Open Mohammedhusen opened 4 years ago
Hi @Mohammedhusen ,
Could you please attach here the full log of the job, and the parameters of the job?
Hi @j-coll ,
This is the only log I can see from the error log file.
cat variant-stats.20200810100544.a87Aod.err
2020-08-10 10:05:48 [main] INFO OpenCgaTool:362 -
2020-08-10 10:05:48 [main] INFO OpenCgaTool:363 - ------- Executing step 'prepare-cohorts' -------
2020-08-10 10:05:48 [main] INFO OpenCgaTool:243 - ------- Tool 'variant-stats' executed in 0.628s [ 00:00:01 ] -------
org.opencb.opencga.core.exceptions.ToolException: Unable to compute variant stats for cohorts [ALL]
at org.opencb.opencga.analysis.variant.stats.VariantStatsAnalysis.lambda$run$3(VariantStatsAnalysis.java:308)
at org.opencb.opencga.analysis.tools.OpenCgaTool.step(OpenCgaTool.java:364)
at org.opencb.opencga.analysis.variant.stats.VariantStatsAnalysis.run(VariantStatsAnalysis.java:267)
at org.opencb.opencga.analysis.tools.OpenCgaTool.start(OpenCgaTool.java:229)
at org.opencb.opencga.analysis.tools.ToolRunner.execute(ToolRunner.java:98)
at org.opencb.opencga.app.cli.internal.executors.VariantInternalCommandExecutor.stats(VariantInternalCommandExecutor.java:431)
at org.opencb.opencga.app.cli.internal.executors.VariantInternalCommandExecutor.execute(VariantInternalCommandExecutor.java:164)
at org.opencb.opencga.app.cli.internal.InternalMain.privateMain(InternalMain.java:117)
at org.opencb.opencga.app.cli.internal.InternalMain.main(InternalMain.java:32)
Hi @j-coll ,
Could you please update on this?
Hi @Mohammedhusen ,
It seems that the cohort "ALL" is empty. Is this possible? Could you copy here the output of these commands?
Full informaiton of the variant stats job:
opencga.sh jobs info --of json --job variant-stats.20200810100544.a87Aod --study <STUDY>
Full informaiton of the cohort ALL:
opencga.sh cohorts info --of json --cohort ALL --study <STUDY>
In case of not being able to share this information, as it might be sensitive data, please just check the number of samples within the cohort
Hi Team,
While using opencga 2.0.0-RC1, we are getting the following error when running stats on the study , could you please help.