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.
