Hi Sayeef, the error I see below is: 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)
It would appear that some of your search results have reference the database c:/ Xcalibur/database/Sprot_Human_20101007.fasta while others reference something else. And the database listed doesn't seem to exist. Is it there? Did it move? Searching all data files that you will process together against the same database may be most successful. In the end, there is no limit to the number of files you can process at once. But if one of the files has a problem, it may cause the entire job to fail, where if that file is not part of the processing, then it will complete correctly. Regards, Eric > -----Original Message----- > From: [email protected] [mailto:spctools- > [email protected]] On Behalf Of Sayeef Mirza > Sent: Monday, October 10, 2011 10:00 AM > To: spctools-discuss > Subject: [spctools-discuss] peptide prophet - command error > > 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. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to spctools- > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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