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implement MEGAHIT #244
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root@kbase-devel:/kbase/arast/assembly# git log --oneline|grep megahit |
The test completed successfully. I'm reopening the issue to make sure the logging is correct. Here's the megahit.out file I see in the work directory (note that the
The actual command seems correct:
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The argument in the list after "input-cmd" is basically "cat " + " ".join(files). Do you want me to test with more than 1 file before closing the issue ? |
I think the command is probably passed correctly. Can you look into how to get the "Command: megabit..." line in the output file to reflect the "cat .." subcommand correctly? |
This can be done by printing the command from within the megahit assembly service plugin. |
MEGAHIT is now part of dev recipes and testing. The issue will be closed when Seb completes the test on big files. |
I tested with a pair of files. seb@kbase-devel:~/bug-167/job-80$ arast get -j 80 seb@kbase-devel:~/bug-167/job-80$ ls -lh seb@kbase-devel:~/bug-167/job-80$ head 80_report.txt Assembly megahit_contigs contigs (>= 0 bp) 2003contigs (>= 1000 bp) 77Total length (>= 0 bp) 2300567 contigs 115Largest contig 132002 seb@kbase-devel:~/bug-167/job-80$ arast stat -d|grep 80 |
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