Hey David, here is the output with the error that I mentioned. Thank you! Ryan
C:/Inetpub/tpp-bin/xinteract (TPP v4.8.0 PHILAE, Build 201411201551-6764 ( mingw-i686)) PPM mode in Accurate Mass Model ... PPM mode in Accurate Mass Model ... running: "C:/Inetpub/tpp-bin/InteractParser "t04803_tc-229_1_light_parse_pp. pep.xml" "t04803_tc-229_1_light_parse.pep.xml" -L"7" -E"nonspecific"" file 1: t04803_tc-229_1_light_parse.pep.xml WARNING: empty raw_data in msms_run_summary tag ... trying mzML ... Failed to open input file 'C:/Inetpub/wwwroot/ISB/data/2015-12-09/t04803_tc-229_1/5_Pep_XML/t04803_tc-229_1.mzML' . WARNING: cannot open data file C:/Inetpub/wwwroot/ISB/data/2015-12-09/ t04803_tc-229_1/5_Pep_XML/t04803_tc-229_1.mzML in msms_run_summary tag ...... trying .mzXML ... SUCCESS: CORRECTED data file C:/Inetpub/wwwroot/ISB/data/2015-12-09/ t04803_tc-229_1/5_Pep_XML/t04803_tc-229_1.mzXML in msms_run_summary tag ... processed altogether 44695 results INFO: Results written to file: c:/Inetpub/wwwroot/ISB/data/2015-12-09/ t04803_tc-229_1/5_Pep_XML/t04803_tc-229_1_light_parse_pp.pep.xml command completed in 79 sec running: "C:/Inetpub/tpp-bin/DatabaseParser "t04803_tc-229_1_light_parse_pp. pep.xml"" command completed in 1 sec running: "C:/Inetpub/tpp-bin/RefreshParser "t04803_tc-229_1_light_parse_pp. pep.xml" "C:\MS-GF+\database\uniprot_homo_sapiens_09292015.fasta"" - Searching the tree... - Linking duplicate entries... - Printing results... - Building Commentz-Walter keyword tree...command completed in 86 sec running: "C:/Inetpub/tpp-bin/PeptideProphetParser "t04803_tc-229 _1_light_parse_pp.pep.xml" MINPROB=0.05 CLEVEL=2.5 PPM PPM ACCMASS NONTT NONMC FORCEDISTR NONPARAM DECOY=XXX_ IGNORECHG=1" using Accurate Mass Bins using PPM mass difference Using Decoy Label "XXX_". Ignoring charge 1+ spectra. Not using ntt model Not using nmc model Forcing output of mixture model Using non-parametric distributions (MS-GF+) WARNING!! The discriminant function for MSGFPL is not yet complete. It is presented here to help facilitate trial and discussion. Reliance on this code for publishable scientific results is not recommended. adding Accurate Mass mixture distr init with MS-GF+ nonspecific MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN PeptideProphet (TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686)) AKeller@ISB read in 0 1+, 10760 2+, 13185 3+, 12462 4+, 6160 5+, 1996 6+, and 0 7+ spectra. Initialising statistical models ... Found 22056 Decoys, and 22507 Non-Decoys Iterations: .........10.........20....... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 28 iterations command completed in 932 sec running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i t04803_tc-229_1_light_parse_pp.pep.xml -d "XXX_"" Analyzing t04803_tc-229_1_light_parse_pp.pep.xml ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "C:/Inetpub/wwwroot/ISB/data/2015-12-09/t04803_tc-229_1/5_Pep_XML/t04803_tc-229_1 (MS-GF+)"... => Found 0 hits. (0 decoys, 0 excluded) => Total so far: 0 hits. (0 decoys, 0 excluded) The system cannot find the path specified. command completed in 4 sec running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/2015-12-09/t04803_tc-229_1/5_Pep_XML/t04803_tc-229_1_light_parse_pp.pep.xml" command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/2015-12-09/t04803_tc-229_1/5_Pep_XML/t04803_tc-229_1_light_parse_pp.pep.xml" failed: Unknown error command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/2015-12-09/t04803_tc-229_1/5_Pep_XML/t04803_tc-229_1_light_parse_pp.pep.xml" exited with non-zero exit code: 255 QUIT - the job is incomplete Warning messages: 1: running command 'C:\WINDOWS\system32\cmd.exe /c cd C:/Inetpub/wwwroot/ISB/data/2015-12-09/t04803_tc-229_1/5_Pep_XML && C:/Inetpub/tpp-bin/xinteract -Nt04803_tc-229_1_light_parse_pp.pep.xml -p0.05 -l7 -c2.5 -PPM -eN -PPM -OANMFPp -dXXX_ -I1 t04803_tc-229_1_light_parse.pep.xml' had status 255 2: In shell(lightanacmd, flag = "/c", intern = FALSE, wait = TRUE, : 'cd C:/Inetpub/wwwroot/ISB/data/2015-12-09/t04803_tc-229_1/5_Pep_XML && C:/Inetpub/tpp-bin/xinteract -Nt04803_tc-229_1_light_parse_pp.pep.xml -p0.05 -l7 -c2.5 -PPM -eN -PPM -OANMFPp -dXXX_ -I1 t04803_tc-229_1_light_parse.pep.xml' execution failed with error code 255 > On Thursday, December 10, 2015 at 10:13:12 AM UTC-8, David Shteynberg wrote: > > Hello Ryan > > It may make it easier to troubleshoot the issues if you post the actual > output generated by the program. > > Thank you, > David > On Dec 9, 2015 10:16 AM, "Ryan Lumpkin" <[email protected] <javascript:>> > wrote: > >> Hello all, >> >> Thank you in advance for your help. I have been using MS-GF+ to search >> spectra prior to analysis with TPP. I had to create a new set of scoring >> parameters for MS-GF+ in order to handle Orbitrap Fusion combined CID/ETD >> data, however after doing so, Peptide Prophet always errors out with 0 hits >> following the accurate mass model and PepXMLViewer crashes. I am aware that >> this can be indicative of bad data, yet my previous scoring parameters had >> no problem dealing with this same dataset. I'm under the impression that >> this is an issue with the settings used to generate those new scoring >> parameters with MS-GF+, but I unfortunately I have not found a better >> location to seek assistance with this. >> >> If anyone could point me in the right direction for resolving this, I >> would greatly appreciate it. >> >> Ryan Lumpkin >> Graduate Student >> University of California, San Diego >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
