10 Oct 2018 23:37:05,289 INFO : Comet search for AG_MAP_Plasma_Bound_F1
10 Oct 2018 23:37:05,289 INFO : =======================================
10 Oct 2018 23:37:05,305 INFO : AG_MAP_Plasma_Bound_F1.mzXML
10 Oct 2018 23:37:05,336 INFO : Starting to run task 'org.labkey.ms2.pipeline.FastaCheckTask' at location 'webserver-fasta-check'
10 Oct 2018 23:37:05,336 INFO : Check FASTA validity
10 Oct 2018 23:37:05,336 INFO : =======================================
10 Oct 2018 23:37:05,351 INFO : Checking sequence file validity of D:\Program Files\LabKey Server\files\DAS - Proteomics\2014_CSF_MCP\@files\databases\20180618_uniprot_human.fasta
10 Oct 2018 23:37:05,742 INFO : 
10 Oct 2018 23:37:05,742 INFO : Successfully completed task 'org.labkey.ms2.pipeline.FastaCheckTask'
10 Oct 2018 23:37:05,773 INFO : Starting to run task 'org.labkey.ms2.pipeline.comet.CometSearchTask' at location 'webserver'
10 Oct 2018 23:37:05,789 INFO : Copying D:\Program Files\LabKey Server\files\DAS - Proteomics\2014_CSF_MCP\@files\MS2\AG_MAP_Plasma_Bound_F1.mzXML to D:\Program Files\LabKey Server\files\DAS - Proteomics\2014_CSF_MCP\@files\MS2\comet\2014_CSF_MCP_no_glycan\AG_MAP_Plasma_Bound_F1.work\AG_MAP_Plasma_Bound_F1.mzXML
10 Oct 2018 23:37:05,914 INFO : Failed to complete task 'org.labkey.ms2.pipeline.comet.CometSearchTask'
10 Oct 2018 23:37:05,914 DEBUG: discarding file: D:\Program Files\LabKey Server\files\DAS - Proteomics\2014_CSF_MCP\@files\MS2\comet\2014_CSF_MCP_no_glycan\AG_MAP_Plasma_Bound_F1.work\AG_MAP_Plasma_Bound_F1.mzXML
10 Oct 2018 23:37:05,945 ERROR: Failed to locate comet. Use the site pipeline tools settings to specify where it can be found. (Currently 'D:\Program Files\LabKey Server\bin')
org.labkey.api.pipeline.PipelineJobException: Failed to locate comet. Use the site pipeline tools settings to specify where it can be found. (Currently 'D:\Program Files\LabKey Server\bin')
    at org.labkey.ms2.pipeline.comet.CometSearchTask.run(CometSearchTask.java:146)
    at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:757)
    at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:988)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.FileNotFoundException: Failed to locate comet. Use the site pipeline tools settings to specify where it can be found. (Currently 'D:\Program Files\LabKey Server\bin')
    at org.labkey.pipeline.api.PipelineJobServiceImpl.getPathToTool(PipelineJobServiceImpl.java:707)
    at org.labkey.pipeline.api.PipelineJobServiceImpl.getVersionedOsPath(PipelineJobServiceImpl.java:739)
    at org.labkey.pipeline.api.PipelineJobServiceImpl.getExecutablePath(PipelineJobServiceImpl.java:722)
    at org.labkey.ms2.pipeline.comet.CometSearchTask.run(CometSearchTask.java:108)
    ... 9 more
10 Oct 2018 23:37:38,664 INFO : Retrying job.
10 Oct 2018 23:37:38,664 DEBUG: Database indicates active task ID is org.labkey.ms2.pipeline.comet.CometSearchTask
10 Oct 2018 23:37:38,664 DEBUG: Retry details: Old Job ID: 8a8a6a31-af00-1036-b9a0-55902533ce00
10 Oct 2018 23:37:38,664 INFO : Starting to run task 'org.labkey.ms2.pipeline.comet.CometSearchTask' at location 'webserver'
10 Oct 2018 23:37:38,664 INFO : Copying D:\Program Files\LabKey Server\files\DAS - Proteomics\2014_CSF_MCP\@files\MS2\AG_MAP_Plasma_Bound_F1.mzXML to D:\Program Files\LabKey Server\files\DAS - Proteomics\2014_CSF_MCP\@files\MS2\comet\2014_CSF_MCP_no_glycan\AG_MAP_Plasma_Bound_F1.work\AG_MAP_Plasma_Bound_F1.mzXML
10 Oct 2018 23:37:38,789 INFO : Failed to complete task 'org.labkey.ms2.pipeline.comet.CometSearchTask'
10 Oct 2018 23:37:38,789 DEBUG: discarding file: D:\Program Files\LabKey Server\files\DAS - Proteomics\2014_CSF_MCP\@files\MS2\comet\2014_CSF_MCP_no_glycan\AG_MAP_Plasma_Bound_F1.work\AG_MAP_Plasma_Bound_F1.mzXML
10 Oct 2018 23:37:38,820 ERROR: Failed to locate comet. Use the site pipeline tools settings to specify where it can be found. (Currently 'D:\Program Files\LabKey Server\bin')
org.labkey.api.pipeline.PipelineJobException: Failed to locate comet. Use the site pipeline tools settings to specify where it can be found. (Currently 'D:\Program Files\LabKey Server\bin')
    at org.labkey.ms2.pipeline.comet.CometSearchTask.run(CometSearchTask.java:146)
    at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:757)
    at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:988)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.FileNotFoundException: Failed to locate comet. Use the site pipeline tools settings to specify where it can be found. (Currently 'D:\Program Files\LabKey Server\bin')
    at org.labkey.pipeline.api.PipelineJobServiceImpl.getPathToTool(PipelineJobServiceImpl.java:707)
    at org.labkey.pipeline.api.PipelineJobServiceImpl.getVersionedOsPath(PipelineJobServiceImpl.java:739)
    at org.labkey.pipeline.api.PipelineJobServiceImpl.getExecutablePath(PipelineJobServiceImpl.java:722)
    at org.labkey.ms2.pipeline.comet.CometSearchTask.run(CometSearchTask.java:108)
    ... 9 more
12 Oct 2018 19:05:50,673 INFO : Retrying job.
12 Oct 2018 19:05:50,673 DEBUG: Database indicates active task ID is org.labkey.ms2.pipeline.comet.CometSearchTask
12 Oct 2018 19:05:50,673 DEBUG: Retry details: Old Job ID: 8a8a6a31-af00-1036-b9a0-55902533ce00
12 Oct 2018 19:18:33,790 INFO : Starting to run task 'org.labkey.ms2.pipeline.comet.CometSearchTask' at location 'webserver'
12 Oct 2018 19:18:33,790 INFO : Copying D:\Program Files\LabKey Server\files\DAS - Proteomics\2014_CSF_MCP\@files\MS2\AG_MAP_Plasma_Bound_F1.mzXML to D:\Program Files\LabKey Server\files\DAS - Proteomics\2014_CSF_MCP\@files\MS2\comet\2014_CSF_MCP_no_glycan\AG_MAP_Plasma_Bound_F1.work\AG_MAP_Plasma_Bound_F1.mzXML
12 Oct 2018 19:18:33,915 INFO : comet output
12 Oct 2018 19:18:33,915 INFO : =======================================
12 Oct 2018 19:18:33,915 INFO : Working directory is D:\Program Files\LabKey Server\files\DAS - Proteomics\2014_CSF_MCP\@files\MS2\comet\2014_CSF_MCP_no_glycan\AG_MAP_Plasma_Bound_F1.work
12 Oct 2018 19:18:33,915 INFO : running: D:\Program Files\LabKey Server\bin\comet AG_MAP_Plasma_Bound_F1.mzXML
12 Oct 2018 19:18:34,681 INFO : Failed to complete task 'org.labkey.ms2.pipeline.comet.CometSearchTask'
12 Oct 2018 19:18:34,681 DEBUG: discarding file: D:\Program Files\LabKey Server\files\DAS - Proteomics\2014_CSF_MCP\@files\MS2\comet\2014_CSF_MCP_no_glycan\AG_MAP_Plasma_Bound_F1.work\AG_MAP_Plasma_Bound_F1.mzXML
12 Oct 2018 19:18:34,712 ERROR: Failed running D:\Program Files\LabKey Server\bin\comet, exit code -1073741515
org.labkey.api.pipeline.ToolExecutionException: Failed running D:\Program Files\LabKey Server\bin\comet, exit code -1073741515
    at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:1273)
    at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:1142)
    at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:1132)
    at org.labkey.ms2.pipeline.comet.CometSearchTask.run(CometSearchTask.java:112)
    at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:757)
    at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:988)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)