• Sign In
  1. Messages

prophet parameter

CPAS Forum (Inactive)

View Message

view list print
prophet parameter mmcfarla  2008-05-20 11:54
Status: Closed
 
Hi.

It looks like the pipeline can't handle pepxml results where there are spectrum queries without search hits (sequest search). We wanted to keep all original search info through out the pipeline so the pipeline prophet min probability was set to 0.

It errors at 'ERROR: MS2 import failed' and 'FATAL: XAR import FAILED'

The peptide and protein prophet reports are generated but the job errors. This only happens when searching data with a tight precursor mass tolerance window.


For searches with a tight precursor mass tolerance (say, 50ppm) there are precursor masses that have no possible molecular weight matches and return no hits.

We have not see this for wide mass tolerance search windows, presumably b/c it is unlikely not to find some peptide w/ in 2Da.

~Melinda
 
 
jeckels responded:  2008-05-20 14:56
Hi Melinda,

Is there additional error information in the log file immediately before or after the error messages that you described? If so, could you include it?

Thanks,
Josh
 
mmcfarla responded:  2008-05-20 15:13
Sorry. Here is from a few lines before through to the end of the log.


14 May 2008 23:58:04,687 INFO : Starting to import FASTA file d:\pipeline\databases\Sprot_040808.fas
14 May 2008 23:58:09,031 INFO : FASTA file "d:/pipeline/databases/Sprot_040808.fas" not imported, but another file, 'd:/pipeline/databases/mascot/Sprot/Sprot_040808.fas', has the same checksum
14 May 2008 23:58:09,047 INFO : 4.35 seconds to import FASTA file d:\pipeline\databases\Sprot_040808.fas
14 May 2008 23:58:09,047 INFO : Starting to import peptide search results for fraction 1, analysis of file null
14 May 2008 23:58:09,047 INFO : Importing MS/MS results is 0% complete
14 May 2008 23:58:09,047 ERROR: MS2 import failed
java.lang.NullPointerException
    at org.labkey.common.tools.PepXmlLoader$PeptideIterator.hasNext(PepXmlLoader.java:416)
    at org.labkey.ms2.PepXmlImporter.importRun(PepXmlImporter.java:114)
    at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:181)
    at org.labkey.ms2.MS2Manager.importRun(MS2Manager.java:424)
    at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:415)
    at org.labkey.ms2.PepXmlExperimentDataHandler.importFile(PepXmlExperimentDataHandler.java:103)
    at org.labkey.experiment.XarReader.loadDataFile(XarReader.java:1083)
    at org.labkey.experiment.XarReader.loadDoc(XarReader.java:314)
    at org.labkey.experiment.XarReader.parseAndLoad(XarReader.java:106)
    at org.labkey.experiment.api.ExperimentServiceImpl.loadXar(ExperimentServiceImpl.java:549)
    at org.labkey.api.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:110)
    at org.labkey.experiment.pipeline.XarImportTask.run(XarImportTask.java:105)
    at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:429)
    at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:534)
    at org.labkey.ms2.pipeline.AbstractMS2SearchPipelineJob.run(AbstractMS2SearchPipelineJob.java:151)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
14 May 2008 23:58:09,062 INFO :
14 May 2008 23:58:09,062 FATAL: Exception during import
java.lang.NullPointerException
    at org.labkey.common.tools.PepXmlLoader$PeptideIterator.hasNext(PepXmlLoader.java:416)
    at org.labkey.ms2.PepXmlImporter.importRun(PepXmlImporter.java:114)
    at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:181)
    at org.labkey.ms2.MS2Manager.importRun(MS2Manager.java:424)
    at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:415)
    at org.labkey.ms2.PepXmlExperimentDataHandler.importFile(PepXmlExperimentDataHandler.java:103)
    at org.labkey.experiment.XarReader.loadDataFile(XarReader.java:1083)
    at org.labkey.experiment.XarReader.loadDoc(XarReader.java:314)
    at org.labkey.experiment.XarReader.parseAndLoad(XarReader.java:106)
    at org.labkey.experiment.api.ExperimentServiceImpl.loadXar(ExperimentServiceImpl.java:549)
    at org.labkey.api.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:110)
    at org.labkey.experiment.pipeline.XarImportTask.run(XarImportTask.java:105)
    at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:429)
    at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:534)
    at org.labkey.ms2.pipeline.AbstractMS2SearchPipelineJob.run(AbstractMS2SearchPipelineJob.java:151)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
14 May 2008 23:58:09,062 FATAL: XAR import FAILED
 
jeckels responded:  2008-05-20 16:09
Hi Melinda,

Thanks for the additional info. You're correct - the problem is tied to the lack of a <search_hit> for the entry in the pepXML file. I've opened a bug to get this fixed.

https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=5904

Thanks,
Josh