predector exit status (137)

Question

[analyst]

Dear all, I got following error while running predector command.

Plus 4 more processes waiting for tasks… [06/6a863f] NOTE: Process signalp_v6 (2) terminated with an error exit status (137) -- Execution is retried (1)

How to avoid this or should i ignore it?

Also predector command is taking days to for 145 fungus proteomes (proteome size range from 7-9mb ). What can be the estimated completion time? Note that server contains 96 cores, 440.5 GiB memory, 10tb space

[GenoMax]

Status 137 related to memory. Looks like 440GB is not enough for what ever you are running.

[analyst]

I am running predector (effector prediction pipeline based on protein properties) using nextflow command given in the usage.

Please find link to tool here

Thank you!

[analyst]

ERROR ~ Error executing process > 'targetp (56)'

Caused by:
  Process `targetp (56)` terminated with an error exit status (1)


Command executed:

  # targetp2 just uses all available cores afaik.
  # Although it seems to use omp, i don't seem to be able to force it
  # to use a specific number of cores.
  export OMP_NUM_THREADS="4"

  run () {
      set -e
      export TMPDIR="tmpdir$$"
      mkdir "${TMPDIR}"

      OUT="out$$"

      targetp           -fasta "${1}"           -org non-pl           -format short           -prefix "${OUT}"         1>&2

      cat "${OUT}_summary.targetp2"
      rm -rf -- "${TMPDIR}" "${OUT}"*
  }

  export -f run

  parallel       --halt now,fail=1       --joblog log.txt       -j 1       -N 1000       --line-buffer       --recstart '>'       --cat       run     < in.fasta     | cat > out.txt

  predutils r2js         --pipeline-version "1.2.7"         --software-version "2.0"       targetp_non_plant "out.txt" in.fasta     > "out.ldjson"

Command exit status:
  1

Command output:
  (empty)

Command error:
  mkdir: cannot create directory ‘tmpdir172’: File exists
  parallel: This job failed:
  run $PARALLEL_TMP

Work dir:
  /home/fungus/Apps/predector/work/25/cf1084dec603b1596a695437f362f3

Container:
  predector/predector:1.2.7

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

Running command again I got above message on bash terminal

[GenoMax]

mkdir: cannot create directory ‘tmpdir172’: File exists

Looks like you need to do some cleanup when you are restarting the pipeline.