Hello, This step is failing because the database you used to search cannot be found on the computer:
error: could not open database file "o:/hoc/12112012/database/decoy_uniprot_mouse(180210).fasta" (No such file or directory) If you moved the database to another location, you should manually update the pepXML file (15N_slice03_interact.pep.xml) to reflect the new location and rerun the analysis (no need to rerun the search). You can also run the RefreshParser command on the command-line to update the database location. Cheers, --Luis On Mon, Nov 12, 2012 at 1:47 AM, Michaela Filiou <[email protected]> wrote: > Hi everyone, > > We are using TPP to analyze data from 14N/15N Orbi-derived mass spectra > (peptide extracts from trypsin digested gel slices). > At the “Analyze Peptides” step, the command fails for some 15N pepxml files. > With the corresponding 14N files the command works fine. > Do you have any idea what the problem may be? > > Below is the complete output from the TPP analysis command failure > > Thanks a lot in advance! > > Michaela > > > c:\Inetpub\tpp-bin\xinteract (TPP v4.6 OCCUPY rev 0, Build 201208170820 > (MinGW)) > > > > running: "C:/Inetpub/tpp-bin/InteractParser "15N_slice03_interact.pep.xml" > "hoc_protein_turnover_pnd28_03.xml" -L"7"" > > file 1: hoc_protein_turnover_pnd28_03.xml > > processed altogether 8636 results > > > > > > results written to file > c:/Inetpub/wwwroot/ISB/data/tpp_data/hoc/12112012/15N_pepxml/15N_slice03_interact.pep.xml > > > > direct your browser to > http://pcj43/ISB/data/tpp_data/hoc/12112012/15N_pepxml/15N_slice03_interact.pep.shtml > > > > > > > > command completed in 5 sec > > > > running: "C:/Inetpub/tpp-bin/DatabaseParser "15N_slice03_interact.pep.xml"" > > command completed in 0 sec > > > > running: "C:/Inetpub/tpp-bin/RefreshParser "15N_slice03_interact.pep.xml" > "O:/hoc/12112012/database/decoy_uniprot_mouse(180210).fasta"" > > - Searching the tree...error: could not open database file > "o:/hoc/12112012/database/decoy_uniprot_mouse(180210).fasta" (No such file > or directory) > > - Building Commentz-Walter keyword tree... > > command "C:/Inetpub/tpp-bin/RefreshParser "15N_slice03_interact.pep.xml" > "O:/hoc/12112012/database/decoy_uniprot_mouse(180210).fasta"" failed: > Unknown error > > > > command "C:/Inetpub/tpp-bin/RefreshParser "15N_slice03_interact.pep.xml" > "O:/hoc/12112012/database/decoy_uniprot_mouse(180210).fasta"" exited with > non-zero exit code: -1 > > QUIT - the job is incomplete > > > > command "c:\Inetpub\tpp-bin\xinteract -N15N_slice03_interact.pep.xml -p0.05 > -l7 -O -dREV: hoc_protein_turnover_pnd28_03.xml" failed: Unknown error > > > > > > Command FAILED > RETURN CODE:65280 > > > > > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/1on0VyDaJRYJ. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [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. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
