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Old 09-02-2010, 12:25 AM   #1
wlnjseu
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Location: China

Join Date: Aug 2010
Posts: 8
Default Help for AB WT Analysis Pipeline(RNA seq)

it is a error when I use ab_wtp_v1.2.1_testData running split_read_mapper.sh -c myconfig.ini. I don't know using Java, so unable to look in detail the error messages.
What does it mean?
Can anyone help me?
Thanks for your suggestions:



USING WT_HOME=/home/corona/wanglei/ab_wtp/ab_wtp_v1.2.1



Logging messages to mapping_output/mapper.log



Aug 30, 2010 9:36:03 AM com.lifetechnologies.solid.wt.mapper.SplitReadsTask doTaskRemotely



SEVERE: Script submission failed.



java.lang.Exception: Script submission failed.



at com.lifetechnologies.solid.wt.cluster.PBSClusterInterface.submitScript(PBSClusterInterface.java:174)



at com.lifetechnologies.solid.wt.cluster.ClusterInterface.executeJob(ClusterInterface.java:161)



at com.lifetechnologies.solid.wt.mapper.SplitReadsTask.doTaskRemotely(SplitReadsTask.java:127)



at com.lifetechnologies.solid.wt.mapper.SplitReadsTask.doTask(SplitReadsTask.java:93)



at com.lifetechnologies.solid.wt.mapper.Mapper.mapReads(Mapper.java:434)



at com.lifetechnologies.solid.wt.cmd.MapperCmd.runCmd(MapperCmd.java:245)



at com.lifetechnologies.solid.wt.cmd.AbstractCmd.run(AbstractCmd.java:221)



at com.lifetechnologies.solid.wt.cmd.CmdRunner.main(CmdRunner.java:20)



Aug 30, 2010 9:36:03 AM com.lifetechnologies.solid.wt.cmd.AbstractCmd run



SEVERE: java.lang.Exception: Script submission failed.



com.lifetechnologies.solid.wt.mapper.TaskException: java.lang.Exception: Script submission failed.



at com.lifetechnologies.solid.wt.mapper.SplitReadsTask.doTaskRemotely(SplitReadsTask.java:143)



at com.lifetechnologies.solid.wt.mapper.SplitReadsTask.doTask(SplitReadsTask.java:93)



at com.lifetechnologies.solid.wt.mapper.Mapper.mapReads(Mapper.java:434)



at com.lifetechnologies.solid.wt.cmd.MapperCmd.runCmd(MapperCmd.java:245)



at com.lifetechnologies.solid.wt.cmd.AbstractCmd.run(AbstractCmd.java:221)



at com.lifetechnologies.solid.wt.cmd.CmdRunner.main(CmdRunner.java:20)



Caused by: java.lang.Exception: Script submission failed.



at com.lifetechnologies.solid.wt.cluster.PBSClusterInterface.submitScript(PBSClusterInterface.java:174)



at com.lifetechnologies.solid.wt.cluster.ClusterInterface.executeJob(ClusterInterface.java:161)



at com.lifetechnologies.solid.wt.mapper.SplitReadsTask.doTaskRemotely(SplitReadsTask.java:127)



... 5 more
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Old 09-02-2010, 10:19 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

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Without knowing much about your computing environment, I would say that you do not have your compute cluster set up correctly. Or perhaps Corona is not set up to work with your cluster. Can you run other Corona programs on your cluster?
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Old 09-02-2010, 01:21 PM   #3
mrawlins
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It looks like a problem submitting your job to the PBS Scheduler. Are you running this on a cluster with PBS/Torque? I don't think their pipeline works without one of the two or three supported schedulers. It's one of the down-sides of the pipeline.
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Old 09-02-2010, 11:10 PM   #4
wlnjseu
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Quote:
Originally Posted by mrawlins View Post
It looks like a problem submitting your job to the PBS Scheduler. Are you running this on a cluster with PBS/Torque? I don't think their pipeline works without one of the two or three supported schedulers. It's one of the down-sides of the pipeline.
Thank for westerman and mrawlins .I did not have my compute cluster set up correctly
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Old 09-02-2010, 11:12 PM   #5
wlnjseu
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Thank for westerman and mrawlins .I did not have my compute cluster set up correctly

Last edited by wlnjseu; 09-02-2010 at 11:25 PM.
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Old 09-02-2010, 11:12 PM   #6
wlnjseu
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Thank for westerman and mrawlins .I did not have my compute cluster set up correctly
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Old 09-06-2010, 02:01 AM   #7
wlnjseu
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hello

I have successfully completed split_read_mapper.sh -c mapping_config.ini and ntr_finder.sh. But ntr_finder.sh -c ntr_config.ini run error.
Thanks for your suggestions:

USING WT_HOME=/share/apps/program/ab_wtp_v1.2.1
Logging messages to ntr_output/ntr_finder.log
Sep 6, 2010 4:47:25 PM com.lifetechnologies.solid.wt.cmd.NTRFinderCmd runCmd
SEVERE: An error has stopped NTR Finding.
java.lang.Exception: All Jobs failed. Cannot continue.
at com.lifetechnologies.solid.wt.NTRFinderLauncher.launch(NTRFinderLauncher.java:205)
at com.lifetechnologies.solid.wt.cmd.NTRFinderCmd.runCmd(NTRFinderCmd.java:107)
at com.lifetechnologies.solid.wt.cmd.AbstractCmd.run(AbstractCmd.java:221)
at com.lifetechnologies.solid.wt.cmd.CmdRunner.main(CmdRunner.java:20)
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