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katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
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grep gene name syntax error #55

Closed cytang19 closed 8 years ago

cytang19 commented 8 years ago

Hi,

I have this issue at the end of running srst2 using resistance gene database. I don't find any problem with the result but I want to clarify this error with you. Is this error a significant one or it just output error with the gene naming but doesn't affect the result?

sh: -c: line 0: syntax error near unexpected token (' sh: -c: line 0:grep 194mph(A)_1_D16251mph(A)_1_D16251__00057 /database/resfinder2016_2.fasta'

Thanks, Cheng

katholt commented 8 years ago

Looks like a problem with the '()' characters in fasta headers. This won't affect your results as it's just occurring when we try to extract additional annotation information for the gene, it's not affecting the output. You could either remove any brackets from the headers in your fasta file, or use the updated resistance gene DB we provide, ie https://github.com/katholt/srst2/blob/master/data/ARGannot.r1.fasta