Error with initialising the "template-config.yaml" for Virsorter2

[sajanraju]

Description of the bug

I am getting an error with Virsorter2. I have analysed the sample dataset from the viroprofiler, and getting this error.

Command used and terminal output

executor >  local (15)
[0e/e464ef] process > VIROPROFILER:FASTQC (HT02)     [100%] 1 of 1, cached: 1 ✔
[f2/56dbcd] process > VIROPROFILER:FASTP (HT02)      [100%] 1 of 1, cached: 1 ✔
[79/b9f74b] process > VIROPROFILER:SPADES (HT02)     [100%] 1 of 1, cached: 1 ✔
[cf/6f2e5e] process > VIROPROFILER:CONTIGLIB         [100%] 1 of 1, cached: 1 ✔
[80/9da85a] process > VIROPROFILER:CHECKV            [100%] 1 of 1 ✔
[e1/4cabb0] process > VIROPROFILER:CONTIGLIB_CLUSTER [100%] 1 of 1 ✔
[0b/6b6263] process > VIROPROFILER:GENEPRED4CTG      [100%] 1 of 1 ✔
[b8/f7e985] process > VIROPROFILER:NRPROT            [100%] 1 of 1 ✔
[70/0c1c75] process > VIROPROFILER:NRGENE            [100%] 1 of 1 ✔
[ec/146d7f] process > VIROPROFILER:CONTIGINDEX       [100%] 1 of 1 ✔
[12/a0317d] process > VIROPROFILER:MAPPING2CONTIG... [100%] 1 of 1 ✔
[-        ] process > VIROPROFILER:ABUNDANCE         [  0%] 0 of 1
[36/02ee83] process > VIROPROFILER:VIBRANT           [100%] 1 of 1 ✔
[62/7b2fb5] process > VIROPROFILER:DVF               [100%] 1 of 1 ✔
[ed/2814e5] process > VIROPROFILER:VIRCONTIGS_PRE    [100%] 1 of 1 ✔
[9d/46aef3] process > VIROPROFILER:VIRSORTER2        [100%] 1 of 1, failed: 1 ✘
[-        ] process > VIROPROFILER:DRAMV             -
[c1/d7d4b9] process > VIROPROFILER:TAXONOMY_VCONTACT [100%] 1 of 1 ✔
[ed/608642] process > VIROPROFILER:TAXONOMY_MMSEQS   [100%] 1 of 1 ✔
[-        ] process > VIROPROFILER:TAXONOMY_MERGE    -
[29/196368] process > VIROPROFILER:VIRALHOST_IPHOP   [100%] 1 of 1, failed: 1 ✘
[02/0d5574] process > VIROPROFILER:BACPHLIP          [100%] 1 of 1 ✔
[-        ] process > VIROPROFILER:RESULTS_TSE       -
[-        ] process > VIROPROFILER:CUSTOM_DUMPSOF... -
[-        ] process > VIROPROFILER:MULTIQC           [  0%] 0 of 1
-[ViroProfiler] Pipeline completed with errors-
Error executing process > 'VIROPROFILER:VIRSORTER2'

Caused by:
  Process `VIROPROFILER:VIRSORTER2` terminated with an error exit status (1)

Command executed:

  #virsorter config --set HMMSEARCH_THREADS=1
  virsorter run --seqname-suffix-off --viral-gene-enrich-off --prep-for-dramv -i putative_vcontigs_pref1.fasta -w out_vs2 --include-groups dsDNAphage --min-length 3000 --min-score 0.5 -j 1 --provirus-off -d /cluster/projects/nn8111k/databases/viroprofiler/virsorter2 all
  grep '^>' out_vs2/final-viral-combined.fa | sed 's/>//' | sed 's/||.*//' > virus_virsorter2.list
  ln -s out_vs2/for-dramv/final-viral-combined-for-dramv.fa .
  ln -s out_vs2/for-dramv/viral-affi-contigs-for-dramv.tab .
  seqkit fx2tab -n final-viral-combined-for-dramv.fa | sed 's/-cat_/,/g' | csvtk add-header -n Contig,vs2_category > vs2_category.csv

  cat <<-END_VERSIONS > versions.yml
  "VIROPROFILER:VIRSORTER2":
      VirSorter2: $(grep 'VirSorter' .command.log | head -n1 | sed 's/.* //')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  [2024-06-20 11:52 INFO] VirSorter 2.2.4
  [2024-06-20 11:52 INFO] /opt/conda/bin/virsorter run --seqname-suffix-off --viral-gene-enrich-off --prep-for-dramv -i putative_vcontigs_pref1.fasta -w out_vs2 --include-groups dsDNAphage --min-length 3000 --min-score 0.5 -j 1 --provirus-off -d /cluster/projects/nn8111k/databases/viroprofiler/virsorter2 all
  [2024-06-20 11:52 INFO] "template-config.yaml" has not been initialized; initializing..
  [2024-06-20 11:52 INFO] saving /cluster/projects/nn8111k/databases/viroprofiler/virsorter2 as DBDIR to config file /VirSorter2/virsorter/template-config.yaml
  Traceback (most recent call last):
    File "/VirSorter2/virsorter/config.py", line 96, in make_config
      with open(TEMPLATE) as fp:
  FileNotFoundError: [Errno 2] No such file or directory: '/VirSorter2/virsorter/template-config.yaml'

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "/opt/conda/bin/virsorter", line 8, in <module>
      sys.exit(cli())
    File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1130, in __call__
      return self.main(*args, **kwargs)
    File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1055, in main
      rv = self.invoke(ctx)
    File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
      return _process_result(sub_ctx.command.invoke(sub_ctx))
    File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
      return ctx.invoke(self.callback, **ctx.params)
    File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 760, in invoke
      return __callback(*args, **kwargs)
    File "/VirSorter2/virsorter/virsorter.py", line 356, in run_workflow
      make_config(
    File "/VirSorter2/virsorter/config.py", line 120, in make_config
      config = init_config_template(SRC_CONFIG_DIR, 
    File "/VirSorter2/virsorter/config.py", line 63, in init_config_template
      with open(template, 'w') as fw:
  OSError: [Errno 30] Read-only file system: '/VirSorter2/virsorter/template-config.yaml'

Work dir:
  /cluster/work/users/sajanr/coco_test/work/9d/46aef375de884c0ad09071fa3620ae

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Relevant files

No response

System information

nextflow version 24.04.2.5914 HPC slurm Singularity Linux ViroProfiler v0.2.4