Error in GISTIC2.0 GISTIC2.0
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Fan Ge
Sep 30, 2023, 10:52:30 AM9/30/23
to GenePattern Help Forum
Hi there,
the id is:
could you tell me how to solve this problem?
The error thrown is
GenePattern Server error preparing job 10224 for execution.
org.genepattern.server.executor.CommandExecutorException: Error running cmd
java.util.concurrent.ExecutionException: org.genepattern.server.executor.CommandExecutorException: Error running cmd
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:206)
at org.genepattern.server.genepattern.GenePatternAnalysisTask.runCommand(GenePatternAnalysisTask.java:1805)
at org.genepattern.server.genepattern.GenePatternAnalysisTask.onJob(GenePatternAnalysisTask.java:1562)
at org.genepattern.server.executor.JobSubmitter.run(JobSubmitter.java:81)
at org.genepattern.server.executor.AnalysisJobScheduler$2$1.run(AnalysisJobScheduler.java:142)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:750)
Caused by: org.genepattern.server.executor.CommandExecutorException: Error running cmd
at org.genepattern.server.executor.slurm.SlurmJobRunner.startJob(SlurmJobRunner.java:429)
at org.genepattern.server.executor.drm.JobExecutor.runCommand(JobExecutor.java:853)
at org.genepattern.server.genepattern.GenePatternAnalysisTask$2.call(GenePatternAnalysisTask.java:1801)
at org.genepattern.server.genepattern.GenePatternAnalysisTask$2.call(GenePatternAnalysisTask.java:1798)
... 4 more
Ted Liefeld
Oct 2, 2023, 12:13:20 PM10/2/23
to GenePattern Help Forum
Hi
There was a problem with the remote compute nodes that we use to execute GISTIC. This has now be corrected and you can reload and re-run your job.
Thanks for your patience,
Ted
p.s. For the details, read on … Our GenePattern server uses several different cloud systems (both commercial and academic) to execute jobs. We attempt to keep costs down, and GenePattern free, by using less expensive, or free services to run computations when we can. Unfortunately less expensive and free also translate into less reliable and sometimes they become unavailable as happened over the weekend with the service we were sending GISTIC to. The next release of GenePattern has an automated failover so that if a job fails on one system, it can be retried automatically on another without requiring user (or administrator) intervention. This update will be released later in October 2023
There was a problem with the remote compute nodes that we use to execute GISTIC. This has now be corrected and you can reload and re-run your job.
Thanks for your patience,
Ted
p.s. For the details, read on … Our GenePattern server uses several different cloud systems (both commercial and academic) to execute jobs. We attempt to keep costs down, and GenePattern free, by using less expensive, or free services to run computations when we can. Unfortunately less expensive and free also translate into less reliable and sometimes they become unavailable as happened over the weekend with the service we were sending GISTIC to. The next release of GenePattern has an automated failover so that if a job fails on one system, it can be retried automatically on another without requiring user (or administrator) intervention. This update will be released later in October 2023
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