Hi everyone, I have downloaded very old (before 2006) tandem mass spectra data from PeptideAtlas and tried to analyze these data using TPP. As these MS/MS were searched by SEQUEST, I used pepXML firstly to convert the output ..out files to ..pep.xml files and then "Analyze Peptides" to run PeptideProphet to analyze these ..pep.xml files. The convert operation ran successfully. However, following errors occurred when running peptide analysis:
c:\Inetpub\tpp-bin\xinteract (TPP v4.7 POLAR VORTEX rev 0, Build 201402281256 (MinGW)) > > running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" > "YAGmem1.pep.xml" "YAGmem1220.pep.xml" "YAGmem1220_rpt1.pep.xml" > "YAGmem48.pep.xml" "YAGmem812.pep.xml" "YAGsn1.pep.xml" "YAGsn2.pep.xml" > "YAGsn2_48rpt.pep.xml" "YAGwall.pep.xml" "pum4.pep.xml" "yagpm.pep.xml" > "yagpm2_1.pep.xml" "yagpm2_2.pep.xml" "yagpm2_3.pep.xml" "yagpm3_1.pep.xml" > "yagpm3_2.pep.xml" "yagpm3_3.pep.xml" "yagpt.pep.xml" > "yagsn1_1120rpt.pep.xml" "yagsn1_48rpt.pep.xml" "yagsn1_712rpt.pep.xml" > "yagsn2_1120rpt.pep.xml" "yagsn2_712rpt.pep.xml" "yagwall_1120rpt.pep.xml" > "yagwall_48rpt.pep.xml" "yagwall_712rpt.pep.xml" -L"5"" > file 1: YAGmem1.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGmem1.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGmem1.(null) in msms_run_summary tag ... > file 2: YAGmem1220.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGmem1220.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGmem1220.(null) in msms_run_summary tag ... > file 3: YAGmem1220_rpt1.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGmem1220_rpt1.(null) in msms_run_summary > tag ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGmem1220_rpt1.(null) in msms_run_summary > tag ... > file 4: YAGmem48.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGmem48.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGmem48.(null) in msms_run_summary tag ... > file 5: YAGmem812.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGmem812.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGmem812.(null) in msms_run_summary tag ... > file 6: YAGsn1.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file c:/Inetpub/wwwroot/ISB/data/dtas/YAGsn1.(null) > in msms_run_summary tag ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGsn1.(null) in msms_run_summary tag ... > file 7: YAGsn2.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file c:/Inetpub/wwwroot/ISB/data/dtas/YAGsn2.(null) > in msms_run_summary tag ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGsn2.(null) in msms_run_summary tag ... > file 8: YAGsn2_48rpt.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGsn2_48rpt.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGsn2_48rpt.(null) in msms_run_summary tag > ... > file 9: YAGwall.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGwall.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/YAGwall.(null) in msms_run_summary tag ... > file 10: pum4.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file c:/Inetpub/wwwroot/ISB/data/dtas/pum4.(null) > in msms_run_summary tag ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/pum4.(null) in msms_run_summary tag ... > file 11: yagpm.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file c:/Inetpub/wwwroot/ISB/data/dtas/yagpm.(null) > in msms_run_summary tag ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpm.(null) in msms_run_summary tag ... > file 12: yagpm2_1.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpm2_1.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpm2_1.(null) in msms_run_summary tag ... > file 13: yagpm2_2.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpm2_2.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpm2_2.(null) in msms_run_summary tag ... > file 14: yagpm2_3.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpm2_3.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpm2_3.(null) in msms_run_summary tag ... > file 15: yagpm3_1.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpm3_1.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpm3_1.(null) in msms_run_summary tag ... > file 16: yagpm3_2.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpm3_2.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpm3_2.(null) in msms_run_summary tag ... > file 17: yagpm3_3.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpm3_3.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpm3_3.(null) in msms_run_summary tag ... > file 18: yagpt.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file c:/Inetpub/wwwroot/ISB/data/dtas/yagpt.(null) > in msms_run_summary tag ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagpt.(null) in msms_run_summary tag ... > file 19: yagsn1_1120rpt.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagsn1_1120rpt.(null) in msms_run_summary > tag ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagsn1_1120rpt.(null) in msms_run_summary > tag ... > file 20: yagsn1_48rpt.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagsn1_48rpt.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagsn1_48rpt.(null) in msms_run_summary tag > ... > file 21: yagsn1_712rpt.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagsn1_712rpt.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagsn1_712rpt.(null) in msms_run_summary tag > ... > file 22: yagsn2_1120rpt.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagsn2_1120rpt.(null) in msms_run_summary > tag ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagsn2_1120rpt.(null) in msms_run_summary > tag ... > file 23: yagsn2_712rpt.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagsn2_712rpt.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagsn2_712rpt.(null) in msms_run_summary tag > ... > file 24: yagwall_1120rpt.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagwall_1120rpt.(null) in msms_run_summary > tag ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagwall_1120rpt.(null) in msms_run_summary > tag ... > file 25: yagwall_48rpt.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagwall_48rpt.(null) in msms_run_summary tag > ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagwall_48rpt.(null) in msms_run_summary tag > ... > file 26: yagwall_712rpt.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagwall_712rpt.(null) in msms_run_summary > tag ...Unknown file type. No file loaded. > WARNING: cannot CORRECT data file > c:/Inetpub/wwwroot/ISB/data/dtas/yagwall_712rpt.(null) in msms_run_summary > tag ... > processed altogether 71134 results > INFO: Results written to file: > c:/Inetpub/wwwroot/ISB/data/dtas/interact.pep.xml > command completed in 1.40194e+009 sec > > running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" > command completed in 1.40194e+009 sec > > running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" > "/dbase/misc/Halobacterium-20040504.fasta"" > - Searching the tree...error: could not open database file > "/dbase/misc/Halobacterium-20040504.fasta" (No such file or directory) > - Building Commentz-Walter keyword tree... > command "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" > "/dbase/misc/Halobacterium-20040504.fasta"" failed: Unknown error > > command "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" > "/dbase/misc/Halobacterium-20040504.fasta"" exited with non-zero exit code: -1 > QUIT - the job is incomplete > > command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.02 -l5 -OI > YAGmem1.pep.xml YAGmem1220.pep.xml YAGmem1220_rpt1.pep.xml YAGmem48.pep.xml > YAGmem812.pep.xml YAGsn1.pep.xml YAGsn2.pep.xml YAGsn2_48rpt.pep.xml > YAGwall.pep.xml pum4.pep.xml yagpm.pep.xml yagpm2_1.pep.xml yagpm2_2.pep.xml > yagpm2_3.pep.xml yagpm3_1.pep.xml yagpm3_2.pep.xml yagpm3_3.pep.xml > yagpt.pep.xml yagsn1_1120rpt.pep.xml yagsn1_48rpt.pep.xml > yagsn1_712rpt.pep.xml yagsn2_1120rpt.pep.xml yagsn2_712rpt.pep.xml > yagwall_1120rpt.pep.xml yagwall_48rpt.pep.xml yagwall_712rpt.pep.xml" failed: > Unknown error > > How can I figure this out? Thanks very much. Jorey -- 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.
