Problem with MzidToTsvConverter in WSL

[JannikSchneider12]

Hey,

I installed msgf+ in WSL and ran the tool on my mgf file. But now when I want to convert it, I am getting this error and I dont know why:

(base) jannik@DELLXPS:~/msgfplus/MzidToTsvConverter$ mono MzidToTsvConverter.exe -mzid /home/jannik/data/consensus_spectra/falcon_run_1_50_conservative.mzid

Error: Unrecognized argument name: home/jannik/data/consensus_spectra/falcon_run_1_50_conservative.mzid

Argument parsing failed: Unknown arguments found

Does someone has an idea what could be the problem?

Thanks for your time and help:)

[FarmGeek4Life]

Please put the argument in quotes, like "/home/jannik/data/consensus_spectra/falcon_run_1_50_conservative.mzid"

---

From: Jannik Schneider @.> Sent: Tuesday, January 9, 2024 3:47:23 AM To: MSGFPlus/msgfplus @.> Cc: Subscribed @.***> Subject: [MSGFPlus/msgfplus] Problem with MzidToTsvConverter in WSL (Issue #149)

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Hey,

I installed msgf+ in WSL and ran the tool on my mgf file. But now when I want to convert it, I am getting this error and I dont know why:

(base) @.***:~/msgfplus/MzidToTsvConverter$ mono MzidToTsvConverter.exe -mzid /home/jannik/data/consensus_spectra/falcon_run_1_50_conservative.mzid

Error: Unrecognized argument name: home/jannik/data/consensus_spectra/falcon_run_1_50_conservative.mzid

Argument parsing failed: Unknown arguments found

Does someone has an idea what could be the problem?

Thanks for your time and help:)

— Reply to this email directly, view it on GitHubhttps://github.com/MSGFPlus/msgfplus/issues/149, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABPPX5MDEMDL4UAL7IOMBVDYNUU4XAVCNFSM6AAAAABBS7DFBCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3TEMRRGQZTANY. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[JannikSchneider12]

Hey,

I also tried it, but the same error occurs:

(base) jannik@DELLXPS:~/msgfplus/MzidToTsvConverter$ mono MzidToTsvConverter.exe -mzid "/home/jannik/data/consensus_spectra/falcon_run_1_50_conservative.mzid"

Error: Unrecognized argument name: home/jannik/data/consensus_spectra/falcon_run_1_50_conservative.mzid

Argument parsing failed: Unknown arguments found

[FarmGeek4Life]

What is happening is the command line parser it uses supports both '-mzid' and '/mzid', and because the path starts with '/' it thinks it's an argument name, not the value, and I hoped the quotes would bypass that but they did not.

Possible options for you to get around this: change -mzid /home/jannik/data/consensus_spectra/falcon_run_1_50_conservative.mzid to:

• -mzid ~/data/consensus_spectra/falcon_run_1_50_conservative.mzid (linux interprets '~' to mean 'current user's home directory', but I'm not sure if that will work properly with mono)
• -mzid:/home/jannik/data/consensus_spectra/falcon_run_1_50_conservative.mzid (the command line parser used supports ':' and '=' as separators between the argument name and value; this is probably the best option)
• "-mzid /home/jannik/data/consensus_spectra/falcon_run_1_50_conservative.mzid" (I think this would work on the same principle as ':' or '=' separators (' ' (space) is also allowed), since the quotes would mean the name and value are passed as a single string, but it definitely looks odd)

[JannikSchneider12]

The second option worked for me. Thank you for the explanation and your help