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mags-building: give MaxBin2 a two-column abundance file - #1540
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paulzierep wants to merge 3 commits into
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MaxBin2 reads the first number after the contig name as the abundance, so the jgi_summarize_bam_contig_depths table made it bin on contig length instead of coverage. Convert the depth table to contig name and totalAvgDepth without header before MaxBin2.
…2 bins With MaxBin2 binning on coverage instead of contig length, Binette selects different bins: the dereplicated set is now bin1 and bin2, and bin1 is 913 kb instead of 803 kb. Assert on stable content instead of an exact contig count.
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Closing in favour of #1454, which replaces this workflow with the modular version and already includes the same fixes: the MaxBin2 abundance conversion (in both the single- and multi-coverage binning subworkflows) and the installable megahit/collection_column_join pins. The standalone binning workflows get the fix in #1538 and #1539. |
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Converts the coverage depth table into the two-column abundance format MaxBin2 expects (contig name and
totalAvgDepth, no header). This adds one Text reformatting step between "Calculate contig depths" and MaxBin2, in the "Abundance utils for Binning" frame. Release 0.9 → 0.10, CHANGELOG updated.The same fix is needed in the modularised workflow in #1454, which embeds the single- and multi-sample binning workflows. It will be carried over there.
Why
MaxBin2 reads the contig name and then only the first number after it as the abundance (
AbundanceLoader::parsecallsatof()on the rest of the line). Thejgi_summarize_bam_contig_depthstable (contigName contigLen totalAvgDepth ...) is therefore accepted without any error, but the contig length is used as the abundance. The header line is read as a contig too.Tested on usegalaxy.eu with a real assembly (859k contigs), MaxBin2
2.2.7+galaxy6, default settings, and CheckM2 1.1.0 on the resulting bins:totalAvgDepth, no header (this PR)Follow-up tool updates
The two tool updates for this workflow will be added to this PR once they are merged and available:
2.2.7+galaxy7(MaxBin2: handle explicit insufficient-marker no-bin outcome tools-iuc#8787): handles gzipped contigs and runs with no bins, and documents the abundance format2.5.0(semibin: update to version 2.5.0 tools-iuc#8885): includes the upstream fix for the crash when no bins pass the size threshold