Error when rerunning VS2

[dnolin13]

Hello, When I was rerunning VS2, which I installed via conda, it ran for several days before spitting out this error message:

`12 merge_split_hmmtbl_by_group 7 merge_split_hmmtbl_by_group_tmp 1 pick_viral_fullseq 844 [2023-03-18 05:35 ERROR] See error details in /home/delaney/SPOT_virome_depth_profiles/quals_subset_depth_profile/13_Viral_Contigs/VirSorter2/DN_SPOT_Anotops_quals_subset_CDHIT_rename_classify.output/log/iter-0/step2-extract-feature/extract-feature-from-hmmout-common.log [Sat Mar 18 05:35:21 2023] Error in rule hmm_sort_to_best_hit_taxon: jobid: 26 output: iter-0/all.pdg.hmm.tax, iter-0/all.pdg.hmm.taxpfam, iter-0/all.pdg.hmm.taxwhm, iter-0/all.pdg.hmm.ftr log: log/iter-0/step2-extract-feature/extract-feature-from-hmmout-common.log (check log file(s) for error message) conda-env: /home/delaney/db/virsorter2-db/conda_envs/cd2ce1e9 shell: python /home/delaney/miniconda3/envs/vs2/lib/python3.9/site-packages/virsorter/./scripts/extract-feature-from-hmmout.py 30 "iter-0/all.pdg.Archaea.hmmtbl,iter-0/all.pdg.Bacteria.hmmtbl,iter-0/all.pdg.Eukaryota.hmmtbl,iter-0/all.pdg.Mixed.hmmtbl,iter-0/all.pdg.Viruses.hmmtbl" "arc,bac,euk,mixed,vir" > iter-0/all.pdg.hmm.tax 2> log/iter-0/step2-extract-feature/extract-feature-from-hmmout-common.log || { echo "See error details in /home/delaney/SPOT_virome_depth_profiles/quals_subset_depth_profile/13_Viral_Contigs/VirSorter2/DN_SPOT_Anotops_quals_subset_CDHIT_rename_classify.output/log/iter-0/step2-extract-feature/extract-feature-from-hmmout-common.log" | python /home/delaney/miniconda3/envs/vs2/lib/python3.9/site-packages/virsorter/./scripts/echo.py --level error; exit 1; } python /home/delaney/miniconda3/envs/vs2/lib/python3.9/site-packages/virsorter/./scripts/add-unaligned-to-hmm-featrues.py iter-0/all.pdg.faa iter-0/all.pdg.hmm.tax > iter-0/all.pdg.hmm.ftr

pfam only annotation

        python /home/delaney/miniconda3/envs/vs2/lib/python3.9/site-packages/virsorter/./scripts/extract-feature-from-hmmout.py 30 "iter-0/all.pdg.Archaea.hmmtbl,iter-0/all.pdg.Bacteria.hmmtbl,iter-0/all.pdg.Eukaryota.hmmtbl,iter-0/all.pdg.Mixed.hmmtbl,iter-0/all.pdg.Pfamviruses.hmmtbl" "arc,bac,euk,mixed,vir" > iter-0/all.pdg.hmm.taxpfam 2>> log/iter-0/step2-extract-feature/extract-feature-from-hmmout-common.log || { echo "See error details in /home/delaney/SPOT_virome_depth_profiles/quals_subset_depth_profile/13_Viral_Contigs/VirSorter2/DN_SPOT_Anotops_quals_subset_CDHIT_rename_classify.output/log/iter-0/step2-extract-feature/extract-feature-from-hmmout-common.log" | python /home/delaney/miniconda3/envs/vs2/lib/python3.9/site-packages/virsorter/./scripts/echo.py --level error; exit 1; }
        python /home/delaney/miniconda3/envs/vs2/lib/python3.9/site-packages/virsorter/./scripts/add-unaligned-to-hmm-featrues.py iter-0/all.pdg.faa iter-0/all.pdg.hmm.taxpfam > iter-0/all.pdg.hmm.ftrpfam
        # add hallmark info to .tax file for making affi-contigs.tab file
        python /home/delaney/miniconda3/envs/vs2/lib/python3.9/site-packages/virsorter/./scripts/add-hallmark-to-taxfile.py iter-0/all.pdg.hmm.tax iter-0/all.pdg.hmm.taxwhm
        # remove split faa files
        echo iter-0/all.pdg.faa.*.split | xargs rm -f

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Exiting because a job execution failed. Look above for error message *** An error occurred. Detailed errors may not be printed for certain rules. Refer to the log file of the failed command for troubleshooting Issues can be raised at: https://github.com/jiarong/VirSorter2/issues`

and this is the note from the log:

(vs2) delaney@ada:~/SPOT_virome_depth_profiles/quals_subset_depth_profile/13_Viral_Contigs/VirSorter2/DN_SPOT_Anotops_quals_subset_CDHIT_rename_classify.output/log/iter-0/step2-extract-feature$ more extract-feature-from-hmmout-common.log Traceback (most recent call last): File "/home/delaney/miniconda3/envs/vs2/lib/python3.9/site-packages/virsorter/./scripts/extract-feature-from-hmmout.py", line 6, in <module> import screed ModuleNotFoundError: No module named 'screed'

[jiarong]

Hi, the error message typically indicates you have multiple package managers interfering each other (conda being one of them). I recommend the installation option 3 to get around.