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ERROR, XML_INPUT NOPLOT

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ERROR, XML_INPUT NOPLOT alkane8  2006-07-14 09:59
Status: Closed
 
I did a search that seemed to work. But when it was finished I got an error. It was very similar to a previous search I had done so I was surprised to see an error. This is the error I received. I cannot interpret what the problem was. Any idea what may have caused this error?

14 Jul 2006 11:46:53,312 INFO : ProteinProphet.pl v2.0 (TPP v2.8 THAW rev.2, Build 200605201719) AKeller August 15, 2003 (xml input) (using degen pep info)
14 Jul 2006 11:46:53,312 INFO : Calling C:\CPASInstall\bin/DatabaseParser C:\CpasPipeline\ExampleFiles\DougP_d071106\xtandem\searchname\filename.work/filename.pep.xml
14 Jul 2006 11:46:56,046 INFO : processing C:\CpasPipeline\ExampleFiles\DougP_d071106\xtandem\searchname\filename.work/filename.pep.xml … read in 0 1+, 470 2+, and 301 3+ spectra with min prob 0.05
14 Jul 2006 11:47:05,218 INFO : Reading results.
14 Jul 2006 11:47:07,109 INFO : cannot find C:\CPASInstall\bin/IPI2LL
14 Jul 2006 11:47:07,156 INFO :
14 Jul 2006 11:47:07,171 INFO : command "C:\CPASInstall\binProteinProphet.pl filename.pep.xml filename.pep-prot.shtml XML_INPUT NOPLOT" exited with non-zero exit code: 2
14 Jul 2006 11:47:07,171 INFO : QUIT - the job is incomplete
14 Jul 2006 11:47:07,171 INFO :
14 Jul 2006 11:47:07,171 INFO : command "perl C:\CPASInstall\bin\ProteinProphet.pl filename.pep.xml filename.pep-prot.shtml XML_INPUT NOPLOT" failed: No such file or directory
14 Jul 2006 11:47:07,171 ERROR: Failed running xinteract.
 
 
brendanx responded:  2006-07-14 10:23
I have attached a copy of the file IPI2LL. Not sure what triggers this case, but it is clearly one we have not seen in testing. I'll make sure this file gets into the next release, though. Thanks for finding.
 
alkane8 responded:  2006-07-14 10:29
This was just a test search of a standard peptide MS2 spectra. The results I posted above resulted from a search for c and z ions. When i repeated the search with b and y ions it worked fine. Perhaps Protein Prophet cannot handle c and z ions? Is there a way to turn off protein prohpet so that I could at least see the xtandem results?
 
brendanx responded:  2006-08-10 07:25
Just a note that I received direct email confirmation that the IPI2LL file did fix this problem for the 1.4 release. It is now included in our 1.5 release.
 
adam responded:  2007-01-04 09:28