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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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Run error in Galaxy 19.05 #123

Closed PHemarajata closed 4 years ago

PHemarajata commented 4 years ago

Hi, I ran into an error trying to run staramr 0.7.1 in Galaxy. I think this happened after I updated the tool. There is no unresolved dependencies. Please see below. I'd really appreciate any suggestion on what I should do. Thank you so much and stay safe!

2020-07-25 13:30:20 INFO: No --pointfinder-organism specified. Will not search the PointFinder databases 2020-07-25 13:30:20 INFO: No --plasmidfinder-database-type specified. Will search the entire PlasmidFinder database 2020-07-25 13:30:20 INFO: --output-dir not set. Files will be output to the respective --output-[type] setting 2020-07-25 13:30:20 INFO: Will exclude ResFinder/PointFinder genes listed in [/home/phemarajata/galaxy/database/dependencies/_conda/envs/__staramr@0.7.1/lib/python3.7/site-packages/staramr/databases/exclude/data/genes_to_exclude.tsv]. Use --no-exclude-genes to disable 2020-07-25 13:30:20 INFO: Making BLAST databases for input files 2020-07-25 13:30:20 ERROR: list index out of range Traceback (most recent call last): File "/home/phemarajata/galaxy/database/dependencies/_conda/envs/staramr@0.7.1/lib/python3.7/site-packages/staramr/blast/JobHandler.py", line 286, in _make_blast_db subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True) File "/home/phemarajata/galaxy/database/dependencies/_conda/envs/staramr@0.7.1/lib/python3.7/subprocess.py", line 512, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['makeblastdb', '-in', '/home/phemarajata/galaxy/database/tmp/tmpxgo6kvxs/input-genomes/plasmid_AA337.fasta.fasta', '-dbtype', 'nucl', '-parse_seqids']' returned non-zero exit status 1.

PHemarajata commented 4 years ago

I'm so sorry. It was my FASTAs that caused it. Should have figured that out earlier.