Okay, I'll try rerunning with the file names changed. Thank you! 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] > <javascript:>> 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > Visit this group at http://groups.google.com/group/spctools-discuss. > > For more options, visit https://groups.google.com/d/optout. >
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