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!!!

[Sawakotx]

Also, before the above problem, the first question I met in the STEP2 was about parameter 'cpu'.
According to the information of error, I just set 'params.cpu = 10' in file"neoflow_msms.nf', then the error seems disappeared, but I'm not sure I'm doing the right thing. Could you help me get back on track？ ：）

There are some details :

WARN: Access to undefined parameter `cpu` -- Initialise it to a default value eg. `params.cpu = some_value`
Error executing process > 'msms_searching (spec-00465.mgf)'

Caused by:
  For input string: "null"

Until now, I set 'params.cpu = 10' in file"neoflow_msms.nf', then the error seems disappeared, but I'm not sure I'm doing the right thing.

Again，Could you help me get back on track？I would really really appreciate it！！！ ：）🫡

[iblacksand]

This thread from the comet support forum seems to be relevant: https://groups.google.com/g/comet-ms/c/aJcontJ9xtU/m/7icBb1snBgAJ.

One comment suggests that it may be due to the amount of threads used, which you set here. Perhaps you can try a lower number for params.cpu. However, the issue in the thread was the program itself, so you may have to run a newer version of comet if changing params.cpu doesn't work. You can download comet from https://uwpr.github.io/Comet/. You would also have to change this section from neoflow_msms.nf to reflect which version you download.

neoflow/neoflow_msms.nf

Line 139 in 1c4f641

/opt/comet.2018014.linux.exe -P${msms_para_file} -N${ms_file.baseName}_rawResults -D${search_db} ${ms_file}

.

And if you haven't seen my latest comment on #10, the spaces are not actually needed, so you should remove them as well.

[Sawakotx]

Thank you very much!!!!! And I did learn many tips from your advice!!!
But it doesn't seem to be a CPU or version issue.
After excluding several possible solutions, according to the tips in #3, which had successfully ran step2, I guess I need to use docker to run it. But I am not familiar with the use of docker and I'm not clear whether the software required by neoflow needs to be installed and used in docker, such as annovar, etc.