf298c96011f1a9dd000d3a96d7dc"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmp3ov999s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8dddf298c96011f1a9dd000d3a96d7dc"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp3ov999s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8dddf298c96011f1a9dd000d3a96d7dc"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmp3ov999s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8dddf298c96011f1a9dd000d3a96d7dc"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmp3ov999s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8dddf298c96011f1a9dd000d3a96d7dc"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmp3ov999s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy4):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8dddf298c96011f1a9dd000d3a96d7dc"`
chromInfo	`"/tmp/tmp3ov999s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
image_content_input	`None`
png_plots	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 8, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 25, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 18, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8dddf298c96011f1a9dd000d3a96d7dc"`
chromInfo	`"/tmp/tmp3ov999s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8dddf298c96011f1a9dd000d3a96d7dc"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmp3ov999s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8dddf298c96011f1a9dd000d3a96d7dc"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmp3ov999s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8dddf298c96011f1a9dd000d3a96d7dc"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmp3ov999s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_gene_stats	`false`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Other invocation details
- history_id
  - 45f6baaf276d0efa
- history_state
  - error
- invocation_id
  - 45f6baaf276d0efa
- invocation_state
  - scheduled
- workflow_id
  - 45f6baaf276d0efa

…bk -> input)

github-actions · 2026-10-16T18:56:57Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Problems:

Output with path /tmp/tmp77_b1hpz/SnpEff eff on dataset 12__3301736f-8a9d-4336-9d5f-7ef0caa5b8e3.vcf different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/variant-calling/generic-variant-calling-wgs-pe/test-data/SnpEff variants.vcf v. /tmp/tmpw_59p_xySnpEff variants.vcf )
--- local_file
+++ history_data
@@ -1,6 +1,7 @@
 ##fileformat=VCFv4.0
-##fileDate=20220601
-##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r KP849471:1-49312 -o /tmp/lofreq2_call_parallelvorvr7qw/0.vcf.gz reads.bam 
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20261016
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r KP849471:1-49312 -o /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/0.vcf.gz reads.bam 
 ##reference=reference.fa
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
@@ -11,104 +12,112 @@
 ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
 ##FILTER=<ID=min_snvqual_51,Description="Minimum SNV Quality (Phred) 51">
 ##FILTER=<ID=min_indelqual_42,Description="Minimum Indel Quality (Phred) 42">
+##contig=<ID=KP849471>
+##FILTER=<ID=min_snvqual_46,Description="Minimum SNV Quality (Phred) 46">
+##FILTER=<ID=min_indelqual_39,Description="Minimum Indel Quality (Phred) 39">
+##FILTER=<ID=min_snvqual_50,Description="Minimum SNV Quality (Phred) 50">
+##FILTER=<ID=min_snvqual_55,Description="Minimum SNV Quality (Phred) 55">
+##FILTER=<ID=min_indelqual_44,Description="Minimum Indel Quality (Phred) 44">
+##bcftools_concatVersion=1.24+htslib-1.24
+##bcftools_concatCommand=concat -a -O z -o /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/concat.vcf.gz /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/0.vcf.gz /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/1.vcf.gz /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/2.vcf.gz /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/3.vcf.gz; Date=Fri Oct 16 18:23:35 2026
 ##FILTER=<ID=min_snvqual_58,Description="Minimum SNV Quality (Phred) 58">
********
*SNIP *
********
+KP849471	177509	.	C	T	67.0	PASS	DP=5;AF=0.4;SB=0;DP4=2,1,1,1;EFF=(MODIFIER||||||||||T|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	177899	.	G	GTT	132.0	PASS	DP=6;AF=0.833333;SB=0;DP4=0,1,1,4;INDEL;HRUN=9;EFF=(MODIFIER||||||||||GTT|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	182243	.	C	A	172.0	PASS	DP=5;AF=1;SB=0;DP4=0,0,2,3;EFF=(MODIFIER||||||||||A|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	183447	.	T	TTAC	203.0	PASS	DP=5;AF=1;SB=0;DP4=0,0,3,2;INDEL;HRUN=2;EFF=(MODIFIER||||||||||TTAC|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	183510	.	A	G	65.0	PASS	DP=7;AF=0.285714;SB=0;DP4=2,3,1,1;EFF=(MODIFIER||||||||||G|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	183610	.	C	T	188.0	PASS	DP=5;AF=1;SB=0;DP4=0,0,1,4;EFF=(MODIFIER||||||||||T|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	188241	.	AAATAT	A	163.0	PASS	DP=5;AF=0.8;SB=6;DP4=1,0,0,4;INDEL;HRUN=3;EFF=(MODIFIER||||||||||A|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	188316	.	G	T	189.0	PASS	DP=5;AF=1;SB=0;DP4=0,0,1,4;EFF=(MODIFIER||||||||||T|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	189106	.	T	C	194.0	PASS	DP=5;AF=1;SB=0;DP4=0,0,1,4;EFF=(MODIFIER||||||||||C|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	189509	.	T	C	180.0	PASS	DP=5;AF=1;SB=0;DP4=0,0,3,2;EFF=(MODIFIER||||||||||C|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	189795	.	G	A	270.0	PASS	DP=7;AF=1;SB=0;DP4=0,0,5,2;EFF=(MODIFIER||||||||||A|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	189808	.	C	A	237.0	PASS	DP=8;AF=0.875;SB=0;DP4=0,0,5,3;EFF=(MODIFIER||||||||||A|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	189835	.	T	A	62.0	PASS	DP=7;AF=0.285714;SB=0;DP4=2,3,1,1;EFF=(MODIFIER||||||||||A|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	189951	.	TAC	T	238.0	PASS	DP=8;AF=0.75;SB=0;DP4=1,1,2,4;INDEL;HRUN=1;EFF=(MODIFIER||||||||||T|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	189971	.	GAT	G	179.0	PASS	DP=5;AF=1;SB=0;DP4=0,1,2,3;INDEL;HRUN=1;EFF=(MODIFIER||||||||||G|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	190055	.	A	G	177.0	PASS	DP=5;AF=1;SB=0;DP4=0,0,2,3;EFF=(MODIFIER||||||||||G|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	190237	.	C	T	229.0	PASS	DP=6;AF=1;SB=0;DP4=0,0,3,3;EFF=(MODIFIER||||||||||T|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	190294	.	T	TA	248.0	PASS	DP=7;AF=1;SB=0;DP4=0,0,4,3;INDEL;HRUN=6;EFF=(MODIFIER||||||||||TA|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	190302	.	T	G	205.0	PASS	DP=8;AF=1;SB=0;DP4=0,0,5,3;EFF=(MODIFIER||||||||||G|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	190494	.	G	T	258.0	PASS	DP=7;AF=1;SB=0;DP4=0,0,4,3;EFF=(MODIFIER||||||||||T|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	190546	.	T	A	262.0	PASS	DP=7;AF=1;SB=0;DP4=0,0,3,4;EFF=(MODIFIER||||||||||A|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	190851	.	GA	G	88.0	PASS	DP=5;AF=0.8;SB=0;DP4=0,1,1,3;INDEL;HRUN=8;EFF=(MODIFIER||||||||||G|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	190951	.	G	A	182.0	sb_fdr	DP=7;AF=1;SB=2147483647;DP4=0,0,0,7;EFF=(MODIFIER||||||||||A|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	190964	.	C	T	190.0	PASS	DP=8;AF=1;SB=0;DP4=0,0,1,7;EFF=(MODIFIER||||||||||T|ERROR_CHROMOSOME_NOT_FOUND)
+KP849471	191034	.	C	T	111.0	PASS	DP=5;AF=1;SB=0;DP4=0,0,1,4;EFF=(MODIFIER||||||||||T|ERROR_CHROMOSOME_NOT_FOUND)

Output with path /tmp/tmp8doh56ob/Call variants on dataset 13__41722f6d-1488-4d09-b5b6-b32dee4db308.vcf different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/variant-calling/generic-variant-calling-wgs-pe/test-data/called_variants.vcf v. /tmp/tmpvk_o5xugcalled_variants.vcf )
--- local_file
+++ history_data
@@ -1,6 +1,7 @@
 ##fileformat=VCFv4.0
-##fileDate=20220601
-##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r KP849471:1-49312 -o /tmp/lofreq2_call_parallelvorvr7qw/0.vcf.gz reads.bam 
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20261016
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r KP849471:1-49312 -o /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/0.vcf.gz reads.bam 
 ##reference=reference.fa
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
@@ -11,98 +12,106 @@
 ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
 ##FILTER=<ID=min_snvqual_51,Description="Minimum SNV Quality (Phred) 51">
 ##FILTER=<ID=min_indelqual_42,Description="Minimum Indel Quality (Phred) 42">
+##contig=<ID=KP849471>
+##FILTER=<ID=min_snvqual_46,Description="Minimum SNV Quality (Phred) 46">
+##FILTER=<ID=min_indelqual_39,Description="Minimum Indel Quality (Phred) 39">
+##FILTER=<ID=min_snvqual_50,Description="Minimum SNV Quality (Phred) 50">
+##FILTER=<ID=min_snvqual_55,Description="Minimum SNV Quality (Phred) 55">
+##FILTER=<ID=min_indelqual_44,Description="Minimum Indel Quality (Phred) 44">
+##bcftools_concatVersion=1.24+htslib-1.24
+##bcftools_concatCommand=concat -a -O z -o /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/concat.vcf.gz /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/0.vcf.gz /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/1.vcf.gz /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/2.vcf.gz /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/3.vcf.gz; Date=Fri Oct 16 18:23:35 2026
 ##FILTER=<ID=min_snvqual_58,Description="Minimum SNV Quality (Phred) 58">
********
*SNIP *
********
 KP849471	189835	.	T	A	62	PASS	DP=7;AF=0.285714;SB=0;DP4=2,3,1,1
-KP849471	189951	.	TAC	T	238	PASS	DP=8;AF=0.750000;SB=0;DP4=1,1,2,4;INDEL;HRUN=1
-KP849471	189971	.	GAT	G	179	PASS	DP=5;AF=1.000000;SB=0;DP4=0,1,2,3;INDEL;HRUN=1
-KP849471	190055	.	A	G	177	PASS	DP=5;AF=1.000000;SB=0;DP4=0,0,2,3
-KP849471	190237	.	C	T	229	PASS	DP=6;AF=1.000000;SB=0;DP4=0,0,3,3
-KP849471	190294	.	T	TA	248	PASS	DP=7;AF=1.000000;SB=0;DP4=0,0,4,3;INDEL;HRUN=6
-KP849471	190302	.	T	G	205	PASS	DP=8;AF=1.000000;SB=0;DP4=0,0,5,3
-KP849471	190494	.	G	T	258	PASS	DP=7;AF=1.000000;SB=0;DP4=0,0,4,3
-KP849471	190546	.	T	A	262	PASS	DP=7;AF=1.000000;SB=0;DP4=0,0,3,4
-KP849471	190851	.	GA	G	88	PASS	DP=5;AF=0.800000;SB=0;DP4=0,1,1,3;INDEL;HRUN=8
-KP849471	190951	.	G	A	182	PASS	DP=7;AF=1.000000;SB=2147483647;DP4=0,0,0,7
-KP849471	190964	.	C	T	190	PASS	DP=8;AF=1.000000;SB=0;DP4=0,0,1,7
-KP849471	191034	.	C	T	111	PASS	DP=5;AF=1.000000;SB=0;DP4=0,0,1,4
+KP849471	189951	.	TAC	T	238	PASS	DP=8;AF=0.75;SB=0;DP4=1,1,2,4;INDEL;HRUN=1
+KP849471	189971	.	GAT	G	179	PASS	DP=5;AF=1;SB=0;DP4=0,1,2,3;INDEL;HRUN=1
+KP849471	190055	.	A	G	177	PASS	DP=5;AF=1;SB=0;DP4=0,0,2,3
+KP849471	190237	.	C	T	229	PASS	DP=6;AF=1;SB=0;DP4=0,0,3,3
+KP849471	190294	.	T	TA	248	PASS	DP=7;AF=1;SB=0;DP4=0,0,4,3;INDEL;HRUN=6
+KP849471	190302	.	T	G	205	PASS	DP=8;AF=1;SB=0;DP4=0,0,5,3
+KP849471	190494	.	G	T	258	PASS	DP=7;AF=1;SB=0;DP4=0,0,4,3
+KP849471	190546	.	T	A	262	PASS	DP=7;AF=1;SB=0;DP4=0,0,3,4
+KP849471	190851	.	GA	G	88	PASS	DP=5;AF=0.8;SB=0;DP4=0,1,1,3;INDEL;HRUN=8
+KP849471	190951	.	G	A	182	PASS	DP=7;AF=1;SB=2147483647;DP4=0,0,0,7
+KP849471	190964	.	C	T	190	PASS	DP=8;AF=1;SB=0;DP4=0,0,1,7
+KP849471	191034	.	C	T	111	PASS	DP=5;AF=1;SB=0;DP4=0,0,1,4

Output with path /tmp/tmpyhxory6j/Samtools stats__83e676b4-bb47-4230-a81f-8c2eedeaca99.tabular different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/variant-calling/generic-variant-calling-wgs-pe/test-data/mapped_reads_stats.tabular v. /tmp/tmpyy491q7jmapped_reads_stats.tabular )
--- local_file
+++ history_data
@@ -1,14 +1,14 @@
-# This file was produced by samtools stats (1.9+htslib-1.9) and can be plotted using plot-bamstats
+# This file was produced by samtools stats (1.22+htslib-1.22) and can be plotted using plot-bamstats
 # This file contains statistics for all reads.
 # The command line was:  stats -@ 0 infile
 # CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
-CHK	89b88d14	bd407c5b	9dde3fd7
+CHK	89b88d14	bd407c5b	c73ad8bf
 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
-SN	raw total sequences:	4626
+SN	raw total sequences:	4626	# excluding supplementary and secondary reads
 SN	filtered sequences:	0
 SN	sequences:	4626
-SN	is sorted:	1
+SN	is sorted:	1	# sorted by coordinate
 SN	1st fragments:	2313
 SN	last fragments:	2313
 SN	reads mapped:	4626
@@ -20,6 +20,7 @@
 SN	reads MQ0:	367	# mapped and MQ=0
 SN	reads QC failed:	0
 SN	non-primary alignments:	0
********
*SNIP *
********
 LRL	149	119
 LRL	150	389
 LRL	151	1766
+# Mapping qualities for reads !(UNMAP|SECOND|SUPPL|QCFAIL|DUP). Use `grep ^MAPQ | cut -f 2-` to extract this part. The columns are: mapq, count
+MAPQ	0	367
+MAPQ	16	1
+MAPQ	30	1
+MAPQ	33	2
+MAPQ	40	22
+MAPQ	60	4233
 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions
 ID	1	102	131
 ID	2	52	47
@@ -1795,7 +1959,7 @@
 COV	[47-47]	47	9
 # GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile
 GCD	0.0	18.182	0.000	0.000	0.000	0.000	0.000
-GCD	31.0	27.273	3.645	3.645	3.645	3.645	3.645
-GCD	32.0	72.727	3.293	3.293	3.525	3.825	3.870
-GCD	33.0	90.909	3.098	3.098	3.098	3.705	3.705
-GCD	34.0	100.000	2.767	2.767	2.767	2.767	2.767
+GCD	31.0	27.273	3.659	3.659	3.659	3.659	3.659
+GCD	32.0	72.727	3.306	3.411	3.539	3.863	3.885
+GCD	33.0	90.909	3.110	3.110	3.415	3.720	3.720
+GCD	34.0	100.000	2.778	2.778	2.778	2.778	2.778

Output with path /tmp/tmpu0332984/Lofreq filter__302ddecb-f73c-48bf-b2c9-17b883d4414e.vcf different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/variant-calling/generic-variant-calling-wgs-pe/test-data/soft_filtered_variants.vcf v. /tmp/tmpsujyl911soft_filtered_variants.vcf )
--- local_file
+++ history_data
@@ -1,6 +1,7 @@
 ##fileformat=VCFv4.0
-##fileDate=20220601
-##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r KP849471:1-49312 -o /tmp/lofreq2_call_parallelvorvr7qw/0.vcf.gz reads.bam 
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20261016
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r KP849471:1-49312 -o /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/0.vcf.gz reads.bam 
 ##reference=reference.fa
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
@@ -11,99 +12,107 @@
 ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
 ##FILTER=<ID=min_snvqual_51,Description="Minimum SNV Quality (Phred) 51">
 ##FILTER=<ID=min_indelqual_42,Description="Minimum Indel Quality (Phred) 42">
+##contig=<ID=KP849471>
+##FILTER=<ID=min_snvqual_46,Description="Minimum SNV Quality (Phred) 46">
+##FILTER=<ID=min_indelqual_39,Description="Minimum Indel Quality (Phred) 39">
+##FILTER=<ID=min_snvqual_50,Description="Minimum SNV Quality (Phred) 50">
+##FILTER=<ID=min_snvqual_55,Description="Minimum SNV Quality (Phred) 55">
+##FILTER=<ID=min_indelqual_44,Description="Minimum Indel Quality (Phred) 44">
+##bcftools_concatVersion=1.24+htslib-1.24
+##bcftools_concatCommand=concat -a -O z -o /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/concat.vcf.gz /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/0.vcf.gz /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/1.vcf.gz /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/2.vcf.gz /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/3.vcf.gz; Date=Fri Oct 16 18:23:35 2026
 ##FILTER=<ID=min_snvqual_58,Description="Minimum SNV Quality (Phred) 58">
********
*SNIP *
********
 KP849471	189835	.	T	A	62	PASS	DP=7;AF=0.285714;SB=0;DP4=2,3,1,1
-KP849471	189951	.	TAC	T	238	PASS	DP=8;AF=0.750000;SB=0;DP4=1,1,2,4;INDEL;HRUN=1
-KP849471	189971	.	GAT	G	179	PASS	DP=5;AF=1.000000;SB=0;DP4=0,1,2,3;INDEL;HRUN=1
-KP849471	190055	.	A	G	177	PASS	DP=5;AF=1.000000;SB=0;DP4=0,0,2,3
-KP849471	190237	.	C	T	229	PASS	DP=6;AF=1.000000;SB=0;DP4=0,0,3,3
-KP849471	190294	.	T	TA	248	PASS	DP=7;AF=1.000000;SB=0;DP4=0,0,4,3;INDEL;HRUN=6
-KP849471	190302	.	T	G	205	PASS	DP=8;AF=1.000000;SB=0;DP4=0,0,5,3
-KP849471	190494	.	G	T	258	PASS	DP=7;AF=1.000000;SB=0;DP4=0,0,4,3
-KP849471	190546	.	T	A	262	PASS	DP=7;AF=1.000000;SB=0;DP4=0,0,3,4
-KP849471	190851	.	GA	G	88	PASS	DP=5;AF=0.800000;SB=0;DP4=0,1,1,3;INDEL;HRUN=8
-KP849471	190951	.	G	A	182	sb_fdr	DP=7;AF=1.000000;SB=2147483647;DP4=0,0,0,7
-KP849471	190964	.	C	T	190	PASS	DP=8;AF=1.000000;SB=0;DP4=0,0,1,7
-KP849471	191034	.	C	T	111	PASS	DP=5;AF=1.000000;SB=0;DP4=0,0,1,4
+KP849471	189951	.	TAC	T	238	PASS	DP=8;AF=0.75;SB=0;DP4=1,1,2,4;INDEL;HRUN=1
+KP849471	189971	.	GAT	G	179	PASS	DP=5;AF=1;SB=0;DP4=0,1,2,3;INDEL;HRUN=1
+KP849471	190055	.	A	G	177	PASS	DP=5;AF=1;SB=0;DP4=0,0,2,3
+KP849471	190237	.	C	T	229	PASS	DP=6;AF=1;SB=0;DP4=0,0,3,3
+KP849471	190294	.	T	TA	248	PASS	DP=7;AF=1;SB=0;DP4=0,0,4,3;INDEL;HRUN=6
+KP849471	190302	.	T	G	205	PASS	DP=8;AF=1;SB=0;DP4=0,0,5,3
+KP849471	190494	.	G	T	258	PASS	DP=7;AF=1;SB=0;DP4=0,0,4,3
+KP849471	190546	.	T	A	262	PASS	DP=7;AF=1;SB=0;DP4=0,0,3,4
+KP849471	190851	.	GA	G	88	PASS	DP=5;AF=0.8;SB=0;DP4=0,1,1,3;INDEL;HRUN=8
+KP849471	190951	.	G	A	182	sb_fdr	DP=7;AF=1;SB=2147483647;DP4=0,0,0,7
+KP849471	190964	.	C	T	190	PASS	DP=8;AF=1;SB=0;DP4=0,0,1,7
+KP849471	191034	.	C	T	111	PASS	DP=5;AF=1;SB=0;DP4=0,0,1,4

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled
Step 3: Name for genome database:
- step_state: scheduled

Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.7+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/fastp:1.3.7
```

Command Line:

ln -sf '/tmp/tmpw08pqdmm/files/a/5/f/dataset_a5fe8de3-c45b-4892-a4e4-c1a2fee51818.dat' 'ERR3485802.fastqsanger.gz' && ln -sf '/tmp/tmpw08pqdmm/files/6/a/c/dataset_6acbb659-781e-4c8e-898b-401cf56b9843.dat' 'ERR3485802_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'ERR3485802.fastqsanger.gz'  -i 'ERR3485802.fastqsanger.gz'   -I 'ERR3485802_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                    --dont_eval_duplication                  && mv first.fastqsanger.gz '/tmp/tmpw08pqdmm/job_working_directory/000/4/outputs/dataset_1e49cdb6-c458-4e6f-ba39-5e9e5bb32778.dat' && mv second.fastqsanger.gz '/tmp/tmpw08pqdmm/job_working_directory/000/4/outputs/dataset_58c158df-1a41-4c4f-9c66-f9eddce60c82.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 2500
total bases: 376657
Q20 bases: 371549(98.6439%)
Q30 bases: 370136(98.2687%)
Q40 bases: 1744(0.463021%)

Read2 before filtering:
total reads: 2500
total bases: 376700
Q20 bases: 355761(94.4415%)
Q30 bases: 351290(93.2546%)
Q40 bases: 131(0.0347757%)

Read1 after filtering:
total reads: 2492
total bases: 375257
Q20 bases: 370593(98.7571%)
Q30 bases: 369355(98.4272%)
Q40 bases: 1744(0.464748%)

Read2 after filtering:
total reads: 2492
total bases: 375297
Q20 bases: 355082(94.6136%)
Q30 bases: 350732(93.4545%)
Q40 bases: 131(0.0349057%)

Filtering result:
reads passed filter: 4984
reads failed due to low quality: 16
reads failed due to too many N: 0
reads failed due to too short: 0
reads failed due to adapter dimer: 0
reads with adapter trimmed: 30
bases trimmed due to adapters: 393

Insert size peak (evaluated by paired-end reads): 263

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title ERR3485802.fastqsanger.gz -i ERR3485802.fastqsanger.gz -I ERR3485802_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz --dont_eval_duplication 
fastp v1.3.7, time used: 0 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e9df53cc98e11f1a9dd3833c5d6d0fe"`
chromInfo	`"/tmp/tmpw08pqdmm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
duplicated_reads	`{"handling_options": {"__current_case__": 0, "eval_dups": "--dont_eval_duplication"}}`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_front_select": {"__current_case__": 1, "cut_front": ""}, "cut_right_select": {"__current_case__": 1, "cut_right": ""}, "cut_tail_select": {"__current_case__": 1, "cut_tail": ""}}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-2104de94fc3275c05faf3d41165a700b6e0c9ef9:328b6a24a575a59e3c8291517564a37ebdc4b7c9-0

Command Line:

python3 '/tmp/shed_data/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/908f2c5fedec/snpeff/gbk2fa.py' '/tmp/tmpw08pqdmm/files/b/0/2/dataset_b02e607f-13dd-4736-9b8f-ee3eb65a425d.dat' '/tmp/tmpw08pqdmm/job_working_directory/000/5/outputs/dataset_53384db7-44d9-49bb-ad59-8d33d2d99a65.dat' --remove_version &&  mkdir -p '/tmp/tmpw08pqdmm/job_working_directory/000/5/outputs/dataset_643eeac4-4653-4469-8b4e-98d389e15137_files/mpxv' && mkdir -p snpeff_output/'mpxv' &&  ln -s '/tmp/tmpw08pqdmm/files/b/0/2/dataset_b02e607f-13dd-4736-9b8f-ee3eb65a425d.dat' 'snpeff_output/mpxv/genes.gbk' &&  snpEff -Xmx${GALAXY_MEMORY_MB:-8192}m build -noCheckCds -noCheckProtein -v -configOption 'mpxv'.genome='mpxv' -configOption 'mpxv'.codonTable='Standard' -genbank -dataDir "$(pwd)/snpeff_output" 'mpxv' && mv snpeff_output/'mpxv'/*.bin '/tmp/tmpw08pqdmm/job_working_directory/000/5/outputs/dataset_643eeac4-4653-4469-8b4e-98d389e15137_files/mpxv' && echo 'mpxv.genome : mpxv' >> '/tmp/tmpw08pqdmm/job_working_directory/000/5/outputs/dataset_643eeac4-4653-4469-8b4e-98d389e15137_files'/snpEff.config && echo 'mpxv.codonTable : Standard' >> '/tmp/tmpw08pqdmm/job_working_directory/000/5/outputs/dataset_643eeac4-4653-4469-8b4e-98d389e15137_files'/snpEff.config

Exit Code:

```
0
```

Standard Error:

00:00:00 SnpEff version SnpEff 5.4c (build 2026-02-23 07:25), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'mpxv'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'mpxv'
00:00:00 Looking for config file: '/tmp/tmpw08pqdmm/job_working_directory/000/5/working/snpEff.config'
00:00:00 Reading config file: /usr/local/share/snpeff-5.4.0c-0/snpEff.config
00:00:01 Codon table 'Standard' for genome 'mpxv'
00:00:01 done
00:00:01 Chromosome: 'KP849471.1'	length: 197248
00:00:01 Create exons from CDS (if needed): 
00:00:01 Exons created for 188 transcripts.
00:00:01 Deleting redundant exons (if needed): 
00:00:01 	Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed): 
00:00:01 	Total collapsed transcripts: 0
00:00:01 		Adding genomic sequences to genes: 
00:00:01 	Done (153 sequences added).
00:00:01 		Adding genomic sequences to exons: 
00:00:01 	Done (188 sequences added, 0 ignored).
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts: 
00:00:01 Adjusting genes: 
00:00:01 Adjusting chromosomes lengths: 
00:00:01 Ranking exons: 
00:00:01 Create UTRs from CDS (if needed): 
00:00:01 Remove empty chromosomes: 
00:00:01 Marking as 'coding' from CDS information: 
00:00:01 Done: 0 transcripts marked
00:00:01 
00:00:01 Caracterizing exons by splicing (stage 1) : 

00:00:01 Caracterizing exons by splicing (stage 2) : 
00:00:01 done.
00:00:01 [Optional] Rare amino acid annotations
WARNING_FILE_NOT_FOUND: Rare Amino Acid analysis: Cannot read protein sequence file '/tmp/tmpw08pqdmm/job_working_directory/000/5/working/snpeff_output/mpxv/protein.fa', nothing done.
00:00:01 Saving database
00:00:01 Saving sequences for small chromosmes to file '/tmp/tmpw08pqdmm/job_working_directory/000/5/working/snpeff_output/mpxv/sequence.bin'
00:00:01 [Optional] Reading regulation elements: GFF
WARNING_FILE_NOT_FOUND: Cannot read optional regulation file '/tmp/tmpw08pqdmm/job_working_directory/000/5/working/snpeff_output/mpxv/regulation.gff', nothing done.
00:00:01 [Optional] Reading regulation elements: BED 
00:00:01 Cannot find optional regulation dir '/tmp/tmpw08pqdmm/job_working_directory/000/5/working/snpeff_output/mpxv/regulation.bed/', nothing done.
00:00:01 [Optional] Reading motifs: GFF
WARNING_FILE_NOT_FOUND: Cannot open PWMs file /tmp/tmpw08pqdmm/job_working_directory/000/5/working/snpeff_output/mpxv/pwms.bin. Nothing done
00:00:01 Done
00:00:01 Done.

Standard Output:

Writing FASTA record: KP849471
............................................................................................................................................................................................

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e9df53cc98e11f1a9dd3833c5d6d0fe"`
chromInfo	`"/tmp/tmpw08pqdmm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": {"values": [{"id": 1, "src": "hda"}]}, "input_type_selector": "gb", "remove_version": true}`

Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:bd996097b6dd518cf788ddd6c586fb23d039cb9c-0

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpw08pqdmm/files/5/3/3/dataset_53384db7-44d9-49bb-ad59-8d33d2d99a65.dat' 'localref.fa' && bwa index 'localref.fa' &&    bwa mem  -t "${GALAXY_SLOTS:-1}" -v 1     -T '30' -h '5'    -Y   -q                'localref.fa' '/tmp/tmpw08pqdmm/files/1/e/4/dataset_1e49cdb6-c458-4e6f-ba39-5e9e5bb32778.dat' '/tmp/tmpw08pqdmm/files/5/8/c/dataset_58c158df-1a41-4c4f-9c66-f9eddce60c82.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpw08pqdmm/job_working_directory/000/6/outputs/dataset_8482425d-048e-44e6-880b-0a4057f2014b.dat'

Exit Code:

```
0
```

Standard Error:

[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.02 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.19-r1273
[main] CMD: bwa index localref.fa
[main] Real time: 0.039 sec; CPU: 0.035 sec
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (277, 334, 393)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (45, 625)
[M::mem_pestat] mean and std.dev: (338.50, 89.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 741)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.19-r1273
[main] CMD: bwa mem -t 1 -v 1 -T 30 -h 5 -Y -q localref.fa /tmp/tmpw08pqdmm/files/1/e/4/dataset_1e49cdb6-c458-4e6f-ba39-5e9e5bb32778.dat /tmp/tmpw08pqdmm/files/5/8/c/dataset_58c158df-1a41-4c4f-9c66-f9eddce60c82.dat
[main] Real time: 0.166 sec; CPU: 0.167 sec

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e9df53cc98e11f1a9dd3833c5d6d0fe"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpw08pqdmm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:8f53bfe77285b2fc8b6545efd875a0b3d1d12061-0

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&        ln -s '/tmp/tmpw08pqdmm/files/8/4/8/dataset_8482425d-048e-44e6-880b-0a4057f2014b.dat' infile && ln -s '/tmp/tmpw08pqdmm/files/_metadata_files/c/4/0/metadata_c4070c00-6ad9-4c95-8b84-9bcc8f53cfe8.dat' infile.bai &&               samtools view -@ $addthreads -b  -f 3 -F 0 -G 0   -o outfile      infile

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e9df53cc98e11f1a9dd3833c5d6d0fe"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpw08pqdmm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/picard:3.1.1--hdfd78af_0

Command Line:

_JAVA_OPTIONS=${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=${TMPDIR:-${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS &&   ln -sf '/tmp/tmpw08pqdmm/files/e/f/b/dataset_efb2da38-770b-4dc9-adee-2fc434a9481c.dat' 'ERR3485802' &&  picard MarkDuplicates  --INPUT 'ERR3485802' --OUTPUT '/tmp/tmpw08pqdmm/job_working_directory/000/8/outputs/dataset_1ef71b8c-f877-4a47-8bd1-1b80bcdd9ce1.dat'  --METRICS_FILE '/tmp/tmpw08pqdmm/job_working_directory/000/8/outputs/dataset_e67fbe59-c5ef-40fd-82a4-9af064adbe17.dat'  --REMOVE_DUPLICATES 'true' --ASSUME_SORTED 'true'  --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES  --OPTICAL_DUPLICATE_PIXEL_DISTANCE '100'   --VALIDATION_STRINGENCY 'LENIENT' --TAGGING_POLICY All --QUIET true --VERBOSITY ERROR

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m -Djava.io.tmpdir=/tmp/tmpw08pqdmm/job_working_directory/000/8/tmp
Oct 16, 2026 6:22:28 PM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e9df53cc98e11f1a9dd3833c5d6d0fe"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpw08pqdmm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/samtools:1.22--h96c455f_0

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   ln -s '/tmp/tmpw08pqdmm/files/e/f/b/dataset_efb2da38-770b-4dc9-adee-2fc434a9481c.dat' infile && ln -s '/tmp/tmpw08pqdmm/files/_metadata_files/6/5/2/metadata_6524efdf-4c80-4893-859b-c18aeae78a37.dat' infile.bai &&       samtools stats       -@ $addthreads infile   > '/tmp/tmpw08pqdmm/job_working_directory/000/9/outputs/dataset_83e676b4-bb47-4230-a81f-8c2eedeaca99.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e9df53cc98e11f1a9dd3833c5d6d0fe"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpw08pqdmm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/lofreq:2.1.5--py313ha7493ab_16

Command Line:

ln -s '/tmp/tmpw08pqdmm/files/5/3/3/dataset_53384db7-44d9-49bb-ad59-8d33d2d99a65.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  lofreq viterbi --ref 'reference.fa'  --defqual 2 --out tmp.bam '/tmp/tmpw08pqdmm/files/1/e/f/dataset_1ef71b8c-f877-4a47-8bd1-1b80bcdd9ce1.dat' &&  samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmpw08pqdmm/job_working_directory/000/10/outputs/dataset_e669e3ca-654e-4530-9928-bb57cbd13fa4.dat' tmp.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e9df53cc98e11f1a9dd3833c5d6d0fe"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpw08pqdmm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy4):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/multiqc:1.35--pyhdfd78af_2

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&         grep -Pq '"before_filtering": {' /tmp/tmpw08pqdmm/files/4/5/3/dataset_45307bba-55d8-4297-b37f-c42b694e5b66.dat || die "Module 'fastp: '"before_filtering": {' not found in the file 'ERR3485802'" && ln -s '/tmp/tmpw08pqdmm/files/4/5/3/dataset_45307bba-55d8-4297-b37f-c42b694e5b66.dat' 'multiqc_WDir/fastp_0/ERR3485802.json'  &&    mkdir multiqc_WDir/samtools_1 &&    mkdir 'multiqc_WDir/samtools_1/stats_0' &&      grep -Pq 'This file was produced by samtools stats' /tmp/tmpw08pqdmm/files/8/3/e/dataset_83e676b4-bb47-4230-a81f-8c2eedeaca99.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file 'ERR3485802'" && ln -s '/tmp/tmpw08pqdmm/files/8/3/e/dataset_83e676b4-bb47-4230-a81f-8c2eedeaca99.dat' 'multiqc_WDir/samtools_1/stats_0/ERR3485802'  &&    mkdir multiqc_WDir/picard_2 &&      mkdir 'multiqc_WDir/picard_2/markdups_0' &&    grep -Pq 'MarkDuplicates' /tmp/tmpw08pqdmm/files/e/6/7/dataset_e67fbe59-c5ef-40fd-82a4-9af064adbe17.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'ERR3485802'" && ln -s '/tmp/tmpw08pqdmm/files/e/6/7/dataset_e67fbe59-c5ef-40fd-82a4-9af064adbe17.dat' 'multiqc_WDir/picard_2/markdups_0/ERR3485802'  &&        multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && { cp ./report_data/*plot*.txt ./plots/ 2>/dev/null || true; }

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.35

       file_search | Search path: /tmp/tmpw08pqdmm/job_working_directory/000/11/working/multiqc_WDir
            picard | Found 1 MarkDuplicates reports
          samtools | Found 1 stats reports
             fastp | Found 1 reports
     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete

Standard Output:

total 1436
-rw-r--r-- 1 1001 1001    5607 Oct 16 18:23 fastp-insert-size-plot.txt
-rw-r--r-- 1 1001 1001    3166 Oct 16 18:23 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    2858 Oct 16 18:23 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    2966 Oct 16 18:23 fastp-seq-content-gc-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001    2789 Oct 16 18:23 fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001    2065 Oct 16 18:23 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    2065 Oct 16 18:23 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    2065 Oct 16 18:23 fastp-seq-content-n-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001    2065 Oct 16 18:23 fastp-seq-content-n-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001    2655 Oct 16 18:23 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    2633 Oct 16 18:23 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    2652 Oct 16 18:23 fastp-seq-quality-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001    2646 Oct 16 18:23 fastp-seq-quality-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001     117 Oct 16 18:23 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 1001   30146 Oct 16 18:23 llms-full.txt
-rw-r--r-- 1 1001 1001   23182 Oct 16 18:23 multiqc.log
-rw-r--r-- 1 1001 1001   51381 Oct 16 18:23 multiqc.parquet
-rw-r--r-- 1 1001 1001     183 Oct 16 18:23 multiqc_citations.txt
-rw-r--r-- 1 1001 1001 1132673 Oct 16 18:23 multiqc_data.json
-rw-r--r-- 1 1001 1001  116812 Oct 16 18:23 multiqc_fastp.txt
-rw-r--r-- 1 1001 1001     796 Oct 16 18:23 multiqc_general_stats.txt
-rw-r--r-- 1 1001 1001     299 Oct 16 18:23 multiqc_picard_dups.txt
-rw-r--r-- 1 1001 1001    1310 Oct 16 18:23 multiqc_samtools_stats.txt
-rw-r--r-- 1 1001 1001      50 Oct 16 18:23 multiqc_software_versions.txt
-rw-r--r-- 1 1001 1001     413 Oct 16 18:23 multiqc_sources.txt
-rw-r--r-- 1 1001 1001       0 Oct 16 18:23 picard_MarkIlluminaAdapters_histogram.txt
-rw-r--r-- 1 1001 1001       0 Oct 16 18:23 picard_MeanQualityByCycle_histogram.txt
-rw-r--r-- 1 1001 1001       0 Oct 16 18:23 picard_MeanQualityByCycle_histogram_1.txt
-rw-r--r-- 1 1001 1001       0 Oct 16 18:23 picard_QualityScoreDistribution_histogram.txt
-rw-r--r-- 1 1001 1001      72 Oct 16 18:23 picard_deduplication.txt
-rw-r--r-- 1 1001 1001     329 Oct 16 18:23 samtools-stats-dp.txt
-rw-r--r-- 1 1001 1001      54 Oct 16 18:23 samtools_alignment_plot.txt
-rw-r--r-- 1 1001 1001    7377 Oct 16 18:23 samtools_insert_size.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e9df53cc98e11f1a9dd3833c5d6d0fe"`
chromInfo	`"/tmp/tmpw08pqdmm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
image_content_input	`None`
png_plots	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 8, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 25, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 18, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/lofreq:2.1.5--py313ha7493ab_16

Command Line:

ln -s '/tmp/tmpw08pqdmm/files/5/3/3/dataset_53384db7-44d9-49bb-ad59-8d33d2d99a65.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  lofreq indelqual --dindel --ref reference.fa -o output.bam /tmp/tmpw08pqdmm/files/e/6/6/dataset_e669e3ca-654e-4530-9928-bb57cbd13fa4.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e9df53cc98e11f1a9dd3833c5d6d0fe"`
chromInfo	`"/tmp/tmpw08pqdmm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/lofreq:2.1.5--py313ha7493ab_16

Command Line:

ln -s '/tmp/tmpw08pqdmm/files/5/3/3/dataset_53384db7-44d9-49bb-ad59-8d33d2d99a65.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  ln -s '/tmp/tmpw08pqdmm/files/7/e/6/dataset_7e61aee7-5a06-46f7-b4af-6c91f773d171.dat' reads.bam && ln -s -f '/tmp/tmpw08pqdmm/files/_metadata_files/c/6/8/metadata_c68f4351-2579-400c-b8ac-f457470a6ee8.dat' reads.bam.bai &&   lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose  --ref 'reference.fa' --out variants.vcf --call-indels   --min-cov 5 --max-depth 1000000  --min-bq 30 --min-alt-bq 30    --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0  --sig 0.0005 --bonf dynamic --no-default-filter  reads.bam 2>&1  || (tool_exit_code=$? && cat "$TMPDIR"/lofreq2_call_parallel*/*.log 1>&2 && exit $tool_exit_code)  && echo set_custom

Exit Code:

```
0
```

Standard Output:

INFO [2026-10-16 18:23:34,620]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter reads.bam

INFO [2026-10-16 18:23:34,628]: Adding 4 commands to mp-pool
Checking the headers and starting positions of 4 files
[W::bcf_hdr_check_sanity] AF should be declared as Number=A
[W::bcf_hdr_check_sanity] SB should be declared as Number=4
Number of substitution tests performed: 324
Number of indel tests performed: 27
INFO [2026-10-16 18:23:35,491]: Executing lofreq filter -i /tmp/tmpw08pqdmm/job_working_directory/000/13/tmp/lofreq2_call_parallelote1ot57/concat.vcf.gz -o variants.vcf --no-defaults --snvqual-thresh 58 --indelqual-thresh 47

set_custom

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e9df53cc98e11f1a9dd3833c5d6d0fe"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpw08pqdmm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/lofreq:2.1.5--py313ha7493ab_16

Command Line:

lofreq filter -i /tmp/tmpw08pqdmm/files/4/1/7/dataset_41722f6d-1488-4d09-b5b6-b32dee4db308.dat --no-defaults --verbose --print-all  -v 0 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001   -o filtered.vcf

Exit Code:

```
0
```

Standard Error:

Skipping default settings
At least one type of multiple testing correction requested. Doing first pass of vcf
MTC application completed
Successful exit.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e9df53cc98e11f1a9dd3833c5d6d0fe"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpw08pqdmm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-b63b6277c1547c8fbbef71582adb7d2600a09ae9:d5f569ec01b5de1e1d3753793b3af0ab899f785f-0

Command Line:

snpEff -Xmx${GALAXY_MEMORY_MB:-8192}m eff -i vcf -o vcf -upDownStreamLen 0 -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -no-utr                    -s snpeff_stats.html -noLog -dataDir '/tmp/tmpw08pqdmm/files/6/4/3/dataset_643eeac4-4653-4469-8b4e-98d389e15137_files' -configOption 'mpxv'.genome='mpxv' -configOption 'mpxv'.codonTable='Standard' 'mpxv' '/tmp/tmpw08pqdmm/files/3/0/2/dataset_302ddecb-f73c-48bf-b2c9-17b883d4414e.dat' > '/tmp/tmpw08pqdmm/job_working_directory/000/15/outputs/dataset_3301736f-8a9d-4336-9d5f-7ef0caa5b8e3.dat' && mkdir '/tmp/tmpw08pqdmm/job_working_directory/000/15/outputs/dataset_607e5d96-3f65-41ae-b656-805b21d2fd1a_files' && mv snpeff_stats.genes.txt /tmp/tmpw08pqdmm/job_working_directory/000/15/outputs/dataset_607e5d96-3f65-41ae-b656-805b21d2fd1a_files

Exit Code:

```
0
```

Standard Error:

00:00:00 Codon table 'Standard' for genome 'mpxv'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4e9df53cc98e11f1a9dd3833c5d6d0fe"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpw08pqdmm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_gene_stats	`false`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Other invocation details
- history_id
  - a58667712b1c330a
- history_state
  - ok
- invocation_id
  - a58667712b1c330a
- invocation_state
  - scheduled
- workflow_id
  - a58667712b1c330a

…tions

github-actions · 2026-10-16T19:52:41Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Generic-variation-analysis-on-WGS-PE-data.ga_0

Problems:

Output with path /tmp/tmpaymq1fl0/Samtools stats__406c081c-2815-4271-8553-e6a26eb25c31.tabular different than expected
Expected line 'SN	average length:	150' in output ('# This file was produced by samtools stats (1.22+htslib-1.22) and can be plotted using plot-bamstats
# This file contains statistics for all reads.
# The command line was:  stats -@ 0 infile
# CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
CHK	89b88d14	bd407c5b	c73ad8bf
# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
SN	raw total sequences:	4626	# excluding supplementary and secondary reads
SN	filtered sequences:	0
SN	sequences:	4626
SN	is sorted:	1	# sorted by coordinate
SN	1st fragments:	2313
SN	last fragments:	2313
SN	reads mapped:	4626
SN	reads mapped and paired:	4626	# paired-end technology bit set + both mates mapped
SN	reads unmapped:	0
SN	reads properly paired:	4626	# proper-pair bit set
SN	reads paired:	4626	# paired-end technology bit set
SN	reads duplicated:	0	# PCR or optical duplicate bit set
SN	reads MQ0:	367	# mapped and MQ=0
SN	reads QC failed:	0
SN	non-primary alignments:	0
SN	supplementary alignments:	3
SN	total length:	696651	# ignores clipping
SN	total first fragment length:	348311	# ignores clipping
SN	total last fragment length:	348340	# ignores clipping
SN	bases mapped:	696651	# ignores clipping
SN	bases mapped (cigar):	694433	# more accurate
SN	bases trimmed:	0
SN	bases duplicated:	0
SN	mismatches:	5244	# from NM fields
SN	error rate:	7.551484e-03	# mismatches / bases mapped (cigar)
SN	average length:	151
SN	average first fragment length:	151
SN	average last fragment length:	151
SN	maximum length:	151
SN	maximum first fragment length:	151
SN	maximum last fragment length:	151
SN	average quality:	37.2
SN	insert size average:	336.9
SN	insert size standard deviation:	91.7
SN	inward oriented pairs:	2308
SN	outward oriented pairs:	5
SN	pairs with other orientation:	0
SN	pairs on different chromosomes:	0
SN	percentage of properly paired reads (%):	100.0
# First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part.
# Columns correspond to qualities and rows to cycles. First column is the cycle number.
FFQ	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	40	0	54	0	0	0	0	0	0	0	0	0	0	86	26	9	727	790	544	36	1	0	0	0	0	0
FFQ	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	0	11	0	0	0	0	0	0	0	0	0	0	37	13	4	587	826	762	58	1	0	0	0	0	0
FFQ	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	3	0	0	0	0	0	0	0	0	0	0	21	7	5	415	817	937	91	6	0	0	0	0	0
FFQ	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	3	0	0	0	0	0	0	0	0	0	0	13	5	6	324	798	989	157	9	0	0	0	0	0
FFQ	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	5	0	0	0	0	0	0	0	0	0	0	14	20	15	339	768	980	148	11	0	0	0	0	0
FFQ	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	13	2	0	0	0	0	0	0	0	0	0	1	3	15	37	146	136	54	0	1893	0	0	0	0
FFQ	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	6	2	6	0	0	0	0	0	0	0	0	2	3	8	50	163	149	72	0	1839	0	0	0	0
FFQ	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	7	3	2	0	0	0	0	0	0	0	0	3	5	16	48	173	135	62	1	1846	0	0	0	0
FFQ	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	1	13	3	3	0	0	0	0	0	1	0	0	2	5	8	41	147	143	59	0	1871	0	0	0	0
FFQ	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	3	9	2	3	0	0	0	0	0	0	0	1	7	1	13	41	145	144	58	3	1873	0	0	0	0
FFQ	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	14	0	5	3	2	0	0	0	1	0	0	1	0	1	2	13	39	159	140	70	4	1858	0	0	0	0
FFQ	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	5	1	1	0	0	0	0	0	0	0	0	3	5	14	50	146	144	70	2	1861	0	0	0	0
FFQ	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	4	2	3	0	0	0	0	0	0	0	0	0	3	1	20	22	17	8	35	107	2081	0	0	0
FFQ	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	1	5	1	3	0	0	0	0	0	0	0	0	0	6	0	9	16	18	13	39	121	2073	0	0	0
FFQ	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	6	2	4	1	0	0	0	0	0	0	1	1	1	0	8	16	13	13	28	109	2095	0	0	0
FFQ	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	6	3	2	0	0	0	0	0	0	0	0	1	2	0	7	19	17	15	24	130	2075	0	0	0
FFQ	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	0	6	4	2	3	0	0	0	0	0	0	0	0	0	1	11	23	16	14	34	114	2071	0	0	0
FFQ	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	1	11	0	3	2	0	0	0	0	0	0	1	0	4	0	10	16	21	11	29	132	2058	0	0	0
FFQ	19	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	15	1	7	2	0	2	0	0	0	0	0	0	0	1	4	0	21	24	29	7	24	120	2051	0	0	0
FFQ	20	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	4	8	0	12	7	3	0	0	0	0	0	1	0	1	0	1	0	17	25	15	9	34	108	2066	0	0	0
FFQ	21	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	6	1	5	2	1	1	0	0	1	0	0	0	0	0	0	0	19	10	21	9	33	125	2078	0	0	0
FFQ	22	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	7	2	13	3	2	1	0	0	0	0	0	1	0	0	2	1	20	15	15	15	22	110	2082	0	0	0
FFQ	23	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2	9	0	5	3	3	0	0	0	0	0	0	0	1	0	0	0	11	20	13	27	38	122	377	1679	0	0
FFQ	24	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	5	10	0	15	4	2	3	0	0	0	0	0	0	0	0	1	0	15	12	8	17	29	117	381	1691	0	0
FFQ	25	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	12	2	7	3	2	1	0	0	1	0	0	0	0	1	4	1	12	23	12	16	36	107	389	1682	0	0
FFQ	26	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	6	9	0	7	2	1	1	0	0	0	0	0	0	0	0	3	0	13	10	11	24	40	112	387	1683	0	0
FFQ	27	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	8	3	1	8	7	1	4	0	0	1	0	0	0	0	0	0	0	12	17	16	18	34	107	374	1699	0	0
FFQ	28	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	7	8	3	10	3	1	1	0	0	1	0	0	0	0	0	1	0	20	20	8	18	27	88	407	1687	0	0
FFQ	29	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	9	5	2	3	6	4	2	0	0	1	0	0	0	0	0	0	0	15	10	9	15	35	116	396	1683	0	0
FFQ	30	0	0	0	0	0	0	0	0	0	0	0	0	3	0	1	4	5	3	6	4	5	0	0	0	0	0	0	0	0	0	3	1	21	21	16	18	29	130	394	1649	0	0
FFQ	31	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	6	5	6	5	1	5	4	0	0	0	0	0	0	0	0	3	1	14	19	18	18	28	107	415	1656	0	0
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FFQ	120	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	3	14	4	3	7	0	0	0	0	0	0	0	1	0	4	6	8	4	21	4	17	40	139	326	1708	0	0
FFQ	121	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	2	9	7	3	6	0	0	0	0	0	0	0	0	0	4	5	5	6	23	8	15	36	124	350	1704	0	0
FFQ	122	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	15	5	6	4	0	0	0	0	0	0	0	0	0	4	6	8	2	28	5	11	53	160	359	1643	0	0
FFQ	123	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	3	10	10	3	6	0	0	0	0	0	0	0	0	0	2	5	9	1	24	7	19	41	116	369	1684	0	0
FFQ	124	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	2	9	7	3	5	0	0	0	0	0	0	0	1	0	8	4	3	2	30	7	11	39	128	400	1647	0	0
FFQ	125	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	1	8	3	5	9	0	0	0	0	0	0	0	0	0	3	6	6	2	18	7	12	37	126	383	1675	0	0
FFQ	126	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	3	10	7	2	5	0	0	0	0	0	0	0	1	0	3	2	1	4	28	4	12	34	133	367	1689	0	0
FFQ	127	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	1	12	12	3	3	0	0	0	0	0	0	0	1	0	6	6	3	4	28	7	8	51	137	376	1627	20	0
FFQ	128	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	2	9	3	4	2	0	0	0	0	0	0	0	1	0	3	5	3	4	16	6	11	28	128	346	1721	15	0
FFQ	129	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	5	13	4	6	0	0	0	0	0	0	0	2	0	3	6	1	0	21	10	11	35	121	348	1696	20	0
FFQ	130	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	10	11	5	5	0	0	0	0	0	0	0	0	0	5	8	4	3	18	7	14	42	108	337	1715	16	0
FFQ	131	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	3	14	11	5	6	0	0	0	0	0	0	0	2	0	6	7	5	3	20	11	13	28	137	368	1652	14	0
FFQ	132	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	9	6	2	9	0	0	0	0	0	0	0	2	0	8	5	3	4	17	12	16	43	116	359	1679	12	0
FFQ	133	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	3	9	10	6	2	0	0	0	0	0	0	0	5	0	6	6	3	3	23	12	10	35	118	374	1664	16	0
FFQ	134	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	1	11	4	7	6	0	0	0	0	0	0	0	1	0	7	1	2	5	23	12	12	41	136	363	1656	12	0
FFQ	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	2	13	6	2	5	0	0	0	0	0	0	0	7	0	4	7	2	2	22	7	16	38	134	359	1660	16	0
FFQ	136	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	3	10	5	6	5	0	0	0	0	0	0	0	1	0	3	7	1	0	21	11	27	41	119	359	1667	13	0
FFQ	137	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	3	10	12	6	3	0	0	0	0	0	0	0	2	0	6	6	3	1	23	14	12	35	137	402	1615	14	0
FFQ	138	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	3	12	8	4	1	0	0	0	0	0	0	0	4	0	4	4	4	4	20	14	22	32	131	361	1664	9	0
FFQ	139	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	2	7	6	3	5	0	0	0	0	0	0	0	2	1	5	8	3	6	14	6	19	26	121	364	1689	11	0
FFQ	140	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	6	5	10	3	2	0	0	0	0	0	0	0	2	0	4	5	1	4	18	9	20	29	118	364	1696	6	0
FFQ	141	0	0	0	0	0	0	0	0	0	0	0	0	0	1	5	2	10	13	3	2	0	0	0	0	0	0	0	4	0	5	9	0	5	26	10	8	25	119	371	1679	11	0
FFQ	142	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	6	5	9	2	3	0	0	0	0	0	0	0	4	0	5	11	1	9	18	13	19	33	128	334	1692	9	0
FFQ	143	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	2	8	6	9	3	0	0	0	0	0	0	0	5	0	6	7	1	4	17	10	22	29	130	352	1678	8	0
FFQ	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	4	8	9	6	1	0	0	0	0	0	0	0	3	0	4	11	1	2	15	11	25	16	122	360	1691	5	0
FFQ	145	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	3	14	3	1	0	0	0	0	0	0	0	3	0	6	10	4	3	29	12	20	16	121	379	1663	7	0
FFQ	146	0	0	0	0	0	0	0	0	0	0	0	0	0	1	11	9	9	8	5	2	0	0	0	0	0	0	0	4	0	1	7	5	1	18	9	14	24	130	390	1646	7	0
FFQ	147	0	0	0	0	0	0	0	0	0	0	0	0	0	1	3	2	12	6	4	3	0	0	0	0	0	0	0	8	1	4	8	5	4	20	14	19	24	138	397	1619	9	0
FFQ	148	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	2	8	13	4	7	0	0	0	0	0	0	0	8	1	3	6	4	6	16	12	27	21	122	412	1609	3	0
FFQ	149	0	0	0	0	0	0	0	0	0	0	0	0	0	1	4	2	11	8	3	5	0	0	0	0	0	0	0	4	0	1	8	6	7	21	12	27	24	94	346	1690	1	0
FFQ	150	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	7	12	11	2	4	0	0	0	0	1	0	0	8	0	2	5	0	5	18	17	12	24	118	334	1548	3	0
FFQ	151	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	3	11	11	8	8	0	0	0	0	0	0	0	10	0	11	26	9	7	41	18	38	30	213	349	958	1	0
# Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part.
# Columns correspond to qualities and rows to cycles. First column is the cycle number.
LFQ	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	133	0	130	0	0	0	0	0	0	0	0	0	0	233	31	3	1087	589	106	1	0	0	0	0	0	0
LFQ	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	156	0	180	0	0	0	0	0	0	0	0	0	0	141	124	63	1003	556	90	0	0	0	0	0	0	0
LFQ	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	117	0	75	0	0	0	0	0	0	0	0	0	0	140	89	45	1075	641	131	0	0	0	0	0	0	0
LFQ	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	0	42	0	0	0	0	0	0	0	0	0	0	121	51	28	990	796	187	0	0	0	0	0	0	0
LFQ	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	0	39	0	0	0	0	0	0	0	0	0	0	67	64	48	890	882	228	0	0	0	0	0	0	0
LFQ	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	49	0	39	14	14	0	0	0	0	0	0	0	0	18	7	30	107	268	66	128	0	1573	0	0	0	0
LFQ	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	61	0	47	27	44	0	0	0	0	0	0	0	0	22	16	37	138	280	49	133	0	1459	0	0	0	0
LFQ	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	1	66	21	38	0	0	0	0	0	0	0	0	30	20	48	133	293	51	162	0	1388	0	0	0	0
LFQ	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	64	1	37	9	11	0	0	0	0	0	0	0	0	19	10	36	121	226	57	149	0	1573	0	0	0	0
LFQ	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	0	32	6	8	0	0	0	0	0	0	0	0	11	9	21	109	234	64	113	0	1652	0	0	0	0
LFQ	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	3	47	9	19	0	0	0	0	0	0	0	0	14	5	25	73	252	57	102	0	1645	0	0	0	0
LFQ	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	60	2	33	5	13	0	0	0	0	0	0	0	0	13	7	19	96	263	65	96	0	1640	0	0	0	0
LFQ	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	52	4	26	5	9	1	0	0	0	0	0	0	0	0	4	0	35	51	47	28	61	255	1733	0	0	0
LFQ	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	53	3	29	4	2	2	0	0	0	0	0	0	0	0	4	0	34	58	35	25	54	217	1790	0	0	0
LFQ	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	62	0	27	5	8	1	0	0	0	0	0	0	0	0	5	0	44	53	42	18	49	237	1760	0	0	0
LFQ	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	54	3	32	5	7	3	0	0	0	0	0	0	0	0	0	0	40	63	45	25	48	236	1751	0	0	0
LFQ	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	59	2	25	5	4	3	0	0	0	0	0	0	0	0	2	0	42	63	47	24	46	248	1738	0	0	0
LFQ	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	46	0	37	5	4	4	0	0	0	0	0	0	0	0	5	0	56	45	40	23	70	238	1738	0	0	0
LFQ	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	43	1	26	5	4	2	0	0	0	0	0	0	0	0	3	0	37	51	42	31	66	209	1786	0	0	0
LFQ	20	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	51	5	32	4	7	1	0	0	0	0	0	0	0	0	9	0	35	53	48	11	76	222	1746	0	0	0
LFQ	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	41	2	28	7	7	3	0	0	0	0	0	0	0	0	4	0	28	48	35	22	64	241	1779	0	0	0
LFQ	22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	42	4	33	9	6	2	0	0	0	0	0	0	0	0	6	0	35	47	47	34	66	207	1757	0	0	0
LFQ	23	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	31	5	38	5	7	3	0	0	0	0	0	0	0	0	3	0	42	60	41	33	57	221	475	1279	0	0
LFQ	24	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22	25	7	28	7	8	6	0	0	0	0	0	0	0	0	1	0	38	46	45	42	54	231	469	1284	0	0
LFQ	25	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	20	25	4	28	5	6	1	0	0	0	0	0	0	0	0	8	0	34	69	31	40	59	222	522	1239	0	0
LFQ	26	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22	28	4	34	16	11	7	0	0	0	0	0	0	0	0	7	0	44	42	45	29	63	221	480	1260	0	0
LFQ	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	26	1	18	8	3	1	0	0	0	0	0	0	0	0	7	0	30	53	36	37	62	239	437	1338	0	0
LFQ	28	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	27	25	5	29	9	6	5	0	0	0	0	0	0	0	0	4	0	34	32	44	39	60	242	446	1305	0	0
LFQ	29	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	30	13	31	9	11	2	0	0	0	0	0	0	0	0	4	0	34	50	36	33	52	229	428	1325	0	0
LFQ	30	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	23	29	8	26	8	7	4	0	0	0	0	0	0	0	0	4	0	39	39	44	26	53	245	456	1301	0	0
LFQ	31	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	36	9	28	7	6	2	0	0	0	0	0	0	0	0	1	0	36	40	42	35	42	248	449	1317	0	0
LFQ	32	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	33	10	33	5	9	1	0	0	0	0	0	0	0	0	6	0	28	45	31	38	43	251	473	1290	0	0
LFQ	33	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	16	19	7	20	5	6	2	0	0	0	0	0	0	0	0	4	0	37	43	35	38	49	250	453	1327	0	0
LFQ	34	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	24	24	16	22	3	5	1	0	0	0	0	0	0	0	0	5	0	35	37	44	40	54	199	462	1340	0	0
LFQ	35	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	24	23	12	23	3	19	2	0	0	0	0	0	0	0	0	7	0	40	39	43	39	65	220	448	1304	0	0
LFQ	36	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	21	37	21	21	1	13	1	0	0	0	0	0	0	0	0	3	0	31	32	45	35	61	210	412	1367	0	0
LFQ	37	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	23	42	23	23	8	13	3	0	0	0	0	0	0	0	0	4	0	31	60	42	56	58	209	460	1255	0	0
LFQ	38	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	28	24	25	23	0	9	1	0	0	0	0	0	0	0	0	6	0	53	54	43	48	66	230	424	1272	0	0
LFQ	39	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	20	30	24	21	5	17	1	0	0	0	0	0	0	0	0	6	0	53	50	28	55	54	221	441	1282	0	0
LFQ	40	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	21	28	27	17	2	7	0	0	0	0	0	0	0	0	0	4	0	42	56	31	37	51	220	429	1339	0	0
LFQ	41	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	20	23	40	18	1	15	2	0	0	0	0	0	0	0	0	9	0	38	47	31	47	64	239	429	1284	0	0
LFQ	42	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	18	22	29	7	2	8	0	0	0	0	0	0	0	0	0	3	0	34	39	39	40	48	222	475	1317	0	0
LFQ	43	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	13	36	42	10	0	15	0	0	0	0	0	0	0	0	0	7	0	43	59	60	55	53	262	477	1173	0	0
LFQ	44	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	22	41	46	11	0	32	0	0	0	0	0	0	0	0	0	6	0	53	82	58	43	80	312	469	1056	0	0
LFQ	45	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	14	39	41	13	0	30	0	0	0	0	0	0	0	0	0	6	0	46	89	25	62	113	330	437	1064	0	0
LFQ	46	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	15	41	51	16	0	26	0	0	0	0	0	0	0	0	0	10	0	55	83	27	67	120	320	477	999	0	0
LFQ	47	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	16	53	49	16	0	29	0	0	0	0	0	0	0	0	1	5	0	49	62	19	42	118	326	488	1033	0	0
LFQ	48	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	18	46	40	10	0	29	0	0	0	0	0	0	0	0	0	2	0	45	79	16	39	96	327	492	1065	0	0
LFQ	49	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	10	35	51	18	0	21	0	0	0	0	0	0	0	0	0	6	1	65	66	22	42	104	311	464	1091	0	0
LFQ	50	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	11	37	31	13	0	21	0	0	0	0	0	0	0	0	0	5	1	54	68	25	48	101	330	449	1109	0	0
LFQ	51	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	9	35	40	18	0	18	0	0	0	0	0	0	0	0	0	11	0	52	56	20	37	117	318	433	1136	0	0
LFQ	52	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	8	29	45	10	0	12	0	0	0	0	0	0	0	0	0	7	0	46	60	19	69	115	309	428	1142	0	0
LFQ	53	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	8	34	38	10	0	22	0	0	0	0	0	0	0	0	1	7	0	46	67	21	60	108	315	467	1094	0	0
LFQ	54	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	9	31	50	15	0	30	0	0	0	0	0	0	0	0	0	6	0	47	49	23	53	104	302	450	1125	0	0
LFQ	55	0	0	0	0	0	0	0	0	0	0	0	0	0	0	20	13	29	43	10	0	21	0	0	0	0	0	0	0	0	0	8	0	48	71	30	50	114	328	449	1079	0	0
LFQ	56	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	11	30	44	5	0	19	0	0	0	0	0	0	0	0	1	6	0	37	70	23	36	121	305	479	1109	0	0
LFQ	57	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	3	55	47	8	0	34	0	0	0	0	0	0	0	0	0	4	0	52	70	27	57	105	299	455	1080	0	0
LFQ	58	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	13	31	47	14	0	16	0	0	0	0	0	0	0	0	0	6	0	53	62	17	55	111	319	471	1076	6	0
LFQ	59	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	39	36	11	0	24	0	0	0	0	0	0	0	0	1	6	0	50	56	22	56	122	301	416	1130	15	0
LFQ	60	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	7	34	38	16	0	20	0	0	0	0	0	0	0	0	1	1	2	61	59	13	59	98	318	438	1118	13	0
LFQ	61	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	14	34	30	9	0	17	0	0	0	0	0	0	0	0	0	3	2	41	59	21	57	110	300	443	1151	11	0
LFQ	62	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	12	38	32	8	0	28	0	0	0	0	0	0	0	0	1	14	2	47	63	21	57	120	280	432	1137	11	0
LFQ	63	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	8	42	38	12	2	20	0	0	0	0	0	0	0	0	0	11	2	45	49	22	52	116	271	437	1167	10	0
LFQ	64	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	8	36	38	13	1	21	0	0	0	0	0	0	0	0	0	4	2	45	75	20	53	116	277	429	1151	12	0
LFQ	65	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	10	43	26	11	1	18	0	0	0	0	0	0	0	0	0	9	3	55	67	20	57	113	292	439	1130	8	0
LFQ	66	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	16	51	40	16	1	22	0	0	0	0	0	0	0	0	0	3	2	29	66	26	40	94	311	435	1137	13	0
LFQ	67	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	12	42	25	12	0	23	0	0	0	0	0	0	0	0	1	11	0	35	56	13	43	109	282	465	1165	6	0
LFQ	68	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	11	40	26	12	1	20	0	0	0	0	0	0	0	0	1	5	0	45	46	16	55	97	302	468	1148	4	0
LFQ	69	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	11	40	37	19	0	28	0	0	0	0	0	0	0	0	0	6	4	41	62	24	42	112	296	418	1150	4	0
LFQ	70	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	15	45	44	13	0	22	0	0	0	0	0	0	0	0	3	7	3	46	55	21	49	113	289	424	1150	2	0
LFQ	71	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	11	37	40	13	1	19	0	0	0	0	0	0	0	0	0	6	1	44	60	23	47	98	317	400	1180	4	0
LFQ	72	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	11	42	37	11	0	30	0	0	0	0	0	0	0	0	2	7	6	41	62	22	41	89	297	458	1143	2	0
LFQ	73	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	37	25	14	1	16	0	0	0	0	0	0	0	0	1	7	2	31	57	19	57	67	285	478	1187	2	0
LFQ	74	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	8	59	27	11	1	21	0	0	0	0	0	0	0	0	2	5	2	34	59	11	51	103	280	409	1213	1	0
LFQ	75	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	14	49	29	15	2	23	0	0	0	0	0	0	0	0	4	5	4	35	54	19	57	93	313	420	1167	0	0
LFQ	76	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	8	36	27	6	3	31	0	0	0	0	0	0	0	0	2	6	7	41	68	16	52	93	271	464	1169	0	0
LFQ	77	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	9	27	31	13	0	22	0	0	0	0	0	0	0	0	3	3	4	43	67	13	44	99	250	480	1194	0	0
LFQ	78	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	12	42	28	6	2	15	0	0	0	0	0	0	0	0	7	4	7	41	54	25	63	85	268	451	1185	0	0
LFQ	79	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	12	38	29	11	1	28	0	0	0	0	0	0	0	0	4	7	3	30	57	21	52	108	312	465	1117	0	0
LFQ	80	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	5	35	39	10	1	23	0	0	0	0	0	0	0	0	3	12	3	42	58	18	59	90	264	444	1192	0	0
LFQ	81	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	11	41	31	8	0	25	0	0	0	0	0	0	0	0	1	5	8	29	59	13	55	112	254	454	1186	0	0
LFQ	82	0	0	0	0	0	0	0	0	0	0	0	0	0	0	28	10	46	29	11	0	33	0	0	0	0	0	0	0	0	5	6	11	34	65	18	42	91	277	441	1166	0	0
LFQ	83	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	12	36	30	12	1	17	0	0	0	0	0	0	0	0	8	9	8	23	59	14	48	95	252	457	1222	0	0
LFQ	84	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	9	40	27	9	3	19	0	0	0	0	0	0	0	0	7	9	14	24	59	18	33	98	281	472	1173	0	0
LFQ	85	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	10	36	29	14	5	18	0	0	0	0	0	0	0	0	10	12	18	23	52	19	38	98	299	435	1178	0	0
LFQ	86	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	7	55	35	14	4	19	0	0	0	0	0	0	0	0	6	17	10	14	66	16	40	93	266	467	1169	0	0
LFQ	87	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	15	28	32	15	6	26	0	0	0	0	0	0	0	0	4	8	20	27	57	15	45	87	231	406	1272	0	0
LFQ	88	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	11	45	33	10	4	18	0	0	0	0	0	0	0	0	7	10	16	24	65	26	34	84	289	438	1181	0	0
LFQ	89	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	4	29	19	10	2	12	0	0	0	0	0	0	0	0	7	14	21	16	63	14	45	103	259	459	1220	0	0
LFQ	90	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	6	40	31	12	4	15	0	0	0	0	0	0	0	0	7	10	21	16	73	11	35	87	270	430	1227	0	0
LFQ	91	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	6	34	29	5	2	17	0	0	0	0	0	0	0	0	7	12	12	14	59	17	26	94	288	453	1220	0	0
LFQ	92	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	6	36	29	10	6	8	0	0	0	0	0	0	0	0	10	6	9	8	52	16	36	85	258	466	1263	0	0
LFQ	93	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	8	30	26	6	9	15	0	0	0	0	0	0	0	0	9	9	15	18	54	18	40	101	291	421	1226	0	0
LFQ	94	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	4	30	19	9	9	18	0	0	0	0	0	0	0	0	11	10	23	4	47	17	31	100	239	472	1258	0	0
LFQ	95	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	13	41	32	14	11	18	0	0	0	0	0	0	1	0	10	5	24	6	75	19	36	86	254	420	1239	0	0
LFQ	96	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	9	32	39	15	9	12	0	0	0	0	0	0	0	0	7	15	25	11	37	17	40	84	263	467	1213	0	0
LFQ	97	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	11	46	27	8	10	5	0	0	0	0	0	0	0	0	14	10	14	3	71	11	40	92	259	456	1223	0	0
LFQ	98	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	6	46	37	19	6	9	0	0	0	0	0	0	0	0	8	10	17	5	69	20	35	91	241	471	1208	0	0
LFQ	99	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	5	30	23	11	4	6	0	0	0	0	0	0	0	0	12	14	21	8	67	9	31	80	244	407	1331	0	0
LFQ	100	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	3	35	24	9	10	6	0	0	0	0	0	0	0	0	10	8	20	7	47	13	35	84	267	427	1291	0	0
LFQ	101	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	9	37	34	14	13	16	0	0	0	0	0	0	2	0	8	9	19	16	62	20	40	80	237	444	1240	0	0
LFQ	102	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	15	36	36	14	10	8	0	0	0	0	0	0	2	0	7	14	23	2	59	20	38	85	248	413	1270	0	0
LFQ	103	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	11	26	37	10	14	4	0	0	0	0	0	0	0	0	8	12	12	6	53	12	32	77	245	416	1319	0	0
LFQ	104	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	10	32	26	10	11	3	0	0	0	0	0	0	0	0	8	8	13	8	61	14	25	86	219	433	1328	0	0
LFQ	105	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	5	30	24	9	11	4	0	0	0	0	0	0	0	0	11	11	13	6	60	10	25	87	248	470	1273	0	0
LFQ	106	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	7	47	22	5	7	5	0	0	0	0	0	0	2	0	9	9	11	5	63	18	32	81	272	441	1259	0	0
LFQ	107	0	0	0	0	0	0	0	0	0	0	0	0	0	0	20	9	40	26	14	10	4	0	0	0	0	0	0	0	0	9	21	25	7	58	18	24	90	251	432	1254	0	0
LFQ	108	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	10	42	31	9	11	4	0	0	0	0	0	0	0	0	13	17	19	4	62	12	27	82	265	449	1243	0	0
LFQ	109	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	9	44	26	11	14	2	0	0	0	0	0	0	0	0	6	18	16	7	53	14	27	89	266	443	1252	0	0
LFQ	110	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	7	29	25	14	17	0	0	0	0	0	0	0	1	0	5	12	14	11	61	14	24	85	246	426	1302	0	0
LFQ	111	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22	7	35	28	14	13	3	0	0	0	0	0	0	1	0	9	17	17	3	81	17	26	76	225	442	1275	0	0
LFQ	112	0	0	0	0	0	0	0	0	0	0	0	0	0	0	23	10	29	27	11	16	0	0	0	0	0	0	0	0	0	15	18	14	3	72	20	27	72	242	423	1289	0	0
LFQ	113	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	8	37	40	14	13	3	0	0	0	0	0	0	0	0	8	17	18	4	60	18	33	91	237	431	1260	0	0
LFQ	114	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	8	24	32	14	16	2	0	0	0	0	0	0	3	0	10	22	18	9	79	16	24	88	227	439	1268	0	0
LFQ	115	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	10	35	24	12	15	1	0	0	0	0	0	0	2	0	11	15	9	4	48	21	32	94	249	446	1272	0	0
LFQ	116	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	10	45	22	20	23	0	0	0	0	0	0	0	1	0	7	14	22	7	71	15	30	93	248	433	1234	0	0
LFQ	117	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	9	36	26	18	18	0	0	0	0	0	0	0	3	0	5	13	24	9	64	23	30	84	257	421	1253	0	0
LFQ	118	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	3	44	25	20	14	0	0	0	0	0	0	0	4	0	12	17	13	6	64	21	39	85	238	439	1253	0	0
LFQ	119	0	0	0	0	0	0	0	0	0	0	0	0	0	0	23	7	36	23	14	32	0	0	0	0	0	0	0	1	0	11	18	17	6	77	19	25	84	239	432	1247	0	0
LFQ	120	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	8	33	31	19	18	0	0	0	0	0	0	0	2	0	12	25	12	5	68	23	33	81	254	433	1236	0	0
LFQ	121	0	0	0	0	0	0	0	0	0	0	0	0	1	0	24	11	34	21	20	9	0	0	0	0	0	0	0	3	0	5	12	8	3	50	12	28	87	248	428	1307	0	0
LFQ	122	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	6	33	26	14	19	0	0	0	0	0	0	0	5	0	14	14	11	5	50	21	21	66	214	443	1334	0	0
LFQ	123	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	11	39	38	13	23	0	0	0	0	0	0	0	3	0	12	19	10	4	53	13	35	77	263	407	1262	0	0
LFQ	124	0	0	0	0	0	0	0	0	0	0	0	0	0	1	22	7	29	29	12	14	0	0	0	0	0	0	0	4	0	13	20	14	6	72	25	21	84	240	428	1269	0	0
LFQ	125	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	7	35	34	23	14	0	0	0	0	0	0	0	4	0	12	15	10	5	54	21	32	88	218	430	1290	0	0
LFQ	126	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	8	23	27	18	19	0	0	0	0	0	0	0	2	0	9	16	15	7	60	12	28	68	245	455	1280	0	0
LFQ	127	0	0	0	0	0	0	0	0	0	0	0	0	0	0	23	15	27	27	10	12	0	0	0	0	0	0	0	3	1	12	17	12	8	59	21	33	83	245	427	1275	0	0
LFQ	128	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22	9	33	26	21	13	0	0	0	0	0	0	0	4	0	13	21	11	7	64	19	29	67	226	440	1285	0	0
LFQ	129	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	8	28	30	16	5	0	0	0	0	0	0	0	8	0	12	17	6	2	53	28	37	74	234	458	1268	0	0
LFQ	130	0	0	0	0	0	0	0	0	0	0	0	0	1	0	15	14	26	32	18	13	0	0	0	0	0	0	0	8	1	7	24	5	4	53	13	41	76	233	484	1242	0	0
LFQ	131	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	11	29	27	16	7	0	0	0	0	0	0	0	3	1	8	21	9	7	67	20	26	77	248	424	1283	0	0
LFQ	132	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	11	21	33	14	15	0	0	0	0	0	0	0	8	0	20	16	4	6	62	25	31	68	240	431	1273	0	0
LFQ	133	0	0	0	0	0	0	0	0	0	0	0	0	1	0	26	9	23	33	8	14	0	0	0	0	0	0	0	12	0	15	13	7	6	70	24	34	72	233	464	1245	0	0
LFQ	134	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22	13	32	37	17	14	0	0	0	0	0	0	0	12	1	8	13	6	7	56	22	34	69	231	457	1257	1	0
LFQ	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	16	43	35	15	22	0	0	0	0	0	0	0	7	0	11	18	3	8	70	22	30	64	243	423	1252	1	0
LFQ	136	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22	13	32	41	14	13	0	0	0	0	0	0	0	8	0	15	32	5	8	84	27	35	72	257	415	1213	3	0
LFQ	137	0	0	0	0	0	0	0	0	0	0	0	0	0	1	19	13	36	32	15	13	0	0	0	0	0	0	0	5	0	17	23	9	9	72	24	41	65	260	439	1216	0	0
LFQ	138	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	14	26	30	11	7	0	0	0	0	0	0	0	6	0	7	23	10	7	71	16	38	64	271	452	1242	1	0
LFQ	139	0	0	0	0	0	0	0	0	0	0	0	0	0	0	23	14	32	40	13	12	0	0	0	0	0	0	0	7	0	7	22	10	12	68	23	27	81	258	448	1212	0	0
LFQ	140	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	6	28	40	13	5	0	0	0	0	0	0	0	8	0	12	16	5	13	75	30	34	59	277	469	1204	0	0
LFQ	141	0	0	0	0	0	0	0	0	0	0	0	0	0	0	23	12	44	25	21	14	0	0	0	0	0	1	0	9	0	9	18	8	7	54	35	38	73	227	431	1259	0	0
LFQ	142	0	0	0	0	0	0	0	0	0	0	0	0	0	1	23	8	23	30	9	11	0	0	0	0	0	0	0	8	1	11	13	7	7	73	23	30	73	244	429	1284	0	0
LFQ	143	0	0	0	0	0	0	0	0	0	0	0	0	1	0	24	9	31	26	13	7	0	0	0	0	0	0	0	11	0	12	15	5	8	41	34	26	47	262	452	1281	0	0
LFQ	144	0	0	0	0	0	0	0	0	0	0	0	0	0	1	21	9	33	47	10	13	0	0	0	0	0	1	0	12	0	8	18	11	13	71	34	46	48	252	401	1256	0	0
LFQ	145	0	0	0	0	0	0	0	0	0	0	0	0	1	0	15	9	24	32	8	11	0	0	0	0	0	0	0	10	0	13	23	6	5	67	40	34	51	268	457	1231	0	0
LFQ	146	0	0	0	0	0	0	0	0	0	0	0	0	0	0	24	16	35	36	6	9	0	0	0	0	0	1	0	10	0	11	19	8	5	62	35	37	56	244	445	1246	0	0
LFQ	147	0	0	0	0	0	0	0	0	0	0	0	0	0	1	25	17	36	29	12	6	0	0	0	0	0	1	0	15	1	7	22	8	7	68	25	44	59	278	438	1202	0	0
LFQ	148	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	10	36	51	10	8	0	0	0	0	0	0	0	10	0	11	21	7	12	59	30	33	62	239	440	1222	0	0
LFQ	149	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	12	38	46	3	7	0	0	0	0	0	0	0	16	0	15	13	10	5	59	28	35	47	246	453	1223	0	0
LFQ	150	0	0	0	0	0	0	0	0	0	0	0	0	1	0	16	11	35	37	1	9	0	0	0	0	0	0	0	10	1	10	21	9	5	58	21	45	55	214	387	1209	0	0
LFQ	151	0	0	0	0	0	0	0	0	0	0	0	0	2	0	36	10	50	48	19	23	0	0	0	0	0	0	0	14	1	20	35	13	7	101	38	66	51	298	331	603	0	0
# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part.
GCF	10.55	0
GCF	21.36	4
GCF	21.86	6
GCF	22.61	11
GCF	23.37	10
GCF	23.87	16
GCF	24.37	13
GCF	24.87	16
GCF	25.38	46
GCF	25.88	57
GCF	26.38	48
GCF	26.88	52
GCF	27.39	83
GCF	27.89	73
GCF	28.39	82
GCF	29.15	139
GCF	29.90	131
GCF	30.40	146
GCF	30.90	153
GCF	31.41	155
GCF	31.91	134
GCF	32.41	124
GCF	32.91	118
GCF	33.42	119
GCF	33.92	127
GCF	34.42	111
GCF	34.92	118
GCF	35.43	113
GCF	35.93	98
GCF	36.43	82
GCF	36.93	48
GCF	37.44	40
GCF	37.94	44
GCF	38.44	61
GCF	38.94	41
GCF	39.45	40
GCF	39.95	41
GCF	40.45	39
GCF	40.95	33
GCF	41.46	26
GCF	41.96	19
GCF	42.46	8
GCF	42.96	17
GCF	43.72	5
GCF	44.47	3
GCF	44.97	1
GCF	45.73	2
GCF	46.48	4
GCF	46.98	3
GCF	47.74	4
GCF	48.49	1
GCF	49.50	0
GCF	50.50	2
GCF	51.01	4
GCF	51.76	0
GCF	52.51	1
GCF	53.02	0
GCF	53.77	1
GCF	56.53	0
GCF	59.05	1
# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part.
GCL	6.78	0
GCL	13.82	1
GCL	15.08	0
GCL	16.83	1
GCL	18.84	0
GCL	20.60	2
GCL	21.36	6
GCL	21.86	9
GCL	22.36	15
GCL	22.86	19
GCL	23.37	12
GCL	23.87	18
GCL	24.37	21
GCL	24.87	24
GCL	25.38	44
GCL	25.88	40
GCL	26.38	52
GCL	26.88	67
GCL	27.39	71
GCL	27.89	62
GCL	28.39	81
GCL	28.89	113
GCL	29.40	109
GCL	29.90	106
GCL	30.40	131
GCL	30.90	127
GCL	31.41	129
GCL	31.91	111
GCL	32.41	155
GCL	32.91	141
GCL	33.42	152
GCL	33.92	128
GCL	34.42	130
GCL	34.92	119
GCL	35.43	110
GCL	35.93	100
GCL	36.43	68
GCL	36.93	66
GCL	37.44	46
GCL	37.94	57
GCL	38.44	68
GCL	38.94	47
GCL	39.45	35
GCL	39.95	44
GCL	40.45	46
GCL	40.95	27
GCL	41.46	26
GCL	41.96	14
GCL	42.46	15
GCL	42.96	10
GCL	43.47	14
GCL	43.97	11
GCL	44.72	3
GCL	45.48	0
GCL	45.98	1
GCL	46.48	4
GCL	46.98	3
GCL	47.49	1
GCL	47.99	2
GCL	48.49	0
GCL	48.99	1
GCL	49.75	0
GCL	50.50	2
GCL	52.01	0
GCL	53.77	1
# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
GCC	1	32.66	17.88	17.60	31.86	0.00	0.00
GCC	2	34.67	15.00	15.02	35.30	0.00	0.00
GCC	3	34.46	16.28	16.32	32.94	0.00	0.00
GCC	4	35.52	15.82	15.69	32.97	0.00	0.00
GCC	5	31.91	15.82	16.82	35.45	0.00	0.00
GCC	6	33.53	17.62	16.30	32.56	0.00	0.00
GCC	7	33.61	15.33	18.59	32.47	0.00	0.00
GCC	8	33.27	16.32	16.32	34.09	0.00	0.00
GCC	9	34.07	15.61	16.75	33.57	0.00	0.00
GCC	10	33.27	16.00	17.27	33.46	0.00	0.00
GCC	11	34.22	17.14	15.24	33.40	0.00	0.00
GCC	12	34.44	16.43	16.43	32.71	0.00	0.00
GCC	13	34.18	15.37	16.43	34.03	0.00	0.00
GCC	14	35.28	16.34	16.86	31.52	0.00	0.00
GCC	15	34.46	16.65	17.14	31.76	0.00	0.00
GCC	16	34.07	16.23	17.12	32.58	0.00	0.00
GCC	17	35.34	15.33	16.95	32.38	0.00	0.00
GCC	18	33.03	14.85	18.55	33.57	0.00	0.00
GCC	19	33.79	16.58	16.04	33.59	0.00	0.00
GCC	20	33.16	16.13	17.42	33.29	0.00	0.00
GCC	21	35.13	16.93	15.50	32.45	0.00	0.00
GCC	22	33.27	16.02	17.36	33.35	0.00	0.00
GCC	23	33.61	16.84	16.86	32.68	0.00	0.00
GCC	24	35.08	14.22	17.12	33.57	0.00	0.00
GCC	25	33.61	16.15	17.44	32.79	0.00	0.00
GCC	26	33.94	16.30	16.62	33.14	0.00	0.00
GCC	27	34.91	16.02	16.67	32.40	0.00	0.00
GCC	28	35.30	15.02	15.61	34.07	0.00	0.00
GCC	29	34.87	15.85	17.01	32.27	0.00	0.00
GCC	30	34.00	16.45	17.53	32.01	0.00	0.00
GCC	31	32.10	17.94	17.38	32.58	0.00	0.00
GCC	32	34.80	15.65	16.30	33.25	0.00	0.00
GCC	33	35.50	15.00	16.34	33.16	0.00	0.00
GCC	34	34.57	15.67	16.13	33.64	0.00	0.00
GCC	35	32.71	17.21	15.80	34.28	0.00	0.00
GCC	36	33.10	16.17	15.67	35.06	0.00	0.00
GCC	37	33.57	15.39	17.25	33.79	0.00	0.00
GCC	38	33.61	15.05	17.81	33.53	0.00	0.00
GCC	39	33.96	15.52	16.65	33.87	0.00	0.00
GCC	40	34.11	16.45	16.34	33.10	0.00	0.00
GCC	41	35.04	15.69	16.95	32.32	0.00	0.00
GCC	42	35.00	16.15	16.21	32.64	0.00	0.00
GCC	43	34.80	17.40	16.02	31.78	0.00	0.00
GCC	44	36.08	15.65	15.76	32.51	0.00	0.00
GCC	45	33.70	15.69	16.86	33.74	0.00	0.00
GCC	46	33.40	16.88	17.92	31.80	0.00	0.00
GCC	47	34.57	16.86	16.52	32.06	0.00	0.00
GCC	48	33.07	16.49	15.74	34.70	0.00	0.00
GCC	49	34.59	15.76	16.39	33.27	0.00	0.00
GCC	50	32.45	18.05	16.77	32.73	0.00	0.00
GCC	51	32.77	17.42	17.57	32.23	0.00	0.00
GCC	52	35.19	16.56	16.26	31.99	0.00	0.00
GCC	53	33.48	15.07	17.21	34.24	0.00	0.00
GCC	54	36.25	15.52	16.60	31.63	0.00	0.00
GCC	55	34.91	16.93	16.73	31.43	0.00	0.00
GCC	56	33.87	15.20	16.52	34.41	0.00	0.00
GCC	57	34.15	16.34	16.54	32.97	0.00	0.00
GCC	58	32.68	16.39	16.43	34.50	0.00	0.00
GCC	59	33.92	14.96	17.12	34.00	0.00	0.00
GCC	60	34.33	15.28	16.26	34.13	0.00	0.00
GCC	61	34.39	15.54	17.64	32.43	0.00	0.00
GCC	62	32.90	16.67	17.08	33.35	0.00	0.00
GCC	63	32.73	16.17	18.16	32.94	0.00	0.00
GCC	64	34.18	15.46	16.26	34.11	0.00	0.00
GCC	65	34.37	17.29	15.26	33.07	0.00	0.00
GCC	66	34.44	16.39	16.02	33.16	0.00	0.00
GCC	67	35.06	16.15	17.19	31.60	0.00	0.00
GCC	68	32.60	15.87	16.00	35.54	0.00	0.00
GCC	69	34.61	16.86	15.97	32.56	0.00	0.00
GCC	70	33.55	16.75	16.28	33.42	0.00	0.00
GCC	71	33.40	15.74	16.80	34.07	0.00	0.00
GCC	72	34.50	15.61	16.80	33.10	0.00	0.00
GCC	73	32.56	16.95	16.71	33.79	0.00	0.00
GCC	74	35.02	16.80	15.74	32.45	0.00	0.00
GCC	75	36.14	15.69	15.93	32.23	0.00	0.00
GCC	76	33.92	16.86	16.75	32.47	0.00	0.00
GCC	77	35.13	15.13	16.39	33.35	0.00	0.00
GCC	78	35.24	16.47	16.15	32.14	0.00	0.00
GCC	79	32.79	16.67	16.86	33.68	0.00	0.00
GCC	80	33.90	17.75	16.41	31.95	0.00	0.00
GCC	81	32.99	15.82	17.86	33.33	0.00	0.00
GCC	82	34.31	14.25	17.73	33.72	0.00	0.00
GCC	83	33.90	14.03	16.77	35.30	0.00	0.00
GCC	84	34.20	16.28	15.93	33.59	0.00	0.00
GCC	85	34.59	17.14	16.67	31.60	0.00	0.00
GCC	86	34.52	15.76	14.70	35.02	0.00	0.00
GCC	87	34.76	16.69	16.34	32.21	0.00	0.00
GCC	88	34.33	15.78	16.71	33.18	0.00	0.00
GCC	89	32.30	15.87	17.27	34.57	0.00	0.00
GCC	90	34.20	15.61	16.60	33.59	0.00	0.00
GCC	91	33.03	16.02	16.17	34.78	0.00	0.00
GCC	92	33.55	16.36	15.65	34.44	0.00	0.00
GCC	93	34.28	15.43	16.28	34.00	0.00	0.00
GCC	94	33.94	14.72	17.27	34.07	0.00	0.00
GCC	95	33.29	16.93	15.72	34.07	0.00	0.00
GCC	96	34.39	17.49	16.49	31.63	0.00	0.00
GCC	97	34.07	18.14	14.25	33.55	0.00	0.00
GCC	98	33.42	17.01	15.76	33.81	0.00	0.00
GCC	99	34.52	16.70	14.51	34.28	0.00	0.00
GCC	100	35.79	15.59	15.90	32.72	0.00	0.00
GCC	101	32.96	14.66	16.48	35.90	0.00	0.00
GCC	102	33.89	16.15	17.37	32.59	0.00	0.00
GCC	103	33.56	17.17	16.80	32.46	0.00	0.00
GCC	104	34.02	16.18	16.41	33.39	0.00	0.00
GCC	105	34.10	15.81	15.53	34.56	0.00	0.00
GCC	106	35.53	16.98	16.24	31.25	0.00	0.00
GCC	107	35.19	15.64	15.25	33.93	0.00	0.00
GCC	108	32.35	15.38	17.46	34.81	0.00	0.00
GCC	109	34.77	15.49	18.00	31.74	0.00	0.00
GCC	110	33.90	15.06	17.44	33.60	0.00	0.00
GCC	111	34.60	15.04	18.04	32.32	0.00	0.00
GCC	112	33.04	16.81	16.57	33.58	0.00	0.00
GCC	113	34.25	17.27	16.70	31.78	0.00	0.00
GCC	114	35.61	15.19	16.40	32.80	0.00	0.00
GCC	115	35.96	15.75	16.90	31.39	0.00	0.00
GCC	116	33.92	15.90	16.27	33.90	0.00	0.00
GCC	117	34.40	15.23	17.20	33.17	0.00	0.00
GCC	118	35.20	15.32	16.03	33.45	0.00	0.00
GCC	119	34.73	16.16	15.82	33.30	0.00	0.00
GCC	120	33.69	15.71	17.46	33.15	0.00	0.00
GCC	121	36.48	15.25	16.31	31.96	0.00	0.00
GCC	122	34.64	16.51	15.86	32.99	0.00	0.00
GCC	123	34.86	15.84	16.62	32.69	0.00	0.00
GCC	124	33.01	16.04	16.75	34.20	0.00	0.00
GCC	125	35.71	14.78	15.65	33.85	0.00	0.00
GCC	126	33.42	16.47	16.17	33.94	0.00	0.00
GCC	127	34.13	14.24	17.51	34.11	0.00	0.00
GCC	128	32.66	14.52	18.38	34.44	0.00	0.00
GCC	129	32.86	16.77	16.32	34.05	0.00	0.00
GCC	130	33.79	16.47	15.76	33.98	0.00	0.00
GCC	131	32.85	16.93	15.66	34.56	0.00	0.00
GCC	132	34.21	15.07	17.26	33.46	0.00	0.00
GCC	133	37.22	15.09	16.96	30.73	0.00	0.00
GCC	134	34.08	16.65	16.41	32.85	0.00	0.00
GCC	135	33.89	16.11	16.96	33.04	0.00	0.00
GCC	136	32.85	16.85	16.76	33.54	0.00	0.00
GCC	137	33.33	16.91	16.09	33.67	0.00	0.00
GCC	138	34.11	14.70	17.13	34.06	0.00	0.00
GCC	139	34.17	15.46	16.46	33.91	0.00	0.00
GCC	140	33.52	15.35	16.44	34.69	0.00	0.00
GCC	141	32.37	16.55	16.92	34.16	0.00	0.00
GCC	142	34.66	17.03	15.32	32.99	0.00	0.00
GCC	143	34.71	16.98	16.42	31.89	0.00	0.00
GCC	144	33.75	15.41	16.17	34.66	0.00	0.00
GCC	145	35.27	16.65	16.17	31.91	0.00	0.00
GCC	146	35.02	15.61	16.37	33.00	0.00	0.00
GCC	147	33.05	15.99	17.01	33.94	0.00	0.00
GCC	148	35.78	16.00	16.81	31.41	0.00	0.00
GCC	149	32.80	16.00	16.38	34.82	0.00	0.00
GCC	150	37.03	13.91	14.78	34.28	0.00	0.00
GCC	151	40.00	10.93	9.83	39.24	0.00	0.00
# ACGT content per cycle, read oriented. Use `grep ^GCT | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]
GCT	1	33.03	18.14	17.34	31.50
GCT	2	35.24	14.46	15.56	34.74
GCT	3	34.00	17.06	15.54	33.40
GCT	4	34.41	16.39	15.13	34.07
GCT	5	31.34	15.63	17.01	36.01
GCT	6	34.31	17.12	16.80	31.78
GCT	7	32.58	16.08	17.83	33.51
GCT	8	33.77	16.84	15.80	33.59
GCT	9	34.91	15.13	17.23	32.73
GCT	10	34.50	15.95	17.32	32.23
GCT	11	33.98	16.06	16.32	33.64
GCT	12	33.48	16.02	16.84	33.66
GCT	13	34.59	15.93	15.87	33.61
GCT	14	33.72	15.20	18.01	33.07
GCT	15	34.54	17.96	15.82	31.67
GCT	16	33.72	17.03	16.32	32.92
GCT	17	32.92	16.82	15.46	34.80
GCT	18	32.43	16.60	16.80	34.18
GCT	19	33.87	16.86	15.76	33.51
GCT	20	33.72	16.41	17.14	32.73
GCT	21	32.79	15.69	16.73	34.78
GCT	22	34.52	15.65	17.73	32.10
GCT	23	33.18	16.43	17.27	33.12
GCT	24	34.82	15.28	16.06	33.83
GCT	25	35.11	16.41	17.19	31.30
GCT	26	33.94	16.15	16.77	33.14
GCT	27	34.74	16.52	16.17	32.58
GCT	28	35.11	15.41	15.22	34.26
GCT	29	33.92	16.99	15.87	33.23
GCT	30	33.38	19.69	14.29	32.64
GCT	31	31.91	17.68	17.64	32.77
GCT	32	34.13	17.42	14.53	33.92
GCT	33	35.99	14.96	16.39	32.66
GCT	34	34.67	16.19	15.61	33.53
GCT	35	34.07	16.82	16.19	32.92
GCT	36	33.66	16.54	15.30	34.50
GCT	37	34.52	15.28	17.36	32.84
GCT	38	34.07	16.21	16.65	33.07
GCT	39	32.77	15.91	16.26	35.06
GCT	40	33.12	16.99	15.80	34.09
GCT	41	34.89	15.52	17.12	32.47
GCT	42	34.52	16.21	16.15	33.12
GCT	43	31.88	17.10	16.32	34.70
GCT	44	34.93	14.92	16.49	33.66
GCT	45	34.67	17.90	14.66	32.77
GCT	46	30.20	16.90	17.90	35.00
GCT	47	33.64	16.13	17.25	32.99
GCT	48	34.00	16.10	16.13	33.77
GCT	49	34.03	16.47	15.67	33.83
GCT	50	32.19	17.12	17.70	32.99
GCT	51	33.05	17.25	17.75	31.95
GCT	52	34.50	17.32	15.50	32.68
GCT	53	33.68	15.63	16.65	34.05
GCT	54	33.29	15.26	16.86	34.59
GCT	55	31.63	16.34	17.32	34.72
GCT	56	35.67	16.10	15.61	32.62
GCT	57	32.81	16.19	16.69	34.31
GCT	58	34.18	15.39	17.42	33.01
GCT	59	34.13	16.10	15.97	33.79
GCT	60	34.46	15.82	15.72	34.00
GCT	61	32.97	16.73	16.45	33.85
GCT	62	34.85	17.16	16.58	31.41
GCT	63	33.05	17.34	16.99	32.62
GCT	64	34.57	14.53	17.19	33.72
GCT	65	33.18	16.43	16.13	34.26
GCT	66	33.83	16.80	15.61	33.77
GCT	67	34.44	16.75	16.58	32.23
GCT	68	34.05	15.65	16.21	34.09
GCT	69	34.65	16.80	16.04	32.51
GCT	70	32.73	16.52	16.52	34.24
GCT	71	33.53	16.32	16.21	33.94
GCT	72	34.00	16.17	16.23	33.59
GCT	73	33.94	17.49	16.17	32.40
GCT	74	33.16	16.04	16.49	34.31
GCT	75	35.30	14.22	17.40	33.07
GCT	76	32.45	16.58	17.03	33.94
GCT	77	35.30	15.80	15.72	33.18
GCT	78	33.14	16.17	16.45	34.24
GCT	79	32.79	15.91	17.62	33.68
GCT	80	31.26	16.86	17.29	34.59
GCT	81	32.97	16.90	16.77	33.35
GCT	82	33.44	14.74	17.23	34.59
GCT	83	34.15	15.48	15.33	35.04
GCT	84	35.34	15.59	16.62	32.45
GCT	85	33.12	15.56	18.24	33.07
GCT	86	36.38	14.87	15.59	33.16
GCT	87	32.47	17.32	15.72	34.50
GCT	88	33.18	16.04	16.45	34.33
GCT	89	33.72	16.67	16.47	33.14
GCT	90	32.75	16.17	16.04	35.04
GCT	91	33.53	15.46	16.73	34.28
GCT	92	33.07	16.04	15.97	34.91
GCT	93	34.09	16.43	15.28	34.20
GCT	94	34.00	15.72	16.28	34.00
GCT	95	33.92	16.45	16.19	33.44
GCT	96	32.32	17.47	16.52	33.70
GCT	97	33.72	15.26	17.12	33.90
GCT	98	33.40	16.45	16.32	33.83
GCT	99	33.15	14.73	16.48	35.64
GCT	100	33.87	15.35	16.13	34.65
GCT	101	34.80	15.64	15.51	34.06
GCT	102	33.48	17.04	16.48	33.00
GCT	103	32.94	16.89	17.08	33.09
GCT	104	33.28	15.53	17.06	34.13
GCT	105	35.40	14.77	16.57	33.26
GCT	106	34.62	15.72	17.50	32.16
GCT	107	36.59	16.18	14.71	32.53
GCT	108	33.69	15.23	17.61	33.47
GCT	109	34.53	17.31	16.18	31.98
GCT	110	33.08	17.24	15.25	34.42
GCT	111	32.65	16.44	16.64	34.27
GCT	112	32.35	16.70	16.68	34.27
GCT	113	32.82	17.55	16.42	33.21
GCT	114	34.68	15.75	15.84	33.73
GCT	115	33.60	15.06	17.59	33.75
GCT	116	34.55	16.68	15.49	33.28
GCT	117	34.47	16.14	16.29	33.10
GCT	118	35.61	14.84	16.51	33.04
GCT	119	35.03	15.84	16.14	32.99
GCT	120	33.58	16.23	16.94	33.25
GCT	121	33.71	14.58	16.98	34.73
GCT	122	34.14	17.37	14.99	33.49
GCT	123	34.03	16.77	15.69	33.51
GCT	124	35.39	16.39	16.41	31.82
GCT	125	33.33	15.00	15.43	36.23
GCT	126	33.70	16.41	16.23	33.66
GCT	127	35.17	15.54	16.21	33.07
GCT	128	33.74	17.08	15.82	33.35
GCT	129	33.35	15.54	17.55	33.55
GCT	130	33.51	16.36	15.87	34.26
GCT	131	34.08	16.89	15.70	33.33
GCT	132	35.06	15.55	16.78	32.61
GCT	133	34.34	16.35	15.70	33.61
GCT	134	33.72	17.35	15.72	33.22
GCT	135	35.02	15.27	17.80	31.92
GCT	136	32.70	16.93	16.67	33.69
GCT	137	34.24	16.76	16.24	32.76
GCT	138	34.54	16.24	15.59	33.63
GCT	139	33.50	16.59	15.33	34.58
GCT	140	33.26	16.85	14.94	34.95
GCT	141	32.63	15.81	17.66	33.90
GCT	142	34.64	15.49	16.85	33.02
GCT	143	32.60	16.85	16.55	33.99
GCT	144	33.06	16.50	15.09	35.36
GCT	145	33.04	15.80	17.02	34.14
GCT	146	34.74	16.61	15.37	33.28
GCT	147	34.64	16.80	16.21	32.36
GCT	148	33.70	16.11	16.70	33.49
GCT	149	34.18	16.64	15.74	33.44
GCT	150	36.75	12.26	16.43	34.56
GCT	151	43.65	0.00	20.76	35.58
# ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
FBC	1	32.51	17.68	17.90	31.91	0.00	0.00
FBC	2	35.32	15.35	15.13	34.20	0.00	0.00
FBC	3	34.85	16.13	15.05	33.98	0.00	0.00
FBC	4	36.88	15.09	14.79	33.25	0.00	0.00
FBC	5	33.33	15.18	15.26	36.23	0.00	0.00
FBC	6	34.20	16.69	17.25	31.86	0.00	0.00
FBC	7	32.34	16.08	19.07	32.51	0.00	0.00
FBC	8	33.94	13.92	17.42	34.72	0.00	0.00
FBC	9	35.80	15.91	16.34	31.95	0.00	0.00
FBC	10	32.56	16.69	17.42	33.33	0.00	0.00
FBC	11	34.28	16.90	14.92	33.90	0.00	0.00
FBC	12	34.98	15.95	16.26	32.81	0.00	0.00
FBC	13	34.72	15.56	15.74	33.98	0.00	0.00
FBC	14	34.07	16.69	16.77	32.47	0.00	0.00
FBC	15	34.89	15.48	16.99	32.64	0.00	0.00
FBC	16	34.89	16.17	17.08	31.86	0.00	0.00
FBC	17	36.75	13.92	17.86	31.47	0.00	0.00
FBC	18	31.91	15.18	18.55	34.37	0.00	0.00
FBC	19	35.11	15.43	15.09	34.37	0.00	0.00
FBC	20	32.90	15.61	17.29	34.20	0.00	0.00
FBC	21	35.19	17.12	15.26	32.43	0.00	0.00
FBC	22	32.99	15.65	17.03	34.33	0.00	0.00
FBC	23	33.81	18.12	16.65	31.43	0.00	0.00
FBC	24	35.80	13.53	17.29	33.38	0.00	0.00
FBC	25	32.99	15.78	17.47	33.77	0.00	0.00
FBC	26	34.15	16.47	17.16	32.21	0.00	0.00
FBC	27	34.67	16.69	16.69	31.95	0.00	0.00
FBC	28	36.10	14.40	16.17	33.33	0.00	0.00
FBC	29	34.03	16.17	17.25	32.56	0.00	0.00
FBC	30	34.93	16.86	17.68	30.52	0.00	0.00
FBC	31	32.21	17.81	16.99	32.99	0.00	0.00
FBC	32	35.62	15.13	15.43	33.81	0.00	0.00
FBC	33	33.29	16.90	16.95	32.86	0.00	0.00
FBC	34	33.68	16.04	15.65	34.63	0.00	0.00
FBC	35	33.59	17.21	15.39	33.81	0.00	0.00
FBC	36	33.29	16.00	15.95	34.76	0.00	0.00
FBC	37	32.94	15.82	16.77	34.46	0.00	0.00
FBC	38	33.16	15.43	17.81	33.59	0.00	0.00
FBC	39	35.75	15.69	15.69	32.86	0.00	0.00
FBC	40	33.55	15.91	16.60	33.94	0.00	0.00
FBC	41	35.02	15.61	16.86	32.51	0.00	0.00
FBC	42	35.88	14.74	17.21	32.17	0.00	0.00
FBC	43	36.14	17.73	14.96	31.17	0.00	0.00
FBC	44	35.88	16.52	15.26	32.34	0.00	0.00
FBC	45	32.56	16.26	17.81	33.38	0.00	0.00
FBC	46	33.68	16.30	17.68	32.34	0.00	0.00
FBC	47	34.50	16.43	17.60	31.47	0.00	0.00
FBC	48	33.55	17.03	14.92	34.50	0.00	0.00
FBC	49	34.76	15.69	16.52	33.03	0.00	0.00
FBC	50	31.39	17.77	18.50	32.34	0.00	0.00
FBC	51	31.73	18.29	17.29	32.68	0.00	0.00
FBC	52	34.33	16.39	16.30	32.99	0.00	0.00
FBC	53	33.68	15.09	17.16	34.07	0.00	0.00
FBC	54	35.58	16.13	15.95	32.34	0.00	0.00
FBC	55	36.58	16.77	17.03	29.62	0.00	0.00
FBC	56	32.68	16.04	16.65	34.63	0.00	0.00
FBC	57	34.15	16.17	17.64	32.04	0.00	0.00
FBC	58	32.17	16.43	16.69	34.72	0.00	0.00
FBC	59	34.46	14.70	16.95	33.90	0.00	0.00
FBC	60	35.32	15.48	15.22	33.98	0.00	0.00
FBC	61	33.90	14.96	19.15	31.99	0.00	0.00
FBC	62	33.68	15.56	17.34	33.42	0.00	0.00
FBC	63	32.68	16.04	17.08	34.20	0.00	0.00
FBC	64	34.85	15.87	15.39	33.90	0.00	0.00
FBC	65	34.03	16.95	15.65	33.38	0.00	0.00
FBC	66	34.37	16.39	15.74	33.51	0.00	0.00
FBC	67	35.06	16.69	16.21	32.04	0.00	0.00
FBC	68	31.56	15.18	16.13	37.14	0.00	0.00
FBC	69	34.11	16.26	16.39	33.25	0.00	0.00
FBC	70	33.55	16.69	15.82	33.94	0.00	0.00
FBC	71	33.42	15.78	18.03	32.77	0.00	0.00
FBC	72	35.37	16.08	16.17	32.38	0.00	0.00
FBC	73	32.43	16.82	16.04	34.72	0.00	0.00
FBC	74	34.50	17.12	16.90	31.47	0.00	0.00
FBC	75	35.32	16.21	16.73	31.73	0.00	0.00
FBC	76	33.94	16.60	16.39	33.07	0.00	0.00
FBC	77	34.76	14.79	16.00	34.46	0.00	0.00
FBC	78	34.67	16.82	16.00	32.51	0.00	0.00
FBC	79	32.21	16.82	15.61	35.37	0.00	0.00
FBC	80	35.11	18.20	16.69	30.00	0.00	0.00
FBC	81	32.34	16.95	17.42	33.29	0.00	0.00
FBC	82	34.33	13.96	17.90	33.81	0.00	0.00
FBC	83	34.11	14.18	17.29	34.41	0.00	0.00
FBC	84	34.15	16.21	16.26	33.38	0.00	0.00
FBC	85	35.11	17.08	16.17	31.65	0.00	0.00
FBC	86	35.71	15.78	14.09	34.41	0.00	0.00
FBC	87	34.80	17.38	16.30	31.52	0.00	0.00
FBC	88	32.51	14.70	18.20	34.59	0.00	0.00
FBC	89	31.00	14.96	18.33	35.71	0.00	0.00
FBC	90	34.50	16.08	15.87	33.55	0.00	0.00
FBC	91	33.46	17.03	15.35	34.15	0.00	0.00
FBC	92	34.59	17.34	14.14	33.94	0.00	0.00
FBC	93	36.06	14.18	16.52	33.25	0.00	0.00
FBC	94	34.67	14.87	16.30	34.15	0.00	0.00
FBC	95	33.64	16.21	16.95	33.20	0.00	0.00
FBC	96	34.07	18.59	16.47	30.87	0.00	0.00
FBC	97	34.37	18.72	13.49	33.42	0.00	0.00
FBC	98	33.03	18.81	16.00	32.17	0.00	0.00
FBC	99	34.99	16.83	14.14	34.04	0.00	0.00
FBC	100	36.63	16.18	14.36	32.83	0.00	0.00
FBC	101	32.14	15.01	16.13	36.72	0.00	0.00
FBC	102	34.73	16.83	17.26	31.19	0.00	0.00
FBC	103	34.26	16.00	17.21	32.53	0.00	0.00
FBC	104	33.74	16.61	15.31	34.34	0.00	0.00
FBC	105	32.01	16.00	15.96	36.03	0.00	0.00
FBC	106	35.03	17.21	16.65	31.10	0.00	0.00
FBC	107	34.21	16.09	16.91	32.79	0.00	0.00
FBC	108	32.11	15.32	18.04	34.53	0.00	0.00
FBC	109	33.06	16.36	19.17	31.41	0.00	0.00
FBC	110	33.58	14.58	17.91	33.92	0.00	0.00
FBC	111	35.14	15.27	17.27	32.32	0.00	0.00
FBC	112	32.54	16.53	16.05	34.88	0.00	0.00
FBC	113	34.27	17.78	16.23	31.72	0.00	0.00
FBC	114	35.70	15.23	16.96	32.11	0.00	0.00
FBC	115	35.48	16.01	16.83	31.67	0.00	0.00
FBC	116	34.10	15.45	15.92	34.53	0.00	0.00
FBC	117	34.27	14.71	17.14	33.88	0.00	0.00
FBC	118	35.31	16.10	15.79	32.80	0.00	0.00
FBC	119	34.92	16.14	15.27	33.67	0.00	0.00
FBC	120	34.36	15.06	17.09	33.49	0.00	0.00
FBC	121	37.39	15.45	16.14	31.03	0.00	0.00
FBC	122	34.53	16.83	16.05	32.58	0.00	0.00
FBC	123	34.31	15.79	16.79	33.10	0.00	0.00
FBC	124	33.38	15.58	18.18	32.86	0.00	0.00
FBC	125	35.84	15.19	15.24	33.72	0.00	0.00
FBC	126	33.16	16.67	15.67	34.50	0.00	0.00
FBC	127	34.68	13.16	17.71	34.46	0.00	0.00
FBC	128	32.64	13.12	18.61	35.63	0.00	0.00
FBC	129	32.55	16.97	16.06	34.42	0.00	0.00
FBC	130	34.72	16.10	14.89	34.29	0.00	0.00
FBC	131	33.52	15.42	16.15	34.91	0.00	0.00
FBC	132	33.09	15.72	17.71	33.48	0.00	0.00
FBC	133	37.25	15.98	16.93	29.84	0.00	0.00
FBC	134	34.47	15.72	16.63	33.17	0.00	0.00
FBC	135	33.74	17.15	16.37	32.74	0.00	0.00
FBC	136	32.83	17.45	15.81	33.91	0.00	0.00
FBC	137	32.35	16.28	16.02	35.34	0.00	0.00
FBC	138	33.65	15.07	17.63	33.65	0.00	0.00
FBC	139	34.21	15.42	16.46	33.91	0.00	0.00
FBC	140	33.52	15.33	16.37	34.78	0.00	0.00
FBC	141	32.93	15.68	17.37	34.01	0.00	0.00
FBC	142	34.88	16.98	15.73	32.41	0.00	0.00
FBC	143	33.67	17.83	16.40	32.10	0.00	0.00
FBC	144	34.19	15.51	15.90	34.40	0.00	0.00
FBC	145	34.06	16.51	15.64	33.80	0.00	0.00
FBC	146	35.07	14.69	16.86	33.38	0.00	0.00
FBC	147	32.38	16.69	17.25	33.68	0.00	0.00
FBC	148	36.10	15.41	16.50	31.99	0.00	0.00
FBC	149	31.65	16.18	16.62	35.56	0.00	0.00
FBC	150	37.45	14.23	14.47	33.85	0.00	0.00
FBC	151	40.65	12.53	7.82	39.00	0.00	0.00
# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
FTC	119017	55861	57404	116029	0
# ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
LBC	1	32.81	18.07	17.29	31.82	0.00	0.00
LBC	2	34.03	14.66	14.92	36.40	0.00	0.00
LBC	3	34.07	16.43	17.60	31.91	0.00	0.00
LBC	4	34.15	16.56	16.60	32.68	0.00	0.00
LBC	5	30.48	16.47	18.37	34.67	0.00	0.00
LBC	6	32.86	18.55	15.35	33.25	0.00	0.00
LBC	7	34.89	14.57	18.12	32.43	0.00	0.00
LBC	8	32.60	18.72	15.22	33.46	0.00	0.00
LBC	9	32.34	15.30	17.16	35.19	0.00	0.00
LBC	10	33.98	15.30	17.12	33.59	0.00	0.00
LBC	11	34.15	17.38	15.56	32.90	0.00	0.00
LBC	12	33.90	16.90	16.60	32.60	0.00	0.00
LBC	13	33.64	15.18	17.12	34.07	0.00	0.00
LBC	14	36.49	16.00	16.95	30.57	0.00	0.00
LBC	15	34.03	17.81	17.29	30.87	0.00	0.00
LBC	16	33.25	16.30	17.16	33.29	0.00	0.00
LBC	17	33.94	16.73	16.04	33.29	0.00	0.00
LBC	18	34.15	14.53	18.55	32.77	0.00	0.00
LBC	19	32.47	17.73	16.99	32.81	0.00	0.00
LBC	20	33.42	16.65	17.55	32.38	0.00	0.00
LBC	21	35.06	16.73	15.74	32.47	0.00	0.00
LBC	22	33.55	16.39	17.68	32.38	0.00	0.00
LBC	23	33.42	15.56	17.08	33.94	0.00	0.00
LBC	24	34.37	14.92	16.95	33.77	0.00	0.00
LBC	25	34.24	16.52	17.42	31.82	0.00	0.00
LBC	26	33.72	16.13	16.08	34.07	0.00	0.00
LBC	27	35.15	15.35	16.65	32.86	0.00	0.00
LBC	28	34.50	15.65	15.05	34.80	0.00	0.00
LBC	29	35.71	15.52	16.77	31.99	0.00	0.00
LBC	30	33.07	16.04	17.38	33.51	0.00	0.00
LBC	31	31.99	18.07	17.77	32.17	0.00	0.00
LBC	32	33.98	16.17	17.16	32.68	0.00	0.00
LBC	33	37.70	13.10	15.74	33.46	0.00	0.00
LBC	34	35.45	15.30	16.60	32.64	0.00	0.00
LBC	35	31.82	17.21	16.21	34.76	0.00	0.00
LBC	36	32.90	16.34	15.39	35.37	0.00	0.00
LBC	37	34.20	14.96	17.73	33.12	0.00	0.00
LBC	38	34.07	14.66	17.81	33.46	0.00	0.00
LBC	39	32.17	15.35	17.60	34.89	0.00	0.00
LBC	40	34.67	16.99	16.08	32.25	0.00	0.00
LBC	41	35.06	15.78	17.03	32.12	0.00	0.00
LBC	42	34.11	17.55	15.22	33.12	0.00	0.00
LBC	43	33.46	17.08	17.08	32.38	0.00	0.00
LBC	44	36.27	14.79	16.26	32.68	0.00	0.00
LBC	45	34.85	15.13	15.91	34.11	0.00	0.00
LBC	46	33.12	17.47	18.16	31.26	0.00	0.00
LBC	47	34.63	17.29	15.43	32.64	0.00	0.00
LBC	48	32.60	15.95	16.56	34.89	0.00	0.00
LBC	49	34.41	15.82	16.26	33.51	0.00	0.00
LBC	50	33.51	18.33	15.05	33.12	0.00	0.00
LBC	51	33.81	16.56	17.86	31.78	0.00	0.00
LBC	52	36.06	16.73	16.21	31.00	0.00	0.00
LBC	53	33.29	15.05	17.25	34.41	0.00	0.00
LBC	54	36.92	14.92	17.25	30.91	0.00	0.00
LBC	55	33.25	17.08	16.43	33.25	0.00	0.00
LBC	56	35.06	14.35	16.39	34.20	0.00	0.00
LBC	57	34.15	16.52	15.43	33.90	0.00	0.00
LBC	58	33.20	16.34	16.17	34.28	0.00	0.00
LBC	59	33.38	15.22	17.29	34.11	0.00	0.00
LBC	60	33.33	15.09	17.29	34.28	0.00	0.00
LBC	61	34.89	16.13	16.13	32.86	0.00	0.00
LBC	62	32.12	17.77	16.82	33.29	0.00	0.00
LBC	63	32.77	16.30	19.24	31.69	0.00	0.00
LBC	64	33.51	15.05	17.12	34.33	0.00	0.00
LBC	65	34.72	17.64	14.87	32.77	0.00	0.00
LBC	66	34.50	16.39	16.30	32.81	0.00	0.00
LBC	67	35.06	15.61	18.16	31.17	0.00	0.00
LBC	68	33.64	16.56	15.87	33.94	0.00	0.00
LBC	69	35.11	17.47	15.56	31.86	0.00	0.00
LBC	70	33.55	16.82	16.73	32.90	0.00	0.00
LBC	71	33.38	15.69	15.56	35.37	0.00	0.00
LBC	72	33.64	15.13	17.42	33.81	0.00	0.00
LBC	73	32.68	17.08	17.38	32.86	0.00	0.00
LBC	74	35.54	16.47	14.57	33.42	0.00	0.00
LBC	75	36.96	15.18	15.13	32.73	0.00	0.00
LBC	76	33.90	17.12	17.12	31.86	0.00	0.00
LBC	77	35.50	15.48	16.77	32.25	0.00	0.00
LBC	78	35.80	16.13	16.30	31.78	0.00	0.00
LBC	79	33.38	16.52	18.12	31.99	0.00	0.00
LBC	80	32.68	17.29	16.13	33.90	0.00	0.00
LBC	81	33.64	14.70	18.29	33.38	0.00	0.00
LBC	82	34.28	14.53	17.55	33.64	0.00	0.00
LBC	83	33.68	13.88	16.26	36.19	0.00	0.00
LBC	84	34.24	16.34	15.61	33.81	0.00	0.00
LBC	85	34.07	17.21	17.16	31.56	0.00	0.00
LBC	86	33.33	15.74	15.30	35.62	0.00	0.00
LBC	87	34.72	16.00	16.39	32.90	0.00	0.00
LBC	88	36.14	16.86	15.22	31.78	0.00	0.00
LBC	89	33.59	16.77	16.21	33.42	0.00	0.00
LBC	90	33.90	15.13	17.34	33.64	0.00	0.00
LBC	91	32.60	15.00	16.99	35.41	0.00	0.00
LBC	92	32.51	15.39	17.16	34.93	0.00	0.00
LBC	93	32.51	16.69	16.04	34.76	0.00	0.00
LBC	94	33.20	14.57	18.24	33.98	0.00	0.00
LBC	95	32.94	17.64	14.48	34.93	0.00	0.00
LBC	96	34.72	16.39	16.52	32.38	0.00	0.00
LBC	97	33.77	17.55	15.00	33.68	0.00	0.00
LBC	98	33.81	15.22	15.52	35.45	0.00	0.00
LBC	99	34.04	16.57	14.88	34.52	0.00	0.00
LBC	100	34.95	15.01	17.43	32.61	0.00	0.00
LBC	101	33.78	14.32	16.83	35.08	0.00	0.00
LBC	102	33.04	15.48	17.47	34.00	0.00	0.00
LBC	103	32.87	18.34	16.39	32.40	0.00	0.00
LBC	104	34.30	15.74	17.52	32.44	0.00	0.00
LBC	105	36.20	15.61	15.10	33.09	0.00	0.00
LBC	106	36.03	16.74	15.83	31.40	0.00	0.00
LBC	107	36.16	15.18	13.58	35.08	0.00	0.00
LBC	108	32.58	15.45	16.88	35.09	0.00	0.00
LBC	109	36.48	14.63	16.83	32.06	0.00	0.00
LBC	110	34.23	15.53	16.96	33.28	0.00	0.00
LBC	111	34.05	14.80	18.82	32.32	0.00	0.00
LBC	112	33.54	17.09	17.09	32.28	0.00	0.00
LBC	113	34.23	16.75	17.18	31.85	0.00	0.00
LBC	114	35.53	15.14	15.84	33.49	0.00	0.00
LBC	115	36.43	15.49	16.96	31.11	0.00	0.00
LBC	116	33.75	16.36	16.62	33.28	0.00	0.00
LBC	117	34.53	15.75	17.27	32.45	0.00	0.00
LBC	118	35.09	14.54	16.27	34.10	0.00	0.00
LBC	119	34.53	16.18	16.36	32.93	0.00	0.00
LBC	120	33.02	16.36	17.83	32.80	0.00	0.00
LBC	121	35.57	15.06	16.49	32.89	0.00	0.00
LBC	122	34.75	16.18	15.66	33.41	0.00	0.00
LBC	123	35.40	15.88	16.44	32.28	0.00	0.00
LBC	124	32.64	16.49	15.32	35.54	0.00	0.00
LBC	125	35.58	14.37	16.06	33.98	0.00	0.00
LBC	126	33.68	16.28	16.67	33.38	0.00	0.00
LBC	127	33.59	15.32	17.32	33.77	0.00	0.00
LBC	128	32.68	15.93	18.14	33.25	0.00	0.00
LBC	129	33.16	16.58	16.58	33.68	0.00	0.00
LBC	130	32.86	16.84	16.62	33.68	0.00	0.00
LBC	131	32.18	18.45	15.16	34.21	0.00	0.00
LBC	132	35.34	14.42	16.80	33.43	0.00	0.00
LBC	133	37.20	14.21	16.98	31.62	0.00	0.00
LBC	134	33.69	17.58	16.20	32.52	0.00	0.00
LBC	135	34.04	15.07	17.54	33.35	0.00	0.00
LBC	136	32.87	16.24	17.71	33.17	0.00	0.00
LBC	137	34.30	17.54	16.15	32.01	0.00	0.00
LBC	138	34.56	14.34	16.63	34.47	0.00	0.00
LBC	139	34.13	15.50	16.46	33.91	0.00	0.00
LBC	140	33.52	15.37	16.50	34.60	0.00	0.00
LBC	141	31.80	17.42	16.46	34.32	0.00	0.00
LBC	142	34.45	17.07	14.90	33.58	0.00	0.00
LBC	143	35.75	16.14	16.44	31.67	0.00	0.00
LBC	144	33.32	15.31	16.44	34.92	0.00	0.00
LBC	145	36.49	16.79	16.70	30.02	0.00	0.00
LBC	146	34.97	16.53	15.88	32.62	0.00	0.00
LBC	147	33.72	15.30	16.78	34.20	0.00	0.00
LBC	148	35.46	16.59	17.12	30.83	0.00	0.00
LBC	149	33.95	15.83	16.14	34.08	0.00	0.00
LBC	150	36.61	13.60	15.08	34.71	0.00	0.00
LBC	151	39.35	9.34	11.83	39.47	0.00	0.00
# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
LTC	118906	55818	57717	115899	0
# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs
IS	0	0	0	0	0
IS	1	0	0	0	0
IS	2	0	0	0	0
IS	3	0	0	0	0
IS	4	0	0	0	0
IS	5	0	0	0	0
IS	6	0	0	0	0
IS	7	0	0	0	0
IS	8	0	0	0	0
IS	9	0	0	0	0
IS	10	0	0	0	0
IS	11	0	0	0	0
IS	12	0	0	0	0
IS	13	0	0	0	0
IS	14	0	0	0	0
IS	15	0	0	0	0
IS	16	0	0	0	0
IS	17	0	0	0	0
IS	18	0	0	0	0
IS	19	1	0	1	0
IS	20	0	0	0	0
IS	21	0	0	0	0
IS	22	0	0	0	0
IS	23	0	0	0	0
IS	24	0	0	0	0
IS	25	0	0	0	0
IS	26	0	0	0	0
IS	27	0	0	0	0
IS	28	0	0	0	0
IS	29	0	0	0	0
IS	30	0	0	0	0
IS	31	0	0	0	0
IS	32	0	0	0	0
IS	33	0	0	0	0
IS	34	0	0	0	0
IS	35	0	0	0	0
IS	36	0	0	0	0
IS	37	0	0	0	0
IS	38	0	0	0	0
IS	39	0	0	0	0
IS	40	0	0	0	0
IS	41	0	0	0	0
IS	42	0	0	0	0
IS	43	0	0	0	0
IS	44	0	0	0	0
IS	45	0	0	0	0
IS	46	0	0	0	0
IS	47	0	0	0	0
IS	48	0	0	0	0
IS	49	0	0	0	0
IS	50	0	0	0	0
IS	51	0	0	0	0
IS	52	0	0	0	0
IS	53	0	0	0	0
IS	54	0	0	0	0
IS	55	0	0	0	0
IS	56	0	0	0	0
IS	57	0	0	0	0
IS	58	0	0	0	0
IS	59	0	0	0	0
IS	60	0	0	0	0
IS	61	0	0	0	0
IS	62	0	0	0	0
IS	63	0	0	0	0
IS	64	0	0	0	0
IS	65	0	0	0	0
IS	66	0	0	0	0
IS	67	0	0	0	0
IS	68	0	0	0	0
IS	69	0	0	0	0
IS	70	0	0	0	0
IS	71	0	0	0	0
IS	72	0	0	0	0
IS	73	0	0	0	0
IS	74	0	0	0	0
IS	75	0	0	0	0
IS	76	0	0	0	0
IS	77	0	0	0	0
IS	78	0	0	0	0
IS	79	0	0	0	0
IS	80	0	0	0	0
IS	81	0	0	0	0
IS	82	0	0	0	0
IS	83	0	0	0	0
IS	84	0	0	0	0
IS	85	0	0	0	0
IS	86	0	0	0	0
IS	87	0	0	0	0
IS	88	0	0	0	0
IS	89	0	0	0	0
IS	90	0	0	0	0
IS	91	0	0	0	0
IS	92	0	0	0	0
IS	93	0	0	0	0
IS	94	0	0	0	0
IS	95	0	0	0	0
IS	96	0	0	0	0
IS	97	0	0	0	0
IS	98	0	0	0	0
IS	99	0	0	0	0
IS	100	0	0	0	0
IS	101	0	0	0	0
IS	102	0	0	0	0
IS	103	0	0	0	0
IS	104	0	0	0	0
IS	105	0	0	0	0
IS	106	0	0	0	0
IS	107	2	2	0	0
IS	108	0	0	0	0
IS	109	0	0	0	0
IS	110	0	0	0	0
IS	111	0	0	0	0
IS	112	0	0	0	0
IS	113	0	0	0	0
IS	114	0	0	0	0
IS	115	0	0	0	0
IS	116	0	0	0	0
IS	117	0	0	0	0
IS	118	0	0	0	0
IS	119	0	0	0	0
IS	120	0	0	0	0
IS	121	0	0	0	0
IS	122	0	0	0	0
IS	123	1	1	0	0
IS	124	0	0	0	0
IS	125	0	0	0	0
IS	126	0	0	0	0
IS	127	0	0	0	0
IS	128	0	0	0	0
IS	129	0	0	0	0
IS	130	1	1	0	0
IS	131	3	0	3	0
IS	132	1	0	1	0
IS	133	0	0	0	0
IS	134	0	0	0	0
IS	135	0	0	0	0
IS	136	0	0	0	0
IS	137	0	0	0	0
IS	138	0	0	0	0
IS	139	0	0	0	0
IS	140	1	1	0	0
IS	141	0	0	0	0
IS	142	3	3	0	0
IS	143	0	0	0	0
IS	144	0	0	0	0
IS	145	0	0	0	0
IS	146	0	0	0	0
IS	147	1	1	0	0
IS	148	0	0	0	0
IS	149	6	6	0	0
IS	150	1	1	0	0
IS	151	0	0	0	0
IS	152	2	2	0	0
IS	153	1	1	0	0
IS	154	0	0	0	0
IS	155	0	0	0	0
IS	156	0	0	0	0
IS	157	1	1	0	0
IS	158	0	0	0	0
IS	159	1	1	0	0
IS	160	0	0	0	0
IS	161	0	0	0	0
IS	162	1	1	0	0
IS	163	1	1	0	0
IS	164	2	2	0	0
IS	165	4	4	0	0
IS	166	0	0	0	0
IS	167	2	2	0	0
IS	168	0	0	0	0
IS	169	0	0	0	0
IS	170	0	0	0	0
IS	171	5	5	0	0
IS	172	3	3	0	0
IS	173	0	0	0	0
IS	174	5	5	0	0
IS	175	1	1	0	0
IS	176	0	0	0	0
IS	177	6	6	0	0
IS	178	0	0	0	0
IS	179	3	3	0	0
IS	180	3	3	0	0
IS	181	4	4	0	0
IS	182	6	6	0	0
IS	183	0	0	0	0
IS	184	9	9	0	0
IS	185	0	0	0	0
IS	186	0	0	0	0
IS	187	3	3	0	0
IS	188	2	2	0	0
IS	189	1	1	0	0
IS	190	5	5	0	0
IS	191	8	8	0	0
IS	192	0	0	0	0
IS	193	0	0	0	0
IS	194	8	8	0	0
IS	195	3	3	0	0
IS	196	2	2	0	0
IS	197	2	2	0	0
IS	198	2	2	0	0
IS	199	1	1	0	0
IS	200	4	4	0	0
IS	201	2	2	0	0
IS	202	3	3	0	0
IS	203	6	6	0	0
IS	204	3	3	0	0
IS	205	3	3	0	0
IS	206	6	6	0	0
IS	207	7	7	0	0
IS	208	1	1	0	0
IS	209	1	1	0	0
IS	210	5	5	0	0
IS	211	4	4	0	0
IS	212	7	7	0	0
IS	213	2	2	0	0
IS	214	6	6	0	0
IS	215	4	4	0	0
IS	216	3	3	0	0
IS	217	7	7	0	0
IS	218	11	11	0	0
IS	219	8	8	0	0
IS	220	5	5	0	0
IS	221	5	5	0	0
IS	222	3	3	0	0
IS	223	5	5	0	0
IS	224	4	4	0	0
IS	225	6	6	0	0
IS	226	4	4	0	0
IS	227	12	12	0	0
IS	228	3	3	0	0
IS	229	3	3	0	0
IS	230	4	4	0	0
IS	231	4	4	0	0
IS	232	0	0	0	0
IS	233	2	2	0	0
IS	234	3	3	0	0
IS	235	6	6	0	0
IS	236	12	12	0	0
IS	237	6	6	0	0
IS	238	4	4	0	0
IS	239	12	12	0	0
IS	240	9	9	0	0
IS	241	13	13	0	0
IS	242	5	5	0	0
IS	243	12	12	0	0
IS	244	6	6	0	0
IS	245	4	4	0	0
IS	246	0	0	0	0
IS	247	4	4	0	0
IS	248	5	5	0	0
IS	249	8	8	0	0
IS	250	6	6	0	0
IS	251	16	16	0	0
IS	252	7	7	0	0
IS	253	7	7	0	0
IS	254	9	9	0	0
IS	255	3	3	0	0
IS	256	12	12	0	0
IS	257	7	7	0	0
IS	258	8	8	0	0
IS	259	5	5	0	0
IS	260	7	7	0	0
IS	261	5	5	0	0
IS	262	4	4	0	0
IS	263	14	14	0	0
IS	264	4	4	0	0
IS	265	10	10	0	0
IS	266	8	8	0	0
IS	267	11	11	0	0
IS	268	11	11	0	0
IS	269	5	5	0	0
IS	270	6	6	0	0
IS	271	18	18	0	0
IS	272	16	16	0	0
IS	273	7	7	0	0
IS	274	5	5	0	0
IS	275	12	12	0	0
IS	276	13	13	0	0
IS	277	4	4	0	0
IS	278	4	4	0	0
IS	279	9	9	0	0
IS	280	6	6	0	0
IS	281	9	9	0	0
IS	282	6	6	0	0
IS	283	8	8	0	0
IS	284	11	11	0	0
IS	285	1	1	0	0
IS	286	12	12	0	0
IS	287	7	7	0	0
IS	288	6	6	0	0
IS	289	12	12	0	0
IS	290	11	11	0	0
IS	291	7	7	0	0
IS	292	7	7	0	0
IS	293	6	6	0	0
IS	294	9	9	0	0
IS	295	6	6	0	0
IS	296	23	23	0	0
IS	297	8	8	0	0
IS	298	16	16	0	0
IS	299	12	12	0	0
IS	300	8	8	0	0
IS	301	12	12	0	0
IS	302	14	14	0	0
IS	303	8	8	0	0
IS	304	14	14	0	0
IS	305	9	9	0	0
IS	306	13	13	0	0
IS	307	16	16	0	0
IS	308	17	17	0	0
IS	309	5	5	0	0
IS	310	4	4	0	0
IS	311	12	12	0	0
IS	312	14	14	0	0
IS	313	7	7	0	0
IS	314	8	8	0	0
IS	315	13	13	0	0
IS	316	7	7	0	0
IS	317	8	8	0	0
IS	318	10	10	0	0
IS	319	5	5	0	0
IS	320	6	6	0	0
IS	321	9	9	0	0
IS	322	8	8	0	0
IS	323	11	11	0	0
IS	324	13	13	0	0
IS	325	13	13	0	0
IS	326	14	14	0	0
IS	327	8	8	0	0
IS	328	18	18	0	0
IS	329	20	20	0	0
IS	330	6	6	0	0
IS	331	11	11	0	0
IS	332	13	13	0	0
IS	333	5	5	0	0
IS	334	9	9	0	0
IS	335	12	12	0	0
IS	336	13	13	0	0
IS	337	10	10	0	0
IS	338	9	9	0	0
IS	339	10	10	0	0
IS	340	14	14	0	0
IS	341	7	7	0	0
IS	342	16	16	0	0
IS	343	9	9	0	0
IS	344	17	17	0	0
IS	345	20	20	0	0
IS	346	11	11	0	0
IS	347	6	6	0	0
IS	348	10	10	0	0
IS	349	8	8	0	0
IS	350	19	19	0	0
IS	351	10	10	0	0
IS	352	11	11	0	0
IS	353	10	10	0	0
IS	354	16	16	0	0
IS	355	11	11	0	0
IS	356	12	12	0	0
IS	357	13	13	0	0
IS	358	9	9	0	0
IS	359	8	8	0	0
IS	360	9	9	0	0
IS	361	9	9	0	0
IS	362	12	12	0	0
IS	363	1	1	0	0
IS	364	9	9	0	0
IS	365	9	9	0	0
IS	366	10	10	0	0
IS	367	4	4	0	0
IS	368	6	6	0	0
IS	369	6	6	0	0
IS	370	11	11	0	0
IS	371	0	0	0	0
IS	372	9	9	0	0
IS	373	8	8	0	0
IS	374	15	15	0	0
IS	375	7	7	0	0
IS	376	9	9	0	0
IS	377	6	6	0	0
IS	378	8	8	0	0
IS	379	9	9	0	0
IS	380	7	7	0	0
IS	381	6	6	0	0
IS	382	10	10	0	0
IS	383	5	5	0	0
IS	384	5	5	0	0
IS	385	9	9	0	0
IS	386	4	4	0	0
IS	387	3	3	0	0
IS	388	13	13	0	0
IS	389	5	5	0	0
IS	390	11	11	0	0
IS	391	8	8	0	0
IS	392	7	7	0	0
IS	393	8	8	0	0
IS	394	14	14	0	0
IS	395	5	5	0	0
IS	396	9	9	0	0
IS	397	3	3	0	0
IS	398	7	7	0	0
IS	399	13	13	0	0
IS	400	7	7	0	0
IS	401	11	11	0	0
IS	402	3	3	0	0
IS	403	1	1	0	0
IS	404	2	2	0	0
IS	405	13	13	0	0
IS	406	9	9	0	0
IS	407	3	3	0	0
IS	408	4	4	0	0
IS	409	6	6	0	0
IS	410	7	7	0	0
IS	411	3	3	0	0
IS	412	2	2	0	0
IS	413	13	13	0	0
IS	414	5	5	0	0
IS	415	8	8	0	0
IS	416	7	7	0	0
IS	417	5	5	0	0
IS	418	1	1	0	0
IS	419	6	6	0	0
IS	420	3	3	0	0
IS	421	4	4	0	0
IS	422	4	4	0	0
IS	423	6	6	0	0
IS	424	13	13	0	0
IS	425	7	7	0	0
IS	426	1	1	0	0
IS	427	5	5	0	0
IS	428	7	7	0	0
IS	429	3	3	0	0
IS	430	6	6	0	0
IS	431	3	3	0	0
IS	432	7	7	0	0
IS	433	6	6	0	0
IS	434	0	0	0	0
IS	435	0	0	0	0
IS	436	0	0	0	0
IS	437	8	8	0	0
IS	438	4	4	0	0
IS	439	2	2	0	0
IS	440	5	5	0	0
IS	441	2	2	0	0
IS	442	7	7	0	0
IS	443	2	2	0	0
IS	444	1	1	0	0
IS	445	2	2	0	0
IS	446	2	2	0	0
IS	447	3	3	0	0
IS	448	7	7	0	0
IS	449	5	5	0	0
IS	450	2	2	0	0
IS	451	3	3	0	0
IS	452	3	3	0	0
IS	453	5	5	0	0
IS	454	2	2	0	0
IS	455	9	9	0	0
IS	456	1	1	0	0
IS	457	7	7	0	0
IS	458	1	1	0	0
IS	459	4	4	0	0
IS	460	1	1	0	0
IS	461	5	5	0	0
IS	462	0	0	0	0
IS	463	4	4	0	0
IS	464	2	2	0	0
IS	465	6	6	0	0
IS	466	2	2	0	0
IS	467	6	6	0	0
IS	468	1	1	0	0
IS	469	0	0	0	0
IS	470	1	1	0	0
IS	471	0	0	0	0
IS	472	2	2	0	0
IS	473	1	1	0	0
IS	474	5	5	0	0
IS	475	1	1	0	0
IS	476	4	4	0	0
IS	477	3	3	0	0
IS	478	2	2	0	0
IS	479	2	2	0	0
IS	480	2	2	0	0
IS	481	3	3	0	0
IS	482	4	4	0	0
IS	483	1	1	0	0
IS	484	5	5	0	0
IS	485	0	0	0	0
IS	486	0	0	0	0
IS	487	2	2	0	0
IS	488	3	3	0	0
IS	489	0	0	0	0
IS	490	5	5	0	0
IS	491	2	2	0	0
IS	492	1	1	0	0
IS	493	4	4	0	0
IS	494	2	2	0	0
IS	495	1	1	0	0
IS	496	1	1	0	0
IS	497	6	6	0	0
IS	498	1	1	0	0
IS	499	2	2	0	0
IS	500	3	3	0	0
IS	501	1	1	0	0
IS	502	0	0	0	0
IS	503	3	3	0	0
IS	504	1	1	0	0
IS	505	2	2	0	0
IS	506	4	4	0	0
IS	507	0	0	0	0
IS	508	0	0	0	0
IS	509	1	1	0	0
IS	510	3	3	0	0
IS	511	3	3	0	0
IS	512	3	3	0	0
IS	513	1	1	0	0
IS	514	0	0	0	0
IS	515	0	0	0	0
IS	516	1	1	0	0
IS	517	3	3	0	0
IS	518	5	5	0	0
IS	519	4	4	0	0
IS	520	3	3	0	0
IS	521	5	5	0	0
IS	522	2	2	0	0
IS	523	1	1	0	0
IS	524	0	0	0	0
IS	525	2	2	0	0
IS	526	3	3	0	0
IS	527	2	2	0	0
IS	528	1	1	0	0
IS	529	1	1	0	0
IS	530	0	0	0	0
IS	531	1	1	0	0
IS	532	0	0	0	0
IS	533	0	0	0	0
IS	534	1	1	0	0
IS	535	2	2	0	0
IS	536	0	0	0	0
IS	537	0	0	0	0
IS	538	0	0	0	0
IS	539	3	3	0	0
IS	540	0	0	0	0
IS	541	0	0	0	0
IS	542	3	3	0	0
IS	543	3	3	0	0
IS	544	0	0	0	0
IS	545	3	3	0	0
IS	546	3	3	0	0
IS	547	2	2	0	0
IS	548	5	5	0	0
IS	549	1	1	0	0
IS	550	2	2	0	0
IS	551	0	0	0	0
IS	552	2	2	0	0
IS	553	0	0	0	0
IS	554	1	1	0	0
IS	555	5	5	0	0
IS	556	2	2	0	0
IS	557	0	0	0	0
IS	558	1	1	0	0
IS	559	0	0	0	0
IS	560	0	0	0	0
IS	561	0	0	0	0
IS	562	1	1	0	0
IS	563	0	0	0	0
IS	564	0	0	0	0
IS	565	1	1	0	0
IS	566	0	0	0	0
IS	567	0	0	0	0
IS	568	0	0	0	0
IS	569	1	1	0	0
IS	570	1	1	0	0
IS	571	1	1	0	0
IS	572	0	0	0	0
IS	573	2	2	0	0
IS	574	0	0	0	0
IS	575	0	0	0	0
IS	576	1	1	0	0
IS	577	0	0	0	0
IS	578	0	0	0	0
IS	579	0	0	0	0
IS	580	0	0	0	0
IS	581	1	1	0	0
IS	582	0	0	0	0
IS	583	0	0	0	0
IS	584	1	1	0	0
IS	585	2	2	0	0
IS	586	0	0	0	0
IS	587	3	3	0	0
IS	588	0	0	0	0
IS	589	0	0	0	0
IS	590	0	0	0	0
IS	591	1	1	0	0
IS	592	4	4	0	0
IS	593	0	0	0	0
IS	594	1	1	0	0
IS	595	1	1	0	0
IS	596	0	0	0	0
IS	597	0	0	0	0
IS	598	3	3	0	0
IS	599	0	0	0	0
IS	600	0	0	0	0
IS	601	0	0	0	0
IS	602	0	0	0	0
IS	603	4	4	0	0
IS	604	0	0	0	0
IS	605	0	0	0	0
IS	606	1	1	0	0
IS	607	0	0	0	0
IS	608	1	1	0	0
IS	609	0	0	0	0
IS	610	1	1	0	0
IS	611	0	0	0	0
IS	612	0	0	0	0
IS	613	0	0	0	0
IS	614	0	0	0	0
IS	615	0	0	0	0
IS	616	2	2	0	0
IS	617	0	0	0	0
IS	618	0	0	0	0
IS	619	1	1	0	0
IS	620	0	0	0	0
IS	621	0	0	0	0
IS	622	2	2	0	0
# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
RL	98	2
RL	107	2
RL	123	2
RL	130	2
RL	140	2
RL	142	6
RL	143	3
RL	145	1
RL	146	4
RL	147	21
RL	148	32
RL	149	258
RL	150	761
RL	151	3530
# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count
FRL	98	1
FRL	107	1
FRL	123	1
FRL	130	1
FRL	140	1
FRL	142	3
FRL	143	3
FRL	145	1
FRL	147	10
FRL	148	16
FRL	149	139
FRL	150	372
FRL	151	1764
# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count
LRL	98	1
LRL	107	1
LRL	123	1
LRL	130	1
LRL	140	1
LRL	142	3
LRL	146	4
LRL	147	11
LRL	148	16
LRL	149	119
LRL	150	389
LRL	151	1766
# Mapping qualities for reads !(UNMAP|SECOND|SUPPL|QCFAIL|DUP). Use `grep ^MAPQ | cut -f 2-` to extract this part. The columns are: mapq, count
MAPQ	0	367
MAPQ	16	1
MAPQ	30	1
MAPQ	33	2
MAPQ	40	22
MAPQ	60	4233
# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions
ID	1	102	131
ID	2	52	47
ID	3	25	43
ID	4	18	7
ID	5	3	6
ID	6	4	8
ID	7	0	13
ID	8	0	3
ID	9	7	2
ID	12	0	8
ID	15	0	6
ID	18	4	0
ID	20	1	0
ID	21	0	1
ID	30	0	2
ID	40	1	0
# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)
IC	5	0	2	1	0
IC	7	0	3	0	1
IC	8	1	0	0	0
IC	9	2	0	0	0
IC	11	1	3	0	0
IC	12	0	1	0	0
IC	13	0	0	1	0
IC	14	0	0	0	1
IC	15	1	0	0	0
IC	16	0	0	1	0
IC	17	2	2	0	0
IC	18	3	0	1	0
IC	19	0	0	0	2
IC	20	1	2	0	0
IC	21	0	3	2	0
IC	22	1	4	1	2
IC	23	0	0	2	0
IC	25	0	0	4	0
IC	26	1	1	0	4
IC	27	2	1	3	1
IC	28	1	0	2	1
IC	29	0	1	1	2
IC	30	0	3	2	0
IC	31	2	2	2	0
IC	32	0	1	1	0
IC	33	0	1	0	0
IC	34	2	3	2	1
IC	35	0	0	1	1
IC	36	1	0	0	0
IC	39	0	0	2	1
IC	40	3	0	1	2
IC	41	0	1	0	1
IC	42	1	1	0	0
IC	43	0	2	6	2
IC	44	0	0	3	3
IC	45	0	1	0	0
IC	46	0	0	0	3
IC	47	1	0	2	1
IC	48	2	1	0	1
IC	49	0	3	3	2
IC	50	0	0	1	0
IC	51	1	0	2	3
IC	52	0	0	1	2
IC	53	0	1	0	4
IC	54	3	3	0	1
IC	55	3	2	1	3
IC	56	2	1	1	2
IC	57	1	0	3	0
IC	58	0	4	0	4
IC	59	0	0	1	0
IC	60	1	0	2	0
IC	61	0	1	2	0
IC	62	3	0	1	0
IC	63	1	1	0	1
IC	64	2	1	0	0
IC	65	1	0	0	4
IC	66	1	0	1	0
IC	67	0	0	1	0
IC	68	0	1	0	0
IC	69	1	0	1	2
IC	70	0	0	1	2
IC	72	0	0	1	0
IC	73	1	1	1	1
IC	74	0	0	1	2
IC	75	0	0	2	2
IC	77	0	0	0	2
IC	79	5	1	1	1
IC	80	3	2	0	0
IC	81	0	0	0	1
IC	82	1	0	2	2
IC	83	1	0	1	2
IC	84	1	2	1	0
IC	85	2	2	3	0
IC	86	1	4	1	1
IC	87	0	0	4	0
IC	88	0	1	3	2
IC	89	1	0	1	1
IC	90	2	1	2	2
IC	91	1	1	0	0
IC	92	0	0	2	0
IC	93	2	0	0	1
IC	94	0	0	0	1
IC	95	1	0	5	0
IC	96	1	1	2	1
IC	97	1	0	1	0
IC	98	0	0	0	1
IC	99	0	3	0	0
IC	100	1	3	2	1
IC	101	0	0	1	2
IC	102	0	0	0	2
IC	103	0	2	0	0
IC	104	0	2	1	1
IC	105	3	2	1	0
IC	106	2	1	3	2
IC	107	1	2	2	4
IC	108	0	0	0	1
IC	110	0	1	2	2
IC	111	1	0	0	0
IC	112	0	1	0	0
IC	113	0	2	1	3
IC	114	0	3	0	1
IC	115	1	1	0	1
IC	116	1	0	0	0
IC	117	0	0	1	3
IC	118	2	1	1	0
IC	120	0	0	1	0
IC	121	1	1	1	2
IC	122	1	2	0	2
IC	123	1	0	0	1
IC	124	0	0	1	0
IC	125	1	0	0	1
IC	126	0	0	0	2
IC	127	4	0	2	3
IC	128	0	1	1	2
IC	129	1	0	2	1
IC	130	0	0	0	1
IC	131	4	0	0	1
IC	132	0	1	0	0
IC	133	1	0	0	1
IC	134	5	0	1	3
IC	135	0	1	1	1
IC	136	0	0	2	1
IC	137	0	2	0	1
IC	138	2	0	2	2
IC	139	2	2	2	2
IC	140	1	0	1	2
IC	142	0	0	0	1
IC	143	2	0	0	0
IC	145	0	0	3	5
IC	147	0	0	3	1
# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.
COV	[1-1]	1	32326
COV	[2-2]	2	30029
COV	[3-3]	3	25917
COV	[4-4]	4	21672
COV	[5-5]	5	15599
COV	[6-6]	6	11614
COV	[7-7]	7	8510
COV	[8-8]	8	5788
COV	[9-9]	9	4914
COV	[10-10]	10	3159
COV	[11-11]	11	2212
COV	[12-12]	12	1562
COV	[13-13]	13	1166
COV	[14-14]	14	816
COV	[15-15]	15	764
COV	[16-16]	16	274
COV	[17-17]	17	204
COV	[18-18]	18	221
COV	[19-19]	19	102
COV	[20-20]	20	75
COV	[21-21]	21	41
COV	[22-22]	22	19
COV	[23-23]	23	13
COV	[24-24]	24	25
COV	[25-25]	25	15
COV	[26-26]	26	7
COV	[27-27]	27	10
COV	[28-28]	28	22
COV	[29-29]	29	23
COV	[30-30]	30	13
COV	[31-31]	31	10
COV	[32-32]	32	6
COV	[33-33]	33	10
COV	[34-34]	34	11
COV	[35-35]	35	12
COV	[37-37]	37	1
COV	[38-38]	38	9
COV	[39-39]	39	6
COV	[40-40]	40	16
COV	[41-41]	41	13
COV	[42-42]	42	3
COV	[43-43]	43	13
COV	[44-44]	44	15
COV	[45-45]	45	16
COV	[46-46]	46	15
COV	[47-47]	47	9
# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile
GCD	0.0	18.182	0.000	0.000	0.000	0.000	0.000
GCD	31.0	27.273	3.659	3.659	3.659	3.659	3.659
GCD	32.0	72.727	3.306	3.411	3.539	3.863	3.885
GCD	33.0	90.909	3.110	3.110	3.415	3.720	3.720
GCD	34.0	100.000	2.778	2.778	2.778	2.778	2.778
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Paired Collection:
- step_state: scheduled
Step 2: GenBank genome:
- step_state: scheduled
Step 3: Name for genome database:
- step_state: scheduled

Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.3.7+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/fastp:1.3.7
```

Command Line:

ln -sf '/tmp/tmpzhosac2u/files/a/8/9/dataset_a896daab-df8c-44c0-b6c8-5ce5f266395d.dat' 'ERR3485802.fastqsanger.gz' && ln -sf '/tmp/tmpzhosac2u/files/e/0/d/dataset_e0d6c01a-4ba7-4272-b654-ce8a1c499add.dat' 'ERR3485802_R2.fastqsanger.gz' &&   fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'ERR3485802.fastqsanger.gz'  -i 'ERR3485802.fastqsanger.gz'   -I 'ERR3485802_R2.fastqsanger.gz' -o first.fastqsanger.gz -O second.fastqsanger.gz                                    --dont_eval_duplication                  && mv first.fastqsanger.gz '/tmp/tmpzhosac2u/job_working_directory/000/4/outputs/dataset_e941f0db-b270-4919-9469-a081b13d8e54.dat' && mv second.fastqsanger.gz '/tmp/tmpzhosac2u/job_working_directory/000/4/outputs/dataset_d5d6f079-6197-4e8f-9041-8ec1b3296530.dat'

Exit Code:

```
0
```

Standard Error:

Read1 before filtering:
total reads: 2500
total bases: 376657
Q20 bases: 371549(98.6439%)
Q30 bases: 370136(98.2687%)
Q40 bases: 1744(0.463021%)

Read2 before filtering:
total reads: 2500
total bases: 376700
Q20 bases: 355761(94.4415%)
Q30 bases: 351290(93.2546%)
Q40 bases: 131(0.0347757%)

Read1 after filtering:
total reads: 2492
total bases: 375257
Q20 bases: 370593(98.7571%)
Q30 bases: 369355(98.4272%)
Q40 bases: 1744(0.464748%)

Read2 after filtering:
total reads: 2492
total bases: 375297
Q20 bases: 355082(94.6136%)
Q30 bases: 350732(93.4545%)
Q40 bases: 131(0.0349057%)

Filtering result:
reads passed filter: 4984
reads failed due to low quality: 16
reads failed due to too many N: 0
reads failed due to too short: 0
reads failed due to adapter dimer: 0
reads with adapter trimmed: 30
bases trimmed due to adapters: 393

Insert size peak (evaluated by paired-end reads): 263

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title ERR3485802.fastqsanger.gz -i ERR3485802.fastqsanger.gz -I ERR3485802_R2.fastqsanger.gz -o first.fastqsanger.gz -O second.fastqsanger.gz --dont_eval_duplication 
fastp v1.3.7, time used: 0 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"79fe72b8c99a11f1a9dd6045bdc951a2"`
chromInfo	`"/tmp/tmpzhosac2u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
duplicated_reads	`{"handling_options": {"__current_case__": 0, "eval_dups": "--dont_eval_duplication"}}`
filter_options	`{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}`
output_options	`{"report_html": true, "report_json": true}`
overrepresented_sequence_analysis	`{"overrepresentation_analysis": false, "overrepresentation_sampling": null}`
read_mod_options	{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_front_select": {"__current_case__": 1, "cut_front": ""}, "cut_right_select": {"__current_case__": 1, "cut_right": ""}, "cut_tail_select": {"__current_case__": 1, "cut_tail": ""}}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}
single_paired	`{"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "detect_adapter_for_pe": false, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "merge_reads": {"__current_case__": 1, "merge": ""}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}`

Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-2104de94fc3275c05faf3d41165a700b6e0c9ef9:328b6a24a575a59e3c8291517564a37ebdc4b7c9-0

Command Line:

python3 '/tmp/shed_data/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/908f2c5fedec/snpeff/gbk2fa.py' '/tmp/tmpzhosac2u/files/c/e/3/dataset_ce3677c3-8df8-464c-bacb-f50c12e0ebb2.dat' '/tmp/tmpzhosac2u/job_working_directory/000/5/outputs/dataset_68a75981-3d85-4a32-bb66-92517310ee92.dat'  &&  mkdir -p '/tmp/tmpzhosac2u/job_working_directory/000/5/outputs/dataset_28944ad4-167d-40b1-bb63-2fc59007c20b_files/mpxv' && mkdir -p snpeff_output/'mpxv' &&  ln -s '/tmp/tmpzhosac2u/files/c/e/3/dataset_ce3677c3-8df8-464c-bacb-f50c12e0ebb2.dat' 'snpeff_output/mpxv/genes.gbk' &&  snpEff -Xmx${GALAXY_MEMORY_MB:-8192}m build -noCheckCds -noCheckProtein -v -configOption 'mpxv'.genome='mpxv' -configOption 'mpxv'.codonTable='Standard' -genbank -dataDir "$(pwd)/snpeff_output" 'mpxv' && mv snpeff_output/'mpxv'/*.bin '/tmp/tmpzhosac2u/job_working_directory/000/5/outputs/dataset_28944ad4-167d-40b1-bb63-2fc59007c20b_files/mpxv' && echo 'mpxv.genome : mpxv' >> '/tmp/tmpzhosac2u/job_working_directory/000/5/outputs/dataset_28944ad4-167d-40b1-bb63-2fc59007c20b_files'/snpEff.config && echo 'mpxv.codonTable : Standard' >> '/tmp/tmpzhosac2u/job_working_directory/000/5/outputs/dataset_28944ad4-167d-40b1-bb63-2fc59007c20b_files'/snpEff.config

Exit Code:

```
0
```

Standard Error:

00:00:00 SnpEff version SnpEff 5.4c (build 2026-02-23 07:25), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'mpxv'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'mpxv'
00:00:00 Looking for config file: '/tmp/tmpzhosac2u/job_working_directory/000/5/working/snpEff.config'
00:00:00 Reading config file: /usr/local/share/snpeff-5.4.0c-0/snpEff.config
00:00:01 Codon table 'Standard' for genome 'mpxv'
00:00:01 done
00:00:01 Chromosome: 'KP849471.1'	length: 197248
00:00:01 Create exons from CDS (if needed): 
00:00:01 Exons created for 188 transcripts.
00:00:01 Deleting redundant exons (if needed): 
00:00:01 	Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed): 
00:00:01 	Total collapsed transcripts: 0
00:00:01 		Adding genomic sequences to genes: 
00:00:01 	Done (153 sequences added).
00:00:01 		Adding genomic sequences to exons: 
00:00:01 	Done (188 sequences added, 0 ignored).
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts: 
00:00:01 Adjusting genes: 
00:00:01 Adjusting chromosomes lengths: 
00:00:01 Ranking exons: 
00:00:01 Create UTRs from CDS (if needed): 
00:00:01 Remove empty chromosomes: 
00:00:01 Marking as 'coding' from CDS information: 
00:00:01 Done: 0 transcripts marked
00:00:01 
00:00:01 Caracterizing exons by splicing (stage 1) : 

00:00:01 Caracterizing exons by splicing (stage 2) : 
00:00:01 done.
00:00:01 [Optional] Rare amino acid annotations
WARNING_FILE_NOT_FOUND: Rare Amino Acid analysis: Cannot read protein sequence file '/tmp/tmpzhosac2u/job_working_directory/000/5/working/snpeff_output/mpxv/protein.fa', nothing done.
00:00:01 Saving database
00:00:01 Saving sequences for small chromosmes to file '/tmp/tmpzhosac2u/job_working_directory/000/5/working/snpeff_output/mpxv/sequence.bin'
00:00:01 [Optional] Reading regulation elements: GFF
WARNING_FILE_NOT_FOUND: Cannot read optional regulation file '/tmp/tmpzhosac2u/job_working_directory/000/5/working/snpeff_output/mpxv/regulation.gff', nothing done.
00:00:01 [Optional] Reading regulation elements: BED 
00:00:01 Cannot find optional regulation dir '/tmp/tmpzhosac2u/job_working_directory/000/5/working/snpeff_output/mpxv/regulation.bed/', nothing done.
00:00:01 [Optional] Reading motifs: GFF
WARNING_FILE_NOT_FOUND: Cannot open PWMs file /tmp/tmpzhosac2u/job_working_directory/000/5/working/snpeff_output/mpxv/pwms.bin. Nothing done
00:00:01 Done
00:00:01 Done.

Standard Output:

Writing FASTA record: KP849471.1
............................................................................................................................................................................................

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"79fe72b8c99a11f1a9dd6045bdc951a2"`
chromInfo	`"/tmp/tmpzhosac2u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
codon_table	`"Standard"`
dbkey	`"?"`
genome_version	`"mpxv"`
input_type	`{"__current_case__": 0, "fasta": "yes", "input": {"values": [{"id": 1, "src": "hda"}]}, "input_type_selector": "gb", "remove_version": false}`

Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:bd996097b6dd518cf788ddd6c586fb23d039cb9c-0

Command Line:

set -o | grep -q pipefail && set -o pipefail;  ln -s '/tmp/tmpzhosac2u/files/6/8/a/dataset_68a75981-3d85-4a32-bb66-92517310ee92.dat' 'localref.fa' && bwa index 'localref.fa' &&    bwa mem  -t "${GALAXY_SLOTS:-1}" -v 1     -T '30' -h '5'    -Y   -q                'localref.fa' '/tmp/tmpzhosac2u/files/e/9/4/dataset_e941f0db-b270-4919-9469-a081b13d8e54.dat' '/tmp/tmpzhosac2u/files/d/5/d/dataset_d5d6f079-6197-4e8f-9041-8ec1b3296530.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpzhosac2u/job_working_directory/000/6/outputs/dataset_44ee835e-364a-43aa-a06a-43da25ad20d9.dat'

Exit Code:

```
0
```

Standard Error:

[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.02 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.19-r1273
[main] CMD: bwa index localref.fa
[main] Real time: 0.038 sec; CPU: 0.035 sec
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (277, 334, 393)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (45, 625)
[M::mem_pestat] mean and std.dev: (338.50, 89.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 741)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.19-r1273
[main] CMD: bwa mem -t 1 -v 1 -T 30 -h 5 -Y -q localref.fa /tmp/tmpzhosac2u/files/e/9/4/dataset_e941f0db-b270-4919-9469-a081b13d8e54.dat /tmp/tmpzhosac2u/files/d/5/d/dataset_d5d6f079-6197-4e8f-9041-8ec1b3296530.dat
[main] Real time: 0.204 sec; CPU: 0.204 sec

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"79fe72b8c99a11f1a9dd6045bdc951a2"`
analysis_type	`{"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}`
chromInfo	`"/tmp/tmpzhosac2u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""}`
output_sort	`"coordinate"`
reference_source	`{"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`

Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:8f53bfe77285b2fc8b6545efd875a0b3d1d12061-0

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&        ln -s '/tmp/tmpzhosac2u/files/4/4/e/dataset_44ee835e-364a-43aa-a06a-43da25ad20d9.dat' infile && ln -s '/tmp/tmpzhosac2u/files/_metadata_files/9/8/7/metadata_987e6b18-e3e1-495c-830b-04f0ae5e971d.dat' infile.bai &&               samtools view -@ $addthreads -b  -f 3 -F 0 -G 0   -o outfile      infile

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"79fe72b8c99a11f1a9dd6045bdc951a2"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpzhosac2u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/picard:3.1.1--hdfd78af_0

Command Line:

_JAVA_OPTIONS=${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=${TMPDIR:-${_GALAXY_JOB_TMPDIR}}"} && export _JAVA_OPTIONS &&   ln -sf '/tmp/tmpzhosac2u/files/7/3/9/dataset_7392bfba-c2ab-489e-bef1-c43e463c2ce7.dat' 'ERR3485802' &&  picard MarkDuplicates  --INPUT 'ERR3485802' --OUTPUT '/tmp/tmpzhosac2u/job_working_directory/000/8/outputs/dataset_ad642ca1-5038-4c83-91bb-f781709e6eba.dat'  --METRICS_FILE '/tmp/tmpzhosac2u/job_working_directory/000/8/outputs/dataset_99c4e50c-740a-4570-949a-182a2aa5f928.dat'  --REMOVE_DUPLICATES 'true' --ASSUME_SORTED 'true'  --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES  --OPTICAL_DUPLICATE_PIXEL_DISTANCE '100'   --VALIDATION_STRINGENCY 'LENIENT' --TAGGING_POLICY All --QUIET true --VERBOSITY ERROR

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m -Djava.io.tmpdir=/tmp/tmpzhosac2u/job_working_directory/000/8/tmp
Oct 16, 2026 7:49:43 PM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"79fe72b8c99a11f1a9dd6045bdc951a2"`
assume_sorted	`true`
barcode_tag	`""`
chromInfo	`"/tmp/tmpzhosac2u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comments	`[]`
dbkey	`"?"`
duplicate_scoring_strategy	`"SUM_OF_BASE_QUALITIES"`
optical_duplicate_pixel_distance	`"100"`
read_name_regex	`""`
remove_duplicates	`true`
validation_stringency	`"LENIENT"`

Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/samtools:1.22--h96c455f_0

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   ln -s '/tmp/tmpzhosac2u/files/7/3/9/dataset_7392bfba-c2ab-489e-bef1-c43e463c2ce7.dat' infile && ln -s '/tmp/tmpzhosac2u/files/_metadata_files/5/d/8/metadata_5d81e4c7-fafd-4330-9202-4cb8f1bcd369.dat' infile.bai &&       samtools stats       -@ $addthreads infile   > '/tmp/tmpzhosac2u/job_working_directory/000/9/outputs/dataset_406c081c-2815-4271-8553-e6a26eb25c31.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"79fe72b8c99a11f1a9dd6045bdc951a2"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpzhosac2u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
cov_threshold	`None`
coverage_cond	`{"__current_case__": 0, "coverage_select": "no"}`
dbkey	`"?"`
filter_by_flags	`{"__current_case__": 1, "filter_flags": "nofilter"}`
gc_depth	`None`
insert_size	`None`
most_inserts	`None`
read_group	`None`
read_length	`None`
remove_dups	`false`
remove_overlaps	`false`
sparse	`false`
split_output_cond	`{"__current_case__": 0, "split_output_selector": "no"}`
trim_quality	`None`

Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/lofreq:2.1.5--py313ha7493ab_16

Command Line:

ln -s '/tmp/tmpzhosac2u/files/6/8/a/dataset_68a75981-3d85-4a32-bb66-92517310ee92.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  lofreq viterbi --ref 'reference.fa'  --defqual 2 --out tmp.bam '/tmp/tmpzhosac2u/files/a/d/6/dataset_ad642ca1-5038-4c83-91bb-f781709e6eba.dat' &&  samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmpzhosac2u/job_working_directory/000/10/outputs/dataset_0d39cd24-695b-403a-b22a-9b9af3f976e6.dat' tmp.bam

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"79fe72b8c99a11f1a9dd6045bdc951a2"`
adv_options	`{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}`
chromInfo	`"/tmp/tmpzhosac2u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`

Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy4):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/multiqc:1.35--pyhdfd78af_2

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastp_0 &&         grep -Pq '"before_filtering": {' /tmp/tmpzhosac2u/files/1/9/d/dataset_19deb8e8-9cf5-4423-b3b3-c901d600f74e.dat || die "Module 'fastp: '"before_filtering": {' not found in the file 'ERR3485802'" && ln -s '/tmp/tmpzhosac2u/files/1/9/d/dataset_19deb8e8-9cf5-4423-b3b3-c901d600f74e.dat' 'multiqc_WDir/fastp_0/ERR3485802.json'  &&    mkdir multiqc_WDir/samtools_1 &&    mkdir 'multiqc_WDir/samtools_1/stats_0' &&      grep -Pq 'This file was produced by samtools stats' /tmp/tmpzhosac2u/files/4/0/6/dataset_406c081c-2815-4271-8553-e6a26eb25c31.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file 'ERR3485802'" && ln -s '/tmp/tmpzhosac2u/files/4/0/6/dataset_406c081c-2815-4271-8553-e6a26eb25c31.dat' 'multiqc_WDir/samtools_1/stats_0/ERR3485802'  &&    mkdir multiqc_WDir/picard_2 &&      mkdir 'multiqc_WDir/picard_2/markdups_0' &&    grep -Pq 'MarkDuplicates' /tmp/tmpzhosac2u/files/9/9/c/dataset_99c4e50c-740a-4570-949a-182a2aa5f928.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'ERR3485802'" && ln -s '/tmp/tmpzhosac2u/files/9/9/c/dataset_99c4e50c-740a-4570-949a-182a2aa5f928.dat' 'multiqc_WDir/picard_2/markdups_0/ERR3485802'  &&        multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && { cp ./report_data/*plot*.txt ./plots/ 2>/dev/null || true; }

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.35

       file_search | Search path: /tmp/tmpzhosac2u/job_working_directory/000/11/working/multiqc_WDir
            picard | Found 1 MarkDuplicates reports
          samtools | Found 1 stats reports
             fastp | Found 1 reports
     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete

Standard Output:

total 1436
-rw-r--r-- 1 1001 1001    5607 Oct 16 19:50 fastp-insert-size-plot.txt
-rw-r--r-- 1 1001 1001    3166 Oct 16 19:50 fastp-seq-content-gc-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    2858 Oct 16 19:50 fastp-seq-content-gc-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    2966 Oct 16 19:50 fastp-seq-content-gc-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001    2789 Oct 16 19:50 fastp-seq-content-gc-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001    2065 Oct 16 19:50 fastp-seq-content-n-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    2065 Oct 16 19:50 fastp-seq-content-n-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    2065 Oct 16 19:50 fastp-seq-content-n-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001    2065 Oct 16 19:50 fastp-seq-content-n-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001    2655 Oct 16 19:50 fastp-seq-quality-plot_Read_1_After_filtering.txt
-rw-r--r-- 1 1001 1001    2633 Oct 16 19:50 fastp-seq-quality-plot_Read_1_Before_filtering.txt
-rw-r--r-- 1 1001 1001    2652 Oct 16 19:50 fastp-seq-quality-plot_Read_2_After_filtering.txt
-rw-r--r-- 1 1001 1001    2646 Oct 16 19:50 fastp-seq-quality-plot_Read_2_Before_filtering.txt
-rw-r--r-- 1 1001 1001     117 Oct 16 19:50 fastp_filtered_reads_plot.txt
-rw-r--r-- 1 1001 1001   30146 Oct 16 19:50 llms-full.txt
-rw-r--r-- 1 1001 1001   23182 Oct 16 19:50 multiqc.log
-rw-r--r-- 1 1001 1001   51378 Oct 16 19:50 multiqc.parquet
-rw-r--r-- 1 1001 1001     183 Oct 16 19:50 multiqc_citations.txt
-rw-r--r-- 1 1001 1001 1132673 Oct 16 19:50 multiqc_data.json
-rw-r--r-- 1 1001 1001  116812 Oct 16 19:50 multiqc_fastp.txt
-rw-r--r-- 1 1001 1001     796 Oct 16 19:50 multiqc_general_stats.txt
-rw-r--r-- 1 1001 1001     299 Oct 16 19:50 multiqc_picard_dups.txt
-rw-r--r-- 1 1001 1001    1310 Oct 16 19:50 multiqc_samtools_stats.txt
-rw-r--r-- 1 1001 1001      50 Oct 16 19:50 multiqc_software_versions.txt
-rw-r--r-- 1 1001 1001     413 Oct 16 19:50 multiqc_sources.txt
-rw-r--r-- 1 1001 1001       0 Oct 16 19:50 picard_MarkIlluminaAdapters_histogram.txt
-rw-r--r-- 1 1001 1001       0 Oct 16 19:50 picard_MeanQualityByCycle_histogram.txt
-rw-r--r-- 1 1001 1001       0 Oct 16 19:50 picard_MeanQualityByCycle_histogram_1.txt
-rw-r--r-- 1 1001 1001       0 Oct 16 19:50 picard_QualityScoreDistribution_histogram.txt
-rw-r--r-- 1 1001 1001      72 Oct 16 19:50 picard_deduplication.txt
-rw-r--r-- 1 1001 1001     329 Oct 16 19:50 samtools-stats-dp.txt
-rw-r--r-- 1 1001 1001      54 Oct 16 19:50 samtools_alignment_plot.txt
-rw-r--r-- 1 1001 1001    7377 Oct 16 19:50 samtools_insert_size.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"79fe72b8c99a11f1a9dd6045bdc951a2"`
chromInfo	`"/tmp/tmpzhosac2u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
image_content_input	`None`
png_plots	`false`
results	[{"__index__": 0, "software_cond": {"__current_case__": 8, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 25, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 18, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
saveLog	`"false"`
title	`""`

Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/lofreq:2.1.5--py313ha7493ab_16

Command Line:

ln -s '/tmp/tmpzhosac2u/files/6/8/a/dataset_68a75981-3d85-4a32-bb66-92517310ee92.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  lofreq indelqual --dindel --ref reference.fa -o output.bam /tmp/tmpzhosac2u/files/0/d/3/dataset_0d39cd24-695b-403a-b22a-9b9af3f976e6.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"79fe72b8c99a11f1a9dd6045bdc951a2"`
chromInfo	`"/tmp/tmpzhosac2u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
strategy	`{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}`

Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/lofreq:2.1.5--py313ha7493ab_16

Command Line:

ln -s '/tmp/tmpzhosac2u/files/6/8/a/dataset_68a75981-3d85-4a32-bb66-92517310ee92.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&  ln -s '/tmp/tmpzhosac2u/files/5/3/6/dataset_5368d323-a0c0-43c4-863f-a71d31abab7f.dat' reads.bam && ln -s -f '/tmp/tmpzhosac2u/files/_metadata_files/7/7/2/metadata_7727d042-7668-4fe8-9a8e-8b5ac83e1288.dat' reads.bam.bai &&   lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose  --ref 'reference.fa' --out variants.vcf --call-indels   --min-cov 5 --max-depth 1000000  --min-bq 30 --min-alt-bq 30    --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0  --sig 0.0005 --bonf dynamic --no-default-filter  reads.bam 2>&1  || (tool_exit_code=$? && cat "$TMPDIR"/lofreq2_call_parallel*/*.log 1>&2 && exit $tool_exit_code)  && echo set_custom

Exit Code:

```
0
```

Standard Output:

INFO [2026-10-16 19:50:56,655]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter reads.bam

INFO [2026-10-16 19:50:56,665]: Adding 4 commands to mp-pool
Checking the headers and starting positions of 4 files
[W::bcf_hdr_check_sanity] AF should be declared as Number=A
[W::bcf_hdr_check_sanity] SB should be declared as Number=4
Number of substitution tests performed: 324
Number of indel tests performed: 27
INFO [2026-10-16 19:50:57,605]: Executing lofreq filter -i /tmp/tmpzhosac2u/job_working_directory/000/13/tmp/lofreq2_call_parallelrusgbtg4/concat.vcf.gz -o variants.vcf --no-defaults --snvqual-thresh 58 --indelqual-thresh 47

set_custom

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"79fe72b8c99a11f1a9dd6045bdc951a2"`
call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
chromInfo	`"/tmp/tmpzhosac2u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_control	`{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}`
reference_source	`{"__current_case__": 1, "ref": {"values": [{"id": 9, "src": "hda"}]}, "ref_selector": "history"}`
regions	`{"__current_case__": 0, "restrict_to_region": "genome"}`
variant_types	`"--call-indels"`

Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/lofreq:2.1.5--py313ha7493ab_16

Command Line:

lofreq filter -i /tmp/tmpzhosac2u/files/b/8/d/dataset_b8d05836-5189-4e07-ab78-6dba0ee553f3.dat --no-defaults --verbose --print-all  -v 0 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001   -o filtered.vcf

Exit Code:

```
0
```

Standard Error:

Skipping default settings
At least one type of multiple testing correction requested. Doing first pass of vcf
MTC application completed
Successful exit.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"79fe72b8c99a11f1a9dd6045bdc951a2"`
af	`{"af_max": "0.0", "af_min": "0.0"}`
chromInfo	`"/tmp/tmpzhosac2u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
coverage	`{"cov_max": "0", "cov_min": "0"}`
dbkey	`"?"`
filter_by_type	`{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}`
flag_or_drop	`"--print-all"`
sb	`{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}`

Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/mulled-v2-b63b6277c1547c8fbbef71582adb7d2600a09ae9:d5f569ec01b5de1e1d3753793b3af0ab899f785f-0

Command Line:

snpEff -Xmx${GALAXY_MEMORY_MB:-8192}m eff -i vcf -o vcf -upDownStreamLen 0 -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -no-utr                    -s snpeff_stats.html -noLog -dataDir '/tmp/tmpzhosac2u/files/2/8/9/dataset_28944ad4-167d-40b1-bb63-2fc59007c20b_files' -configOption 'mpxv'.genome='mpxv' -configOption 'mpxv'.codonTable='Standard' 'mpxv' '/tmp/tmpzhosac2u/files/b/8/1/dataset_b8197b87-afed-4af6-8b88-7e2f8208f3f5.dat' > '/tmp/tmpzhosac2u/job_working_directory/000/15/outputs/dataset_fd6b78c1-5e83-44f9-b021-5fddb34196ee.dat' && mkdir '/tmp/tmpzhosac2u/job_working_directory/000/15/outputs/dataset_bd9297fd-fd0e-4d8e-a4c2-c06b2490f955_files' && mv snpeff_stats.genes.txt /tmp/tmpzhosac2u/job_working_directory/000/15/outputs/dataset_bd9297fd-fd0e-4d8e-a4c2-c06b2490f955_files

Exit Code:

```
0
```

Standard Error:

00:00:00 Codon table 'Standard' for genome 'mpxv'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"79fe72b8c99a11f1a9dd6045bdc951a2"`
annotations	`["-formatEff", "-classic"]`
chr	`""`
chromInfo	`"/tmp/tmpzhosac2u/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
csvStats	`false`
dbkey	`"?"`
filter	`{"__current_case__": 0, "specificEffects": "no"}`
filterOut	`["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"]`
generate_gene_stats	`false`
generate_stats	`true`
inputFormat	`"vcf"`
intervals	`None`
noLog	`true`
offset	`"default"`
outputConditional	`{"__current_case__": 0, "outputFormat": "vcf"}`
outputFormat	`"vcf"`
snpDb	`{"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 8, "src": "hda"}]}}`
spliceRegion	`{"__current_case__": 0, "setSpliceRegions": "no"}`
spliceSiteSize	`None`
transcripts	`None`
udLength	`"0"`

Other invocation details
- history_id
  - a8b73d2152f2793f
- history_state
  - ok
- invocation_id
  - a8b73d2152f2793f
- invocation_state
  - scheduled
- workflow_id
  - a8b73d2152f2793f

SnpEff 5.4 needs versioned sequence ids, so mapping and variant calling now use e.g. KP849471.1. A new boolean input (default false) also outputs the reference FASTA with ids as in 0.1.1 (KP849471).

mvdbeek · 2026-10-17T10:19:25Z

@nekrut you're listed as the creator of this workflow. Could you check whether this change makes sense?

What changed. snpEff 5.4 names chromosomes after the GenBank VERSION field (KP849471.1). This workflow stripped the version from the reference, so snpEff couldn't match any variant to a chromosome (ERROR_CHROMOSOME_NOT_FOUND). The PR now keeps the version (remove_version: false). As a result, the reference FASTA, the BAMs and all the VCFs use KP849471.1 rather than KP849471. The variant calls and annotations are otherwise unchanged:

92 records, 90 of them PASS and 2 sb_fdr
about 54 annotated
the K393E, T101, D627Y and A4V effects are identical to the snpEff 4.3 results

New optional output. There is a new boolean input, Strip version from reference sequence ids, which defaults to false. When it is set, the workflow also outputs Fasta sequences for genbank file without version: the reference FASTA with ids as in 0.1.1. Mapping and variant calling still use the versioned ids, so this FASTA won't match the VCF/BAM contig names. It is only meant for downstream use with files keyed on the bare accession.

Questions:

Is the versioned id change OK?
Is the optional unversioned FASTA useful, or should it be dropped?
Would you rather stay on snpEff 4.3 instead?

gxydevbot · 2026-10-19T12:46:51Z

There are new updates, if you want to integrate them, close the PR and delete branch.

Galaxy refuses to import a workflow whose steps (inputs included) share a label ("Duplicated step label ... in request."), but neither lint_ga nor lint_format2 checked for it, so planemo workflow_lint passed workflows that then failed at import (galaxyproject/iwc#310). Add a StepLabelNotUnique structural rule, checked per workflow level like Galaxy (subworkflows have their own namespace, empty labels ignored). The Format2 check uses the same label helpers as conversion, now shared as native_input_label / native_step_label, so it flags exactly the native labels Galaxy would see.

gxydevbot · 2026-10-23T11:02:25Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2026-10-26T13:01:45Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2026-10-30T11:44:44Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2026-11-02T15:34:49Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2026-11-06T16:49:12Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2026-11-09T16:05:19Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2026-11-13T03:22:31Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot changed the title ~~Updating workflows/variant-calling/generic-variant-calling-wgs-pe from 0.1.1 to 0.1.2~~ Updating workflows/variant-calling/generic-variant-calling-wgs-pe from 0.1.1 to 0.1.2 Mar 5, 2024

gxydevbot force-pushed the workflows/variant-calling/generic-variant-calling-wgs-pe branch from 4fd752a to efa4703 Compare September 23, 2024 14:55

gxydevbot force-pushed the workflows/variant-calling/generic-variant-calling-wgs-pe branch from efa4703 to 7c636a0 Compare September 24, 2024 14:31

gxydevbot force-pushed the workflows/variant-calling/generic-variant-calling-wgs-pe branch from 7c636a0 to 3bc0713 Compare October 7, 2024 05:31

gxydevbot force-pushed the workflows/variant-calling/generic-variant-calling-wgs-pe branch from 3bc0713 to 828ad55 Compare October 21, 2024 05:20

gxydevbot force-pushed the workflows/variant-calling/generic-variant-calling-wgs-pe branch from 828ad55 to c44a614 Compare October 28, 2024 05:13

gxydevbot force-pushed the workflows/variant-calling/generic-variant-calling-wgs-pe branch from c44a614 to 80b0cbe Compare November 18, 2024 05:43

gxydevbot force-pushed the workflows/variant-calling/generic-variant-calling-wgs-pe branch from 80b0cbe to 64ba12f Compare January 27, 2025 05:44

gxydevbot force-pushed the workflows/variant-calling/generic-variant-calling-wgs-pe branch from 64ba12f to fe71741 Compare February 10, 2025 05:52

gxydevbot force-pushed the workflows/variant-calling/generic-variant-calling-wgs-pe branch from fe71741 to 1aadbc1 Compare February 17, 2025 05:59

Updating workflows/variant-calling/generic-variant-calling-wgs-pe fro…

507cb8f

…m 0.1.1 to 0.1.2

gxydevbot force-pushed the workflows/variant-calling/generic-variant-calling-wgs-pe branch from d55acf8 to 507cb8f Compare September 21, 2026 13:20

Merge branch 'main' into workflows/variant-calling/generic-variant-ca…

9696c4a

…lling-wgs-pe

Reconnect GenBank input to snpEff_build_gb 5.4 (param renamed input_g…

bac0965

…bk -> input)

Keep GenBank sequence version for snpEff 5.4 and use robust VCF asser…

ec2db37

…tions

mvdbeek added 4 commits October 16, 2026 21:59

Accept samtools stats average length 150 or 151 (fastp 1.3)

f9cb186

Clarify average length comment

3225bf5

Add optional output of the reference FASTA without sequence versions

1a04d56

SnpEff 5.4 needs versioned sequence ids, so mapping and variant calling now use e.g. KP849471.1. A new boolean input (default false) also outputs the reference FASTA with ids as in 0.1.1 (KP849471).

Give the sed step a label distinct from its input

3334a65

mvdbeek approved these changes Oct 17, 2026

View reviewed changes

This was referenced Oct 17, 2026

Lint duplicate step labels as errors galaxyproject/gxformat2#268

Merged

Lint duplicate step labels as errors (port gxformat2 StepLabelNotUnique) jmchilton/galaxy-tool-util-ts#192

Merged

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