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bhattlab / MGEfinder

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
MIT License
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mgefinder issue #25

Closed Rick-meinersmann closed 3 years ago

Rick-meinersmann commented 3 years ago

mgefinder is giving me an error code I don't understand. As far as I can tell the input files follow the specifications and everything should be up to date, loaded or updated in the last week. Entire screen dump in in attached file. mge_screen-out.txt

Pertinent part would seem to be: click.echo('Loading file {num1}/{num2}: {f}'.format(num1=1, num2=len(inferseq_files), f=inferseq_files[0])) IndexError: list index out of range Error in job clusterseq while creating output file /home/rick/Documents/Campy-mge-test/03.results/AL111168/01.clusterseq.AL111168.tsv. RuleException: CalledProcessError in line 259 of /home/rick/anaconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.Snakefile: Command ' mgefinder clusterseq -minsize 70 -maxsize 200000 --threads 1 --memory 50000 /home/rick/Documents/Campy-mge-test/01.mgefinder/AL111168/AL111168.all_inferseq_database.txt -o /home/rick/Documents/Campy-mge-test/03.results/AL111168/01.clusterseq.AL111168.tsv ' returned non-zero exit status 1. File "/home/rick/anaconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.Snakefile", line 259, in __rule_clusterseq File "/home/rick/anaconda3/envs/mgefinder/lib/python3.6/concurrent/futures/thread.py", line 56, in run Will exit after finishing currently running jobs. Exiting because a job execution failed. Look above for error message

Thank you for any help, Rick

durrantmm commented 3 years ago

Thank you for reporting this issue. Please follow my responses in #16, and see if that clarifies the issue. My guess is that it didn't find any insertions and it failed as a result on the clusterseq step.

Rick-meinersmann commented 3 years ago

I missed the format on the bam file names to include the name of the reference genome sequence. On fixing that the program ran without any error calls. Thank you.

durrantmm commented 3 years ago

Great! Glad you got it working.