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Hi PULpy developers,
I am running your pipeline, but encountered an error message that I don't know how to fix. I installed the package witin a conda environment as you instructed, and installed moose package sudo apt-get install libmoose-perl on my system. But it didn't fix the problem. Could you please help?
$ snakemake --use-conda
Building DAG of jobs...
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 all
285 dbcan_filter
107 gff2table
285 pfam_scan
285 puls
963
rule pfam_scan:
input: proteins/MSK18_37_protein.faa
output: pfam/MSK18_37.pfam
jobid: 672
wildcards: id=MSK18_37
Activating conda environment /home/pamerlab/Documents/Eddi/PULpy/.snakemake/conda/59de0edf.
/bin/bash: activate: No such file or directory
Can't locate Moose.pm in @INC (you may need to install the Moose module) (@INC contains: /home/pamerlab/miniconda3/envs/PULpy/share/pfam_scan-1.6-4 /home/pamerlab/miniconda3/envs/PULpy/lib/perl5/5.32/site_perl /home/pamerlab/miniconda3/envs/PULpy/lib/perl5/site_perl /home/pamerlab/miniconda3/envs/PULpy/lib/perl5/5.32/vendor_perl /home/pamerlab/miniconda3/envs/PULpy/lib/perl5/vendor_perl /home/pamerlab/miniconda3/envs/PULpy/lib/perl5/5.32/core_perl /home/pamerlab/miniconda3/envs/PULpy/lib/perl5/core_perl .) at /home/pamerlab/miniconda3/envs/PULpy/share/pfam_scan-1.6-4/Bio/Pfam/HMM/HMMResultsIO.pm line 50.
BEGIN failed--compilation aborted at /home/pamerlab/miniconda3/envs/PULpy/share/pfam_scan-1.6-4/Bio/Pfam/HMM/HMMResultsIO.pm line 50.
Compilation failed in require at /home/pamerlab/miniconda3/envs/PULpy/share/pfam_scan-1.6-4/Bio/Pfam/Scan/PfamScan.pm line 33.
BEGIN failed--compilation aborted at /home/pamerlab/miniconda3/envs/PULpy/share/pfam_scan-1.6-4/Bio/Pfam/Scan/PfamScan.pm line 33.
Compilation failed in require at /home/pamerlab/miniconda3/envs/PULpy/share/pfam_scan-1.6-4/pfam_scan.pl line 8.
BEGIN failed--compilation aborted at /home/pamerlab/miniconda3/envs/PULpy/share/pfam_scan-1.6-4/pfam_scan.pl line 8.
Error in rule pfam_scan:
jobid: 672
output: pfam/MSK18_37.pfam
RuleException:
CalledProcessError in line 106 of /home/pamerlab/Documents/Eddi/PULpy/Snakefile:
Command 'source activate /home/pamerlab/Documents/Eddi/PULpy/.snakemake/conda/59de0edf; source /etc/profile; pfam_scan.pl -outfile pfam/MSK18_37.pfam -as -cpu 1 -fasta proteins/MSK18_37_protein.faa -dir pfam_data ' returned non-zero exit status 2.
File "/home/pamerlab/Documents/Eddi/PULpy/Snakefile", line 106, in __rule_pfam_scan
File "/usr/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
Complete log: .snakemake/log/2021-11-08T105040.143971.snakemake.log
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