Error with demo in STEP2: executing process > 'msms_searching (spec-00139.mgf)'

[Sawakotx]

I succeeded in running the STEP1, but failed in STEP2, all information I know about error are as follows :

Error executing process > 'msms_searching (spec-00139.mgf)'

Caused by:
  Process `msms_searching (spec-00139.mgf)` terminated with an error exit status (2)

Command executed:

  #!/bin/sh
  /opt/comet.2018014.linux.exe -Pcomet_parameter.txt -Nspec-00139_rawResults -Dneoflow_crc_target_decoy.fasta spec-00139.mgf
  sed -i '1d' spec-00139_rawResults.txt
  sed -i '1 s/$/ "2018.0na/' spec-00139_rawResults.txt

Command exit status:
  2

Command output:
   Comet version "2018.01 rev. 4"

Command error:
   Comet version "2018.01 rev. 4"
  
  Segmentation fault (core dumped)
  sed: can't read spec-00139_rawResults.txt: No such file or directory
  sed: can't read spec-00139_rawResults.txt: No such file or directory

Work dir:
  /root/work/8c/e6ebc4108dbc902d529873b78827ae

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`

I'm not sure if I need to install the MS/MS searching engines like comet (the example of STEP2 in demo).

Also, I supported the command lines I used in STEP2, which may give more details:

nextflow run /root/neoflow/neoflow_msms.nf --ms /root/work/example_data/mgf/ --msms_para_file /root/work/example_data/comet_parameter.txt --search_engine comet --db /root/output/customized_database/neoflow_crc_target_decoy.fasta --out_dir /root/output --pv_refdb /root/output/customized_database/ref.fasta --pv_tol 20 --pv_itol 0.05

I am a complete novice in this field and really hope to meet someone to give advice～ Thanks in advance!!!