25 Jan 2012 16:19:23,675 INFO : Mascot search for all 25 Jan 2012 16:19:23,679 INFO : ======================================= 25 Jan 2012 16:19:23,708 INFO : Starting to run task 'org.labkey.ms2.pipeline.FastaCheckTask' at location 'webserver-fasta-check' 25 Jan 2012 16:19:23,714 INFO : Check FASTA validity 25 Jan 2012 16:19:23,716 INFO : ======================================= 25 Jan 2012 16:19:23,720 INFO : Checking sequence file validity of /home/massspec/cpas/pipeline/databases/ToxoGT1_7.1FR.fasta 25 Jan 2012 16:19:25,498 INFO : 25 Jan 2012 16:19:25,502 INFO : Successfully completed task 'org.labkey.ms2.pipeline.FastaCheckTask' 25 Jan 2012 16:25:42,160 INFO : Submitting job to Globus SGE with queue labkey: /share/apps/java/jdk1.5.0_12/bin/java -cp /share/apps/cpas/bin/labkey/labkeyBootstrap.jar org.labkey.bootstrap.ClusterBootstrap -modulesdir=/share/apps/cpas/bin/labkey/modules -webappdir=/share/apps/cpas/bin/labkey/labkeywebapp -configdir=/share/apps/cpas/bin/labkey/config file:/home/massspec/cpas/pipeline/projects/LynnGroup/Lynn/PVM/@files/mascot/PVM_mascot_Copy15/all.job.xml 25 Jan 2012 16:26:01,835 INFO : Starting to run task 'org.labkey.ms2.pipeline.TPPTask:join' at location 'cluster' 25 Jan 2012 16:26:01,921 INFO : xinteract output 25 Jan 2012 16:26:01,923 INFO : ======================================= 25 Jan 2012 16:26:01,925 INFO : Working directory is /home/massspec/cpas/pipeline/projects/LynnGroup/Lynn/PVM/@files/mascot/PVM_mascot_Copy15/all.work 25 Jan 2012 16:26:01,927 INFO : running: /share/apps/cpas/bin/tpp/bin/xinteract -x20 -Opt -nR -Nall.pep.xml ../faction1_raw.pep.xml ../fraction10_raw.pep.xml ../fraction11_raw.pep.xml ../fraction2_raw.pep.xml ../fraction3_raw.pep.xml ../fraction4_raw.pep.xml ../fraction5_raw.pep.xml ../fraction6_raw.pep.xml ../fraction7_raw.pep.xml ../fraction8_raw.pep.xml ../fraction9_raw.pep.xml ../frqaction12_raw.pep.xml 25 Jan 2012 16:26:01,952 INFO : 25 Jan 2012 16:26:01,968 INFO : /share/apps/cpas/bin/tpp/bin/xinteract (TPP v4.3 JETSTREAM rev 1, Build 201002051140 (linux)) 25 Jan 2012 16:26:01,970 INFO : 25 Jan 2012 16:26:01,972 INFO : running: "InteractParser 'all.pep.xml' '../faction1_raw.pep.xml' '../fraction10_raw.pep.xml' '../fraction11_raw.pep.xml' '../fraction2_raw.pep.xml' '../fraction3_raw.pep.xml' '../fraction4_raw.pep.xml' '../fraction5_raw.pep.xml' '../fraction6_raw.pep.xml' '../fraction7_raw.pep.xml' '../fraction8_raw.pep.xml' '../fraction9_raw.pep.xml' '../frqaction12_raw.pep.xml' -L'7'" 25 Jan 2012 16:26:02,908 INFO : file 1: ../faction1_raw.pep.xml 25 Jan 2012 16:26:03,121 INFO : file 2: ../fraction10_raw.pep.xml 25 Jan 2012 16:26:03,305 INFO : file 3: ../fraction11_raw.pep.xml 25 Jan 2012 16:26:03,499 INFO : file 4: ../fraction2_raw.pep.xml 25 Jan 2012 16:26:03,695 INFO : file 5: ../fraction3_raw.pep.xml 25 Jan 2012 16:26:03,897 INFO : file 6: ../fraction4_raw.pep.xml 25 Jan 2012 16:26:04,100 INFO : file 7: ../fraction5_raw.pep.xml 25 Jan 2012 16:26:04,276 INFO : file 8: ../fraction6_raw.pep.xml 25 Jan 2012 16:26:04,454 INFO : file 9: ../fraction7_raw.pep.xml 25 Jan 2012 16:26:04,614 INFO : file 10: ../fraction8_raw.pep.xml 25 Jan 2012 16:26:04,779 INFO : file 11: ../fraction9_raw.pep.xml 25 Jan 2012 16:26:04,949 INFO : file 12: ../frqaction12_raw.pep.xml 25 Jan 2012 16:26:05,493 INFO : processed altogether 13634 results 25 Jan 2012 16:26:07,211 INFO : command completed in 6 sec 25 Jan 2012 16:26:07,214 INFO : 25 Jan 2012 16:26:07,217 INFO : running: "PeptideProphetParser 'all.pep.xml' EXTRAITRS=20" 25 Jan 2012 16:26:07,256 INFO : (MASCOT) 25 Jan 2012 16:26:07,501 INFO : results for charge 1: 757 id tot and 17 adj scores 25 Jan 2012 16:26:07,997 INFO : results for charge 2: 6796 id tot and 124 adj scores 25 Jan 2012 16:26:08,000 INFO : results for charge 2: 5.92561 adj_ion_mean and 16.8452 adj_ion_hom mean 37.6441id mean0.92452 correlation (r) 25 Jan 2012 16:26:08,009 INFO : 2+ ion - id = 1.10336*(ion - hom) + -12.6607 with error = 6.597 25 Jan 2012 16:26:08,011 INFO : mean ion - id: 5.92561, mean ion - hom: 16.8452 25 Jan 2012 16:26:08,458 INFO : results for charge 3: 6081 id tot and 17 adj scores 25 Jan 2012 16:26:08,551 INFO : results for charge 4: 0 id tot and 0 adj scores 25 Jan 2012 16:26:08,645 INFO : results for charge 5: 0 id tot and 0 adj scores 25 Jan 2012 16:26:08,738 INFO : results for charge 6: 0 id tot and 0 adj scores 25 Jan 2012 16:26:08,833 INFO : results for charge 7: 0 id tot and 0 adj scores 25 Jan 2012 16:26:08,835 INFO : init with MASCOT trypsin 25 Jan 2012 16:26:09,379 INFO : ERROR: two instrument manufacturers: Thermo Finnigan and ThermoFinnigan 25 Jan 2012 16:26:09,381 INFO : 25 Jan 2012 16:26:09,383 INFO : command "PeptideProphetParser 'all.pep.xml' EXTRAITRS=20" exited with non-zero exit code: 256 25 Jan 2012 16:26:09,385 INFO : QUIT - the job is incomplete 25 Jan 2012 16:26:09,391 INFO : Failed to complete task 'org.labkey.ms2.pipeline.TPPTask:join' 25 Jan 2012 16:26:09,395 ERROR: Failed to remove work directory /home/massspec/cpas/pipeline/projects/LynnGroup/Lynn/PVM/@files/mascot/PVM_mascot_Copy15/all.work unexpected files found: all.pep.xml 25 Jan 2012 16:26:21,652 ERROR: Fault received from Globus on "submit" command 25 Jan 2012 16:26:21,689 ERROR: Parameter not supported 25 Jan 2012 16:26:21,698 ERROR: Fault received from Globus 25 Jan 2012 16:26:21,706 ERROR: org.globus.exec.generated.FaultType 25 Jan 2012 16:26:21,714 ERROR: Fault received from Globus 25 Jan 2012 16:26:21,722 ERROR: ProcessDied 25 Jan 2012 16:26:21,731 ERROR: Fault received from Globus 25 Jan 2012 16:26:21,739 ERROR: java.lang.Exception 25 Jan 2012 16:26:21,748 ERROR: Fault received from Globus 25 Jan 2012 16:26:21,756 ERROR: org.oasis.wsrf.faults.BaseFaultType 25 Jan 2012 16:26:21,765 INFO : Reading log file /home/massspec/cpas/pipeline/projects/LynnGroup/Lynn/PVM/@files/mascot/PVM_mascot_Copy15/all.cluster.out, which is now of size 2057 25 Jan 2012 16:26:21,794 INFO : Content of stdout: Deploying resources from exploded modules to web app directory... Module extraction and deployment complete. Cleaning up web app directory... Web app directory cleanup complete. INFO 2012-01-25 16:25:59,520 [main] org.labkey.pipeline.AbstractPipelineStartup: Loading Spring configuration for the Pipeline module from [file:/share/apps/cpas/bin/labkey/modules/pipeline/config/pipelineContext.xml, file:/share/apps/cpas/bin/labkey/config/pipelineConfig.xml] INFO 2012-01-25 16:25:59,899 [main] org.labkey.pipeline.AbstractPipelineStartup: Loading Spring configuration for the Experiment module from [file:/share/apps/cpas/bin/labkey/modules/experiment/config/experimentContext.xml] INFO 2012-01-25 16:25:59,992 [main] org.labkey.pipeline.AbstractPipelineStartup: Loading Spring configuration for the MS2 module from [file:/share/apps/cpas/bin/labkey/modules/ms2/config/ms2Context.xml, file:/share/apps/cpas/bin/labkey/config/ms2Config.xml] INFO 2012-01-25 16:26:00,521 [main] org.labkey.pipeline.AbstractPipelineStartup: Loading Spring configuration for the MS1 module from [file:/share/apps/cpas/bin/labkey/modules/ms1/config/ms1Context.xml, file:/share/apps/cpas/bin/labkey/config/ms1Config.xml] INFO 2012-01-25 16:26:00,814 [main] org.labkey.pipeline.AbstractPipelineStartup: Loading Spring configuration for the Study module from [file:/share/apps/cpas/bin/labkey/modules/study/config/studyContext.xml] Starting to run task for job (NOT SUBMITTED) @files (PVM_mascot_Copy15) INFO 2012-01-25 16:26:01,830 [main] org.labkey.api.util.Job: Starting to run task 'org.labkey.ms2.pipeline.TPPTask:join' for job '(NOT SUBMITTED) @files (PVM_mascot_Copy15)' with log file /home/massspec/cpas/pipeline/projects/LynnGroup/Lynn/PVM/@files/mascot/PVM_mascot_Copy15/all.log INFO 2012-01-25 16:26:09,393 [main] org.labkey.api.util.Job: Failed to complete task 'org.labkey.ms2.pipeline.TPPTask:join' for job '(NOT SUBMITTED) @files (PVM_mascot_Copy15)' with log file /home/massspec/cpas/pipeline/projects/LynnGroup/Lynn/PVM/@files/mascot/PVM_mascot_Copy15/all.log 25 Jan 2012 16:26:31,804 INFO : Deleting log file /home/massspec/cpas/pipeline/projects/LynnGroup/Lynn/PVM/@files/mascot/PVM_mascot_Copy15/all.cluster.out, which is now of size 2057 25 Jan 2012 16:26:31,811 INFO : Reading log file /home/massspec/cpas/pipeline/projects/LynnGroup/Lynn/PVM/@files/mascot/PVM_mascot_Copy15/all.cluster.err, which is now of size 901 25 Jan 2012 16:26:31,827 INFO : Content of stderr: Unwrapping InvocationTargetException Exception in thread "main" org.labkey.api.pipeline.PipelineJobException: Failed running /share/apps/cpas/bin/tpp/bin/xinteract, exit code 1 at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:1106) at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:966) at org.labkey.ms2.pipeline.TPPTask.run(TPPTask.java:419) at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:626) at org.labkey.pipeline.cluster.ClusterStartup.run(ClusterStartup.java:58) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.labkey.bootstrap.ClusterBootstrap.main(ClusterBootstrap.java:50) 25 Jan 2012 16:26:41,835 INFO : Deleting log file /home/massspec/cpas/pipeline/projects/LynnGroup/Lynn/PVM/@files/mascot/PVM_mascot_Copy15/all.cluster.err, which is now of size 901