Problem with X-tandem search
01 ноя 2008 02:49:40,421 ERROR: Failed to remove work directory F:\labkey_repository\moss\organells\chloroplasts\2\mzXML\mascot\moss_ncbi\xtandem\moss_ncbi\Ch-2-10_1-F,8_01_3755.work
java.io.IOException: Failed to remove work directory F:\labkey_repository\moss\organells\chloroplasts\2\mzXML\mascot\moss_ncbi\xtandem\moss_ncbi\Ch-2-10_1-F,8_01_3755.work
at org.labkey.pipeline.api.WorkDirectoryLocal.remove(WorkDirectoryLocal.java:184)
at org.labkey.ms2.pipeline.TPPTask.run(TPPTask.java:233)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:464)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:569)
at org.labkey.ms2.pipeline.AbstractMS2SearchPipelineJob.run(AbstractMS2SearchPipelineJob.java:167)
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) |
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| jeckels responded: |
2008-11-05 16:44 |
Hello,
What version of LabKey Server are you running?
Have you run other searches run successfully on this installation?
Please include the full log file for the job that failed, as well as the directory contents for F:\labkey_repository\moss\organells\chloroplasts\2\mzXML\mascot\moss_ncbi\xtandem\moss_ncbi and F:\labkey_repository\moss\organells\chloroplasts\2\mzXML\mascot\moss_ncbi\xtandem\moss_ncbi\Ch-2-10_1-F,8_01_3755.work
Thanks,
Josh |
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| polyakovnb responded: |
2009-01-13 04:23 |
I'm sorry for silence, i had a lot of other work. I use last version of labkey server and all searches on this installation was not successfull. I think the problem is with directory permissions, but i don't know how-to fix it . Please see logfile and directory content |
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| brendanx responded: |
2009-01-13 06:30 |
The problem is that somehow you have a 4.0.2 version of ProteinProphet on your path:
running: "ProteinProphet "9_1-F,8_01_3855.pep.xml" "9_1-F,8_01_3855.pep-prot.xml" XML NOPLOT"
29 дек 2008 13:11:05,807 INFO : ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.0 JETSTREAM rev 2, Build 200807011544 (MinGW))
Built with MinGW. You are running v3.4.1 of xinteract, which is the currently supported version for CPAS, but xinteract in turn runs ProteinProphet, and it is getting the wrong version. The v4.0.2 version of ProteinProphet apparently leaves behind a xml_senserr.txt file, and this causes the error you get.
Fix the path your server uses so that you see it running ProteinProphet 3.4.1, and you should get much better results.
--Brendan |
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| adina-chuang responded: |
2009-02-08 17:32 |
Brenden,
I think I'm having this very issue. I'm not sure where to change the path of Protein Prophet. I uninstalled TPP and it seemed to help my results but I'm still having some issues with a second search with a similar error. Can you send me additional info on what exactly I need to change and/or where it is located?
I'm installing CPAS on a local computer. It is not used as as server.
Thanks,
Adina |
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| wnels2 responded: |
2009-02-09 03:27 |
Hi Adina,
Your pipeline looks to be opperating correctly now. I suspect that the last error is related to your xtandem search params. The error says that there is no good data in the pep.xml file. I beleive the sample you are running is the TPP mudpit icat tutorial sample. Double check that the Cys modifications are set correctly. Fractions and Xpress should also be used with these files but it will not crash if they are left out. If the Cys mods don't fix it the next step would be to post your xtandem.xml file.
Bill |
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logfile.txt
9_1-F,8_01_3855.work.rar