Permission issues - Githubissues

I am encountering a permissions issue when running the pipeline under docker profile.


Launching `Katmon/main.nf` [cranky_mclean] DSL2 - revision: a3ec2e25a6

executor >  local (9)
[7a/742485] concat (Concatenating fasta files into all_sequences.fasta)            | 1 of 1 ✔
[19/4f589a] pangolin (Lineage assignment using pangolin tool)                      | 0 of 1
[58/56f008] nextclade (Lineage assignment using nextclade)                         | 0 of 1
[-        ] lineage_assignment                                                     -
[-        ] bammix                                                                 -
[-        ] bam_filter                                                             -
[-        ] makevcf                                                                -
[0a/36d21b] vir…in (Identifying lineage assignment for barcode07 using VirsStrain) | 0 of 3
[-        ] virstrain_summary                                                      -
[72/d2d734] fre…lative lineage abundances of samples to see potential coinfection) | 0 of 3
[-        ] freyja_demix                                                           -
[-        ] freyja_aggregate                                                       -
[-        ] freyja_plot                                                            -
[-        ] bammixplot                                                             -
[-        ] aafplot_mutations                                                      -
[-        ] aafplot_amplicons                                                      -
[-        ] ampliconsorting_DeltaReads                                             -
[-        ] ampliconsorting_OmicronReads                                           -
[-        ] ampliconsorting_samtools                                               -
[-        ] ampliconsorting_bgzip                                                  -
[-        ] ampliconsorting_fasta                                                  -
[-        ] ampliconsorting_lineageAssignment_Pangolin                             -
[-        ] ampliconsorting_lineageAssignment_Nextclade                            -
[-        ] report                                                                 -
ERROR ~ Error executing process > 'virstrain (Identifying lineage assignment for barcode09 using VirsStrain)'

executor >  local (9)
[7a/742485] concat (Concatenating fasta files into all_sequences.fasta)            | 1 of 1 ✔
[-        ] pangolin (Lineage assignment using pangolin tool)                      -
[-        ] nextclade (Lineage assignment using nextclade)                         -
[-        ] lineage_assignment                                                     -
[-        ] bammix                                                                 -
[-        ] bam_filter                                                             -
[-        ] makevcf                                                                -
[0a/36d21b] vir…in (Identifying lineage assignment for barcode07 using VirsStrain) | 1 of 1, failed: 1
[-        ] virstrain_summary                                                      -
[-        ] fre…lative lineage abundances of samples to see potential coinfection) -
[-        ] freyja_demix                                                           -
[-        ] freyja_aggregate                                                       -
[-        ] freyja_plot                                                            -
[-        ] bammixplot                                                             -
[-        ] aafplot_mutations                                                      -
[-        ] aafplot_amplicons                                                      -
[-        ] ampliconsorting_DeltaReads                                             -
[-        ] ampliconsorting_OmicronReads                                           -
[-        ] ampliconsorting_samtools                                               -
[-        ] ampliconsorting_bgzip                                                  -
[-        ] ampliconsorting_fasta                                                  -
[-        ] ampliconsorting_lineageAssignment_Pangolin                             -
[-        ] ampliconsorting_lineageAssignment_Nextclade                            -
[-        ] report                                                                 -
ERROR ~ Error executing process > 'virstrain (Identifying lineage assignment for barcode09 using VirsStrain)'

Caused by:
  Process `virstrain (Identifying lineage assignment for barcode09 using VirsStrain)` terminated with an error exit status (1)

Command executed:

  virstrain         -i barcode09.fastq         -d /home/iwantsaul/Katmon/assets/Custom_DB         -o /home/iwantsaul/Results/03-Virstrain/barcode09

  cp /home/iwantsaul/Results/03-Virstrain/barcode09/VirStrain_report.txt barcode09_VirStrain.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
  /bin/bash: .command.sh: Permission denied

Work dir:
  /home/iwantsaul/work/b3/4530d4156b4422bf99a34f0d0753dc

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

I managed to fix this by putting this in the nextflow.config file:

runOptions = '-u $(id -u):$(id -g)'

docker {
    enabled = true
    temp = 'auto'
    runOptions = '-u $(id -u):$(id -g)'
    }

nice work on the pipeline.

lanadelrea / Katmon

Permission issues #16