Provide FASTA via --gene_db but SRST2 seems to expect bowtie index?

katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens

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Provide FASTA via --gene_db but SRST2 seems to expect bowtie index? #79

Closed mw55309 closed 7 years ago

mw55309 commented 7 years ago

Hey

So the documentation definitely states that --gene_db should be a fasta file, and I used ARGannot.r1.fasta in my tests.

However, all my jobs failed as Bowtie2 failed; and bowtie2 failed because ARGannot.r1.fasta is not an index...

This could be because I submitted 48 jobs simultaneously.

Is it possible that all 48 jobs tried to create the same index??

Cheers Mick

mw55309 commented 7 years ago

OK, answered my own question!

My guess is 1st time run creates faidx and bowtie2 indices, so submitting multiple jobs simulatenously creates clashes as multiple jobs attempt the first time index build.

katholt commented 7 years ago

See https://github.com/katholt/srst2#known-issues