Error while setting up databases

Description of the bug

I'm getting the following error when trying to setup database.

Command used:

nextflow run deng-lab/viroprofiler -r main -profile docker --mode "setup" --db /media/BRIANDATA2/sidd/viroprofiler_db --max_cpus 20 --max_memory 200GB

Error:

  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  mkdir: cannot create directory ‘/media/BRIANDATA2/sidd/viroprofiler_db’: Permission denied

However, when I use the relative path in --db option I get some success but get another error:

Command used: nextflow run deng-lab/viroprofiler -r main -profile docker --mode "setup" --db viroprofiler_db --max_cpus 20 --max_memory 200GB

Error:

  2023-06-20 19:47:51 (30.5 MB/s) - ‘taxdump.zip’ saved [58628855/58628855]

  Archive:  taxdump.zip
    inflating: citations.dmp
    inflating: delnodes.dmp
    inflating: division.dmp
    inflating: gencode.dmp
    inflating: merged.dmp
    inflating: names.dmp
    inflating: nodes.dmp
    inflating: gc.prt
    inflating: readme.txt
  viroprofiler_db/taxonomy/mmseqs_vrefseq.tar.gz: No such file or directory

Work dir:
  /media/BRIANDATA2/sidd/work/a3/a1f7bb952801c534dba57b2aa6dec0

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

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

Command used and terminal output

# This is the command when using absolute path
nextflow run deng-lab/viroprofiler -r main -profile docker --mode "setup" --db /media/BRIANDATA2/sidd/viroprofiler_db --max_cpus 20 --max_memory 200GB

-[ViroProfiler] Pipeline completed with errors-
ERROR ~ Error executing process > 'VIROPROFILER:SETUP:DB_VIBRANT'

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

Command executed:

  if [ ! -d /media/BRIANDATA2/sidd/viroprofiler_db/vibrant ]; then
      mkdir -p /media/BRIANDATA2/sidd/viroprofiler_db/vibrant
executor >  local (6)
[60/d37bfe] process > VIROPROFILER:SETUP:DB_CHECKV     [100%] 1 of 1, failed: 1 ✘
[a2/f8216d] process > VIROPROFILER:SETUP:DB_VIBRANT    [100%] 1 of 1, failed: 1 ✘
[8a/3b8bb6] process > VIROPROFILER:SETUP:DB_VIRSORTER2 [100%] 1 of 1, failed: 1 ✘
[b7/780b5b] process > VIROPROFILER:SETUP:DB_DRAM       [100%] 1 of 1, failed: 1 ✘
[19/e6e121] process > VIROPROFILER:SETUP:DB_IPHOP      [100%] 1 of 1, failed: 1 ✘
[6f/7e476f] process > VIROPROFILER:SETUP:DB_VREFSEQ    [100%] 1 of 1, failed: 1 ✘
Execution cancelled -- Finishing pending tasks before exit
-[ViroProfiler] Pipeline completed with errors-
ERROR ~ Error executing process > 'VIROPROFILER:SETUP:DB_VIBRANT'

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

Command executed:

  if [ ! -d /media/BRIANDATA2/sidd/viroprofiler_db/vibrant ]; then
      mkdir -p /media/BRIANDATA2/sidd/viroprofiler_db/vibrant
      export VIBRANT_DATA_PATH="/opt/conda/share/vibrant-1.2.1/db"
      download-db.sh /media/BRIANDATA2/sidd/viroprofiler_db/vibrant
  else
      echo "VIBRANT database already exists"
  fi

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  mkdir: cannot create directory ‘/media/BRIANDATA2/sidd/viroprofiler_db’: Permission denied

Work dir:
  /media/BRIANDATA2/sidd/work/a2/f8216dcace4d0e2ef6e56c399b5c5a

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`

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

Relevant files

nextflow_relativePath.log nextflow_absPath.log

System information

Nextflow version 23.04.1 nf-core/viroprofiler - revision: c2a1f1871b [main]. But while running the version displayed is ViroProfiler v0.2.4

deng-lab / viroprofiler