virstrain module error: expecting python is already installed

[abulenciamiguel]

The error below shows that I have no python installed in my environment which is true. You can make a yaml file to set up the environment or have all modules run on a docker container.

N E X T F L O W  ~  version 23.04.1
Launching `CoPi/main.nf` [big_legentil] DSL2 - revision: 9a59f5b6be
executor >  local (7)
[5b/a4d801] process > concat (Concatenating fasta files into all_sequences.fasta)            [  0%] 0 of 1
[-        ] process > pangolin                                                               -
[-        ] process > nextclade                                                              -
[-        ] process > lineage_assignment                                                     -
[-        ] process > bammix                                                                 -
[-        ] process > bam_filter                                                             -
[06/141427] process > virstrain (Identifying lineage assignment for barcode08 using Virst... [  0%] 0 of 3
[68/76fa2b] process > freyja (Identifying relative lineage abundances of samples to see p... [  0%] 0 of 3
[-        ] process > freyja_demix                                                           -
[-        ] process > freyja_aggregate                                                       -
[-        ] process > freyja_plot                                                            -
[-        ] process > makevcf                                                                -
[-        ] process > bammixplot                                                             -
[-        ] process > aafplot_mutations                                                      -
[-        ] process > aafplot_amplicons                                                      -
[-        ] process > ampliconsorting_DeltaReads                                             -
[-        ] process > ampliconsorting_OmicronReads                                           -
[-        ] process > ampliconsorting_samtools                                               -
[-        ] process > ampliconsorting_bgzip                                                  -
[-        ] process > ampliconsorting_fasta                                                  -
[-        ] process > ampliconsorting_lineageAssignment_Pangolin                             -
[-        ] process > ampliconsorting_lineageAssignment_Nextclade                            -
executor >  local (7)
[5b/a4d801] process > concat (Concatenating fasta files into all_sequences.fasta)            [100%] 1 of 1, failed: 1 ✘
[-        ] process > pangolin                                                               -
[-        ] process > nextclade                                                              -
[-        ] process > lineage_assignment                                                     -
[-        ] process > bammix                                                                 -
[-        ] process > bam_filter                                                             -
[06/141427] process > virstrain (Identifying lineage assignment for barcode08 using Virst... [100%] 3 of 3, failed: 3 ✘
[-        ] process > freyja (Identifying relative lineage abundances of samples to see p... -
[-        ] process > freyja_demix                                                           -
[-        ] process > freyja_aggregate                                                       -
[-        ] process > freyja_plot                                                            -
[-        ] process > makevcf                                                                -
[-        ] process > bammixplot                                                             -
[-        ] process > aafplot_mutations                                                      -
[-        ] process > aafplot_amplicons                                                      -
[-        ] process > ampliconsorting_DeltaReads                                             -
[-        ] process > ampliconsorting_OmicronReads                                           -
[-        ] process > ampliconsorting_samtools                                               -
[-        ] process > ampliconsorting_bgzip                                                  -
[-        ] process > ampliconsorting_fasta                                                  -
[-        ] process > ampliconsorting_lineageAssignment_Pangolin                             -
[-        ] process > ampliconsorting_lineageAssignment_Nextclade                            -
[-        ] process > report                                                                 -
ERROR ~ Error executing process > 'virstrain (Identifying lineage assignment for barcode09 using Virstrain)'

Caused by:
  Process `virstrain (Identifying lineage assignment for barcode09 using Virstrain)` terminated with an error exit status (127)

Command executed:

  python /home/ufuoma/coinfection/CoPi/bin/VirStrain/VirStrain.py         -i Samples//barcode09.fastq         -d /home/ufuoma/coinfection/CoPi/bin/VirStrain/Custom_DB         -o result/03-Virstrain/barcode09

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 2: python: command not found

Work dir:
  /home/ufuoma/coinfection/work/3d/d40f649707af33cc06542f44367751

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

[lanadelrea]

The VirStrain docker container seems to be working fine now. Thank you sir u da best!