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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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Error message returned non-zero exit status 1 #20

Closed SK-N-BE closed 6 years ago

SK-N-BE commented 6 years ago

I have never had problems when using staramr, but suddenly I am getting this error message:

2018-06-29 11:45:58,535 ERROR: Command '['makeblastdb', '-in', '/tmp/tmp426ql20e/input-genomes/Patient_2_A.fasta', '-dbtype', 'nucl', '-parse_seqids']' returned non-zero exit status 1 What may I do?

apetkau commented 6 years ago

staramr first runs makeblastdb to make a BLAST database of your input genomes. It seems like this command failed. To get more details, you can run the command outside of staramr, that is:

makeblastdb -in Patient_2_A.fasta -dbtype nucl -parse_seqids

I've sometimes had trouble in cases where there are duplicate sequence ids in an input fasta file (in which case you just have to make them unique). But, there could be a number of reasons this command failed.

SK-N-BE commented 6 years ago

Thank you. Using your command, I am getting this error message:

BLAST Database creation error: Error: Duplicate seq_ids are found: LCL|PATIENT

Thus, there seems to be the error you describe: duplicate sequence ids in an input fasta file. I am using a multi-fasta file.

apetkau commented 6 years ago

Great. You can try opening up the file and renaming the sequence ids so they are unique. For example, if there are multiple ids like >patient, you can rename them >patient1, >patient2, and so on.

SK-N-BE commented 6 years ago

Thank you! It is working. I have done the following:

I opened the multi-fasta file in Artemis and generated a "single-fasta" file that I used as an input for staramr instead of the multi-fasta file

apetkau commented 6 years ago

That's awesome :smile:. I'm glad it's working. Let me know if you have any more questions.