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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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Error in job genotype while creating output #20

Closed MKorzhanova closed 3 years ago

MKorzhanova commented 3 years ago

Hello! I have an error while running workflow denovo. I had the same problem with my samples and with your test directory. 

Finished job 3.
75 of 79 steps (95%) done

rule genotype:
    input: test_workdir/03.results/efae_GCF_900639545/01.clusterseq.efae_GCF_900639545.tsv, test_workdir/01.mgefinder/efae_GCF_900639545/efae_GCF_900639545.all_pair.txt
    output: test_workdir/03.results/efae_GCF_900639545/02.genotype.efae_GCF_900639545.tsv
    log: test_workdir/03.results/efae_GCF_900639545/log/efae_GCF_900639545.genotype.log
    jobid: 4
    benchmark: test_workdir/03.results/efae_GCF_900639545/log/efae_GCF_900639545.genotype.benchmark.txt
    wildcards: genome=efae_GCF_900639545

zsh:2: = not found
Error in job genotype while creating output file test_workdir/03.results/efae_GCF_900639545/02.genotype.efae_GCF_900639545.tsv.
RuleException:
CalledProcessError in line 286 of /home/mk/miniconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.Snakefile:
Command '
        if [ "True" == "True" ]; then
            mgefinder genotype --filter-clusters-inferred-assembly test_workdir/03.results/efae_GCF_900639545/01.clusterseq.efae_GCF_900639545.tsv test_workdir/01.mgefinder/efae_GCF_900639545/efae_GCF_900639545.all_pair.txt -o test_workdir/03.results/efae_GCF_900639545/02.genotype.efae_GCF_900639545.tsv 1> test_workdir/03.results/efae_GCF_900639545/log/efae_GCF_900639545.genotype.log 2> test_workdir/03.results/efae_GCF_900639545/log/efae_GCF_900639545.genotype.log.err ||             (cat test_workdir/03.results/efae_GCF_900639545/log/efae_GCF_900639545.genotype.log.err; exit 1)
        else
            mgefinder genotype --no-filter-clusters-inferred-assembly test_workdir/03.results/efae_GCF_900639545/01.clusterseq.efae_GCF_900639545.tsv test_workdir/01.mgefinder/efae_GCF_900639545/efae_GCF_900639545.all_pair.txt -o test_workdir/03.results/efae_GCF_900639545/02.genotype.efae_GCF_900639545.tsv 1> test_workdir/03.results/efae_GCF_900639545/log/efae_GCF_900639545.genotype.log 2> test_workdir/03.results/efae_GCF_900639545/log/efae_GCF_900639545.genotype.log.err ||             (cat test_workdir/03.results/efae_GCF_900639545/log/efae_GCF_900639545.genotype.log.err; exit 1)
        fi
        ' returned non-zero exit status 1.
  File "/home/mk/miniconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.Snakefile", line 286, in __rule_genotype
  File "/home/mk/miniconda3/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

test_workdir/03.results/efae_GCF_900639545/log directory is empty.

durrantmm commented 3 years ago

I haven't seen this error before. This looks like you are using the Z shell instead of the default bash. Could you try running it in a bash shell?

wshropshire commented 2 years ago

New MacOS updates have the default terminal shell scripting in Zsh now. Is there any way to go around this bash script error?