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Mascot 2.3 Pipeline Error with CPAS 10.3

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Mascot 2.3 Pipeline Error with CPAS 10.3 donw  2011-02-21 09:11
Status: Closed
 
Hi,

We recently upgraded our mascot server from 2.2 to 2.3 and our CPAS server from 9.0 to 10.30. I was testing out the searches before we bring it live and noticed some TPP pipeline errors when kicking off a Mascot server search.

Attached is the Log file and our mascot.xml params file

Basically It searches fine, downloads the *.dat and *.fasta fine, but fails to generate a *.pep.xml from the *.dat file with Mascot2XML which then causes Xinteract to fail with exit code 1 due to not having anything in the *.pep.xml file to process.

running: D:\LabKey Server\bin\Mascot2XML 110111_E2_TiO2Elu_neulossMS3.dat -DD:\LabKey Server\files\Don_Test\@files\databases\mascot\SwissProt\SwissProt_2011_01.fasta -xml -notgz -desc

10 Feb 2011 22:18:36,812 INFO : D:\LabKey Server\bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909211148 (MSVC))
10 Feb 2011 22:18:36,812 INFO :
10 Feb 2011 22:18:36,812 INFO : running: "InteractParser "110111_E2_TiO2Elu_neulossMS3.pep.xml" "..\110111_E2_TiO2Elu_neulossMS3_raw.pep.xml" -L"7""
10 Feb 2011 22:18:36,828 INFO : file 1: ..\110111_E2_TiO2Elu_neulossMS3_raw.pep.xml
10 Feb 2011 22:18:36,828 INFO : processed altogether 0 results
10 Feb 2011 22:18:36,828 INFO : ERROR: output file created, d:/LabKey Server/files/Don_Test/@files/mascot/110210_MascotSearch_Test3/110111_E2_TiO2Elu_neulossMS3.work/110111_E2_TiO2Elu_neulossMS3.pep.xml, appears incomplete. Please check the input files for completeness.
10 Feb 2011 22:18:36,828 INFO : command completed in 0 sec

Any thoughts what to troubleshoot next?
Thanks
Don Wolfgeher donw@uchicago.edu
 
 
jeckels responded:  2011-02-22 12:33
Hi Don,

Have you had a chance to inspect the .dat file to verify that it contains valid results? It looks like it's grabbing a sizeable file, so there are likely results, but it's good to double check.

Also, can you check the .pep.xml file and see if it looks OK?

I've seen cases where having a protein name with a " or < can produce invalid XML files, which then confuse downstream tools.

Thanks,
Josh
 
donw responded:  2011-02-25 10:07
Feb 25 2011

Update -

For us this was a version issue with Mascot2XML module. Version 4.3.1 was giving the error, but when we swapped in the binaries for Ver 4.4.1 it worked fine.

Note: Since there was still a known bug with Xinteract Ver 4.4, we only used the Mascot2XML 4.4 module binaries at this time, the rest of our CPAS TPP is ver 4.3.1. Will wait for the 4.4 code to pass the CPAS check in then update.