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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

improt gcnvkernel fails. somehting to do with theano lock



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    simon lee

    I should just add one more thing:

    When running in non-parellel mode, or when running the first or even the second job on the hpc, I do not get this error. the module load executes without a problem and retruns a result of 0. It's only after a few jobs are running that this seems to occur and I cant figure out the pattern. At the moment I am staggering the running of my jobs and that seems to help, but I don't know why, other than to think it is some kind of threadsafe protection protocol that I am avoiding by staggering the runs.


    06:21:26.223 DEBUG ScriptExecutor -   python
    06:21:26.223 DEBUG ScriptExecutor -   -c
    06:21:26.223 DEBUG ScriptExecutor -   import gcnvkernel

    06:21:34.416 DEBUG ScriptExecutor - Result: 0

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    Genevieve Brandt (she/her)

    Hi simon lee,

    Thank you for writing into the forum! I hope we can figure out why you are getting this error. 

    It looks like you are not using the correct version of java that we recommend: You are also using an old version of GATK. I know there have been some bugs we fixed in gCNV, so I would recommend you upgrade your GATK version.

    Have you set up the proper Conda environment for GermlineCNVCaller?

    The error message you are getting looks related to the python environment so that's why I think it's important to start there.

    Let me know,


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    Genevieve Brandt (she/her)

    Hi simon,

    We haven't heard from you in a couple of days so we're going to close out this ticket. If you still require assistance, simply respond to this thread and we'll be happy to pick up where we left off!

    Kind regards,


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