It seems the crash is due to tab characters in the fasta file (probably legal, but ProteinProphet wasn't expecting it). Replace those tabs with spaces and it should all work.
Brian _____ From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of QuanZe He Sent: Wednesday, July 15, 2009 1:14 AM To: spctools-discuss@googlegroups.com Subject: [spctools-discuss] Re: Why not run Analyze Proteins when sample label by iTRAQ Dear Brian Pratt I have zip up the pepXML and fasta files to Analyze_Proteins_Error.rar and send it to ftp://insilicos.serveftp.net/pub. Thank you very much. I will waiting your replay. Best wish Bright 2009/7/15 Brian Pratt <brian.pr...@insilicos.com> Hard to say what is happening there - you might zip up the pepXML and fasta files and FTP them to ftp://insilicos.serveftp.net/pub and I could take a quick look. Brian -----Original Message----- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Bright Sent: Monday, July 13, 2009 10:52 PM To: spctools-discuss Subject: [spctools-discuss] Why not run Analyze Proteins when sample label by iTRAQ Hi everyone I use TPP v4.2 JETSTREAM rev 1, Build 200904071723 to analyse the sample which when label by iTRAQ but the Analyze Protein can't normal finish. The error report is following: running: "C:/Inetpub/tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ ISB/data/LiuXiaoHui/interact.pep.xml" command completed in 1 sec running: "C:/Inetpub/tpp-bin/ProteinProphet "interact.pep.xml" "interact.prot.xml" XML" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.2 JETSTREAM rev 1, Build 200904071723 (MinGW)) (xml input) (report Protein Length) (using degen pep info) . . . reading in c:/Inetpub/wwwroot/ISB/data/LiuXiaoHui/ interact.pep.xml. . . . . . read in 1 1+, 83 2+, 20 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 command "C:/Inetpub/tpp-bin/ProteinProphet "interact.pep.xml" "interact.prot.xml" XML" failed: Unknown error command "C:/Inetpub/tpp-bin/ProteinProphet "interact.pep.xml" "interact.prot.xml" XML" exited with non-zero exit code: -1073741676 QUIT - the job is incomplete command "C:\Inetpub\tpp-bin\xinteract.exe -Ninteract.pep.xml -p0.05 - l7 -Ofp -Lcondition.xml-1 c:/Inetpub/wwwroot/ISB/data/LiuXiaoHui/ F003217.pep.xml" failed: Unknown error Command FAILED Can you tell me the reasons why happend it. I will appreciate for your help. Thank your Bright --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
