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assembleAll.pl: quast --min-contig 1 to avoid errors on bad assemblies
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SneakerNet.plugins/assembleAll.pl

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -190,7 +190,9 @@ sub assembleAll{
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if(!-e "$outdir/quast/report.html"){
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logmsg "Running quast on $outassembly > $outdir/quast";
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command("quast $outassembly --glimmer --output-dir $outdir/quast --threads $$settings{numcpus} --rna-finding");
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# 2024-09-23 adding --min-contig 1 to accept assemblies of very small contig lengths:
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# we just want to know if it's a bad assembly and we don't want quast to crash.
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command("quast $outassembly --glimmer --output-dir $outdir/quast --threads $$settings{numcpus} --rna-finding --min-contig 1");
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}
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else{
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logmsg "Found $outdir/quast/report.html. Not rerunning";

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