Can you make sure that the files are all complete, meaning that the searches completed? You can look at the file sizes to see if any are incomplete or look at the last few lines for closing tags that should look something like this:
</search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> -David On Thu, Jun 5, 2014 at 1:51 PM, Krystalle S. Diaz <[email protected]> wrote: > The same error occured with the renamed files, again on the same file. I'm > assuming it has something to do with the contents or set up of this file > itself, so I'll look further into it as mch as I can > > On Thursday, June 5, 2014 12:52:09 PM UTC-7, David Shteynberg wrote: >> >> One problem I see is that your file base names contain '.' This is >> probably causing the parser to break. >> >> -David >> >> On Thu, Jun 5, 2014 at 12:37 PM, Krystalle S. Diaz <[email protected]> >> wrote: >> > I'm using the Amazon Cloud to run the TPP. I ran an X!tandem search >> > yesterday, which appeared to process fine, and subsequently converted >> > all >> > .tandem files to .pep.xml files for use in PeptideProphet, which also >> > appeared to work fine. Initially the xinteract process (all defaults >> > run >> > through, using Petunia for the TPP) appeared to work fine, with my first >> > four files appearing to go through, but my 5th file appears to cause a >> > segmentation fault. Has anyone had a similar problem? This is a rerun >> > of >> > an analysis we did back in December with TPP 4.6.2. Everything but our >> > database is identical to our former search, although it has recently >> > been >> > annotated. Here are the logs: >> > >> > EXECUTING: cd /mnt/tppdata/MO3_1; xinteract >> > >> > -NMO3_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_Runs1thru3_interact.pep.xml >> > -p0.05 -l7 -PPM -O >> > >> > M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_01.2014_06_04_23_00_51.t.tandem.pep.xml >> > >> > M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_02.2014_06_05_00_08_27.t.tandem.pep.xml >> > >> > M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_03.2014_06_05_00_46_54.t.tandem.pep.xml >> > >> > M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082013_Run2_02.2014_06_05_01_39_09.t.tandem.pep.xml >> > >> > M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082013_Run2_03.2014_06_05_02_32_02.t.tandem.pep.xml >> > >> > M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082013_Run2_04.2014_06_05_03_03_01.t.tandem.pep.xml >> > >> > MO3_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082513_Run3_02.2014_06_05_03_42_49.t.tandem.pep.xml >> > >> > MO3_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082513_Run3_03.2014_06_05_04_36_54.t.tandem.pep.xml >> > >> > MO3_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082513_Run3_04.2014_06_05_05_02_56.t.tandem.pep.xml >> > >> > xinteract (TPP v4.7 POLAR VORTEX (AMI) rev 1, Build 201405271720 >> > (linux)) >> > PPM mode in Accurate Mass Model ... >> > >> > running: "/opt/tpp/bin/InteractParser >> > >> > '/opt/tpp/tmp/VBLNyi/MO3_1/MO3_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_Runs1thru3_interact.pep.xml' >> > >> > 'M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_01.2014_06_04_23_00_51.t.tandem.pep.xml' >> > >> > 'M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_02.2014_06_05_00_08_27.t.tandem.pep.xml' >> > >> > 'M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_03.2014_06_05_00_46_54.t.tandem.pep.xml' >> > >> > 'M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082013_Run2_02.2014_06_05_01_39_09.t.tandem.pep.xml' >> > >> > 'M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082013_Run2_03.2014_06_05_02_32_02.t.tandem.pep.xml' >> > >> > 'M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082013_Run2_04.2014_06_05_03_03_01.t.tandem.pep.xml' >> > >> > 'MO3_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082513_Run3_02.2014_06_05_03_42_49.t.tandem.pep.xml' >> > >> > 'MO3_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082513_Run3_03.2014_06_05_04_36_54.t.tandem.pep.xml' >> > >> > 'MO3_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082513_Run3_04.2014_06_05_05_02_56.t.tandem.pep.xml' >> > -L'7'" >> > file 1: >> > >> > M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_01.2014_06_04_23_00_51.t.tandem.pep.xml >> > SUCCESS: CORRECTED data file >> > >> > /mnt/tppdata/MO3_1/M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_01.mzXML.gz >> > in msms_run_summary tag ... >> > file 2: >> > >> > M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_02.2014_06_05_00_08_27.t.tandem.pep.xml >> > SUCCESS: CORRECTED data file >> > >> > /mnt/tppdata/MO3_1/M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_02.mzXML.gz >> > in msms_run_summary tag ... >> > file 3: >> > >> > M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_03.2014_06_05_00_46_54.t.tandem.pep.xml >> > SUCCESS: CORRECTED data file >> > >> > /mnt/tppdata/MO3_1/M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_03.mzXML.gz >> > in msms_run_summary tag ... >> > file 4: >> > >> > M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082013_Run2_02.2014_06_05_01_39_09.t.tandem.pep.xml >> > SUCCESS: CORRECTED data file >> > >> > /mnt/tppdata/MO3_1/M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082013_Run2_02.mzXML.gz >> > in msms_run_summary tag ... >> > file 5: >> > >> > M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082013_Run2_03.2014_06_05_02_32_02.t.tandem.pep.xml >> > Segmentation fault (core dumped) >> > >> > command "/opt/tpp/bin/InteractParser >> > >> > '/opt/tpp/tmp/VBLNyi/MO3_1/MO3_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_Runs1thru3_interact.pep.xml' >> > >> > 'M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_01.2014_06_04_23_00_51.t.tandem.pep.xml' >> > >> > 'M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_02.2014_06_05_00_08_27.t.tandem.pep.xml' >> > >> > 'M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_050213_Run1_03.2014_06_05_00_46_54.t.tandem.pep.xml' >> > >> > 'M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082013_Run2_02.2014_06_05_01_39_09.t.tandem.pep.xml' >> > >> > 'M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082013_Run2_03.2014_06_05_02_32_02.t.tandem.pep.xml' >> > >> > 'M03_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082013_Run2_04.2014_06_05_03_03_01.t.tandem.pep.xml' >> > >> > 'MO3_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082513_Run3_02.2014_06_05_03_42_49.t.tandem.pep.xml' >> > >> > 'MO3_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082513_Run3_03.2014_06_05_04_36_54.t.tandem.pep.xml' >> > >> > 'MO3_1_Normal_Lyses_Buff_SCX_250uL_6hr_QExactive_082513_Run3_04.2014_06_05_05_02_56.t.tandem.pep.xml' >> > -L'7'" exited with non-zero exit code: 35584 >> > QUIT - the job is incomplete >> > >> > Command FAILED >> > RETURN CODE:35584 >> > >> > -- >> > 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. > > -- > 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. -- 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.
