I have 360 pepxml files I want to analyze using peptide prophet. When that didn't work, I tried analyzing just 30. One set of 30 worked fine, but another set of 30 did not work. Here is the following command error: (what does it meant that it is skipping files, is there a way to analyze all the files at once and not have to split?)
Command 1 [Mon Oct 10 12:34:42 2011] [ Show / Hide ] run_in c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef; c:\Inetpub \tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -O c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_11-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_11- run2.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_11-run3.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_12-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_12-run2.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_12-run3.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_13- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_13-run2.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_13-run3.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_14-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_14-run2.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_14- run3.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_15-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_15-run2.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_15-run3.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_16-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_16- run2.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_16-run3.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_17-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_17-run2.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_17-run3.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_18- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_18-run2.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_18-run3.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_19-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_19-run2.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_19- run3.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_20-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_20-run2.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_20-run3.pep.xml -------------------------------------------------------------------------------- c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909091257 (MinGW)) running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_11- run1.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_11-run2.pep.xml" "c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_11-run3.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_12-run1.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_12- run2.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_12-run3.pep.xml" "c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_13-run1.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_13-run2.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_13- run3.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_14-run1.pep.xml" "c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_14-run2.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_14-run3.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_15- run1.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_15-run2.pep.xml" "c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_15-run3.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_16-run1.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_16- run2.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_16-run3.pep.xml" "c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_17-run1.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_17-run2.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_17- run3.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_18-run1.pep.xml" "c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_18-run2.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_18-run3.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_19- run1.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_19-run2.pep.xml" "c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_19-run3.pep.xml" "c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_20-run1.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_20- run2.pep.xml" "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_20-run3.pep.xml" -L"7"" file 1: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_11-run1.pep.xml file 2: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_11-run2.pep.xml file 3: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_11-run3.pep.xml file 4: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_12-run1.pep.xml file 5: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_12-run2.pep.xml file 6: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_12-run3.pep.xml file 7: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_13-run1.pep.xml file 8: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_13-run2.pep.xml file 9: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_13-run3.pep.xml file 10: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_14-run1.pep.xml file 11: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_14-run2.pep.xml file 12: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_14-run3.pep.xml file 13: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_15-run1.pep.xml file 14: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_15-run2.pep.xml file 15: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_15-run3.pep.xml file 16: c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_16-run1.pep.xml -------------------------------------------------------------------------------- ...skipping 93 lines of output... -------------------------------------------------------------------------------- Parsing search results "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010- Sayeef/110110_LR5_20-run1 (SEQUEST)"... => Total of 2003 hits. Parsing search results "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010- Sayeef/110110_LR5_20-run2 (SEQUEST)"... => Total of 2061 hits. Parsing search results "c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010- Sayeef/110110_LR5_20-run3 (SEQUEST)"... => Total of 1879 hits. command completed in 39 sec running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" command completed in 3 sec running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" "C: \Xcalibur\database\Sprot_Human_20101007.fasta"" - Searching the tree...error: could not open database file "c:/ Xcalibur/database/Sprot_Human_20101007.fasta" (No such file or directory) - Building Commentz-Walter keyword tree... command "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" "C: \Xcalibur\database\Sprot_Human_20101007.fasta"" failed: Unknown error command "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" "C: \Xcalibur\database\Sprot_Human_20101007.fasta"" exited with non-zero exit code: -1 QUIT - the job is incomplete command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -O c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_11- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_11-run2.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_11-run3.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_12-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_12-run2.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_12- run3.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_13-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_13-run2.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_13-run3.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_14-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_14- run2.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_14-run3.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_15-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_15-run2.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_15-run3.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_16- run1.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_16-run2.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_16-run3.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_17-run1.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_17-run2.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_17- run3.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_18-run1.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_18-run2.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_18-run3.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_19-run1.pep.xml c:/ Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_19- run2.pep.xml c:/Inetpub/wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/ 110110_LR5_19-run3.pep.xml c:/Inetpub/wwwroot/ISB/data/ MyelomaGelLC2010-Sayeef/110110_LR5_20-run1.pep.xml c:/Inetpub/wwwroot/ ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_20-run2.pep.xml c:/Inetpub/ wwwroot/ISB/data/MyelomaGelLC2010-Sayeef/110110_LR5_20-run3.pep.xml" failed: Unknown error Command FAILED -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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