Error in job genotype while creating output file

[Oelsakha]

Hi all

I am trying to run test files of MGEfinder but I got this error

CHECKING DEPENDENCIES

Current version of snakemake: 3.13.3 Expected version of snakemake: 3.13.3 Current version of einverted: EMBOSS:6.6.0.0 Expected version of einverted: EMBOSS:6.6.0.0 Current version of bowtie2: 2.3.5 Expected version of bowtie2: 2.3.5 Current version of samtools: 1.9 Expected version of samtools: 1.9 Current version of cd-hit: 4.8.1 Expected version of cd-hit: 4.8.1 : : 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 /Users/mo/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 "/Users/mo/miniconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.Snakefile", line 286, in __rule_genotype File "/Users/mo/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

: subprocess.CalledProcessError: Command 'snakemake -s /Users/mo/miniconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.Snakefile --config wd=test_workdir/ memory=16000 --cores 1 --configfile /Users/mo/miniconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.config.yml ' returned non-zero exit status 1.

[durrantmm]

Looks like an issue with snakemake. How did you install MGEfinder?

[Oelsakha]

I already have conda so i did this step git clone https://github.com/bhattlab/MGEfinder.git cd MGEfinder/ bash install.sh However, I removed MGEfinder and reinstall it and found this new error.

 Traceback (most recent call last):

File "/Users/mo/miniconda3/bin/mgefinder", line 33, in sys.exit(load_entry_point('mgefinder==1.0.6', 'console_scripts', 'mgefinder')()) File "/Users/mo/miniconda3/bin/mgefinder", line 25, in importlib_load_entry_point return next(matches).load() File "/Users/mo/miniconda3/lib/python3.9/importlib/metadata.py", line 86, in load module = import_module(match.group('module')) File "/Users/mo/miniconda3/lib/python3.9/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1030, in _gcd_import File "", line 1007, in _find_and_load File "", line 986, in _find_and_load_unlocked File "", line 680, in _load_unlocked File "", line 850, in exec_module File "", line 228, in _call_with_frames_removed File "/Users/mo/miniconda3/lib/python3.9/site-packages/mgefinder-1.0.6-py3.9.egg/mgefinder/main.py", line 5, in from mgefinder.workflow import _workflow File "/Users/mo/miniconda3/lib/python3.9/site-packages/mgefinder-1.0.6-py3.9.egg/mgefinder/workflow.py", line 2, in from snakemake import shell ModuleNotFoundError: No module named 'snakemake'

[durrantmm]

Seems like a clean install is needed here. I assume you're also calling conda activate mgefinder?

[Oelsakha]

can you explain more? I removed it then reinstalled and conda activate mgefinder now give me this error zsh: command not found: mgefinder

[durrantmm]

You need to activate the conda environment that includes the mgefinder installation. This seems like an issue with your conda installation. Could you give me the exact output when you run the command:

conda activate mgefinder

[Oelsakha]

Yes, I did and mgefinder env is activated but if I run it give me zsh: command not found: mgefinder

[durrantmm]

Then it didn't install properly. Could you uninstall, reinstall, and send me the complete output?