command "C:/TPP/bin/PeptideProphetParser" failed

[Asif Ahmed]

Hi, 

I did a comet search (Comet version "2020.01 rev. 0") in Linux HPC, update the paths of .mzML files, but when I tried to combine and run peptide-prophet (on TPP v5.2.0), I am getting this error. I tried to combine all the files, without running peptide-prophet and it works!

Can you please advice me- what to do?

ASIF

[Jimmy Eng]

Stick with Comet 2019.01.5.  In version 2020.01.0, I deprecated the "deltacnstar" score in Comet and it looks like PeptideProphet can't run w/o it.  Alternately, run this Perl command on your pep.xml files before running PeptideProphet if you want a workaround with the latest Comet:

perl -i -pe 's/<search_score name="deltacn"/<search_score name="deltacnstar" value="0.0"\/>\n <search_score name="deltacn"/g;' yourfile.pep.xml

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[David Shteynberg]

I have updated PeptideProphetParser so that it CAN run with the new version of Comet.  You will have to get it from the TPP SVN repository.

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[Asif Ahmed]

Thanks Jimmy, i will try your suggestion. It took a while to generate the pep.xml files, So I would prefer your perl script. 

David, is it possible to share the link? i was going to source forge website, but could not find it.

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Khandaker Asif Ahmed

PhD Student| Applied BioSciences, Macquarie University, NSW, Australia

Postgraduate Research Student| CSIRO Land and Water Flagship, Black Mountain, ACT, Australia

Address: Room No: S1.03, Building No: 101, CSIRO Clunies Ross Street, Black Mountain, ACT 2601, Australia

Alternative Email: khandaker...@csiro.au; khandaker-...@students.mq.edu.au. 

Mobile: (+61)0434018803, Skype ID: kh.asifratul

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[David Shteynberg]

 Are you building the TPP from source?  All the code is here:  https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/ but if building from SVN source is too much headache we should have an official release coming up in the next few weeks give or take.  Meanwhile, Jimmy's solution will also have the same result.

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[Asif Ahmed]

I am using the windows version, 

any suggestion for that?

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[David Shteynberg]

Use Jimmy's solution until the next release.

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[Asif Ahmed]

The script works perfectly without any error! Thanks for your help.

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