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opencb / opencga

An Open Computational Genomics Analysis platform for big data genomics analysis. OpenCGA is maintained and develop by its parent company Zetta Genomics. Please contact support@zettagenomics.com for bug report and feature requests.
Apache License 2.0
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Unable to execute storage operation #1663

Open Mohammedhusen opened 4 years ago

Mohammedhusen commented 4 years ago

Hi Team,

We are getting a strange error below could you please help. The job creating a folder and then giving an error folder should be empty!

org.opencb.opencga.storage.core.exceptions.StorageEngineException: Unable to execute storage operation. Outdir '/opt/opencga/sessions/jobs/J_2513' must be empty!
    at org.opencb.opencga.storage.core.manager.variant.operations.StorageOperation.outdirMustBeEmpty(StorageOperation.java:91)
    at org.opencb.opencga.storage.core.manager.variant.operations.VariantFileIndexerStorageOperation.index(VariantFileIndexerStorageOperation.java:116)
    at org.opencb.opencga.storage.core.manager.variant.VariantStorageManager.index(VariantStorageManager.java:183)
    at org.opencb.opencga.storage.core.manager.variant.VariantStorageManager.index(VariantStorageManager.java:174)
    at org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.index(VariantCommandExecutor.java:307)
    at org.opencb.opencga.app.cli.analysis.executors.VariantCommandExecutor.execute(VariantCommandExecutor.java:116)
    at org.opencb.opencga.app.cli.analysis.AnalysisMain.privateMain(AnalysisMain.java:102)
    at org.opencb.opencga.app.cli.analysis.AnalysisMain.main(AnalysisMain.java:35)
Mohammedhusen commented 4 years ago

Hi @j-coll ,

Could you please update on this error?

j-coll commented 4 years ago

Hi @Mohammedhusen ,

This is strange, indeed. Could you list the content of that directory, please? Are you using the "local" executor? Are you running multiple instances of the opencga-master (opencga-admin.sh catalog daemon) ?

Mohammedhusen commented 4 years ago

Hi @j-coll ,

Thanks for your response.

Here is the content of the directory.

Screen Shot 2020-10-22 at 9 55 28 AM

This error we are getting when using SGE executor in the 1.4.1 version.

j-coll commented 4 years ago

Thanks! I think I know how to fix this. Are you planning to upgrade to v2.0.0 ?

Mohammedhusen commented 4 years ago

@j-coll ,

Glad to know that you have a solution to this issue. Regarding upgrade to v2.0.0 yes we are planing if there is a stable version for both openCGA and IVA available. Do you guys have a stable version of V2? if yes please share the link.