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New error (Validation errors: Extra inputs) running somatic calling pipeline: problem with Cromwell 48?

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9 comments

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    Jason Cerrato

    Hi lck,

    Would you be willing to share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in either the icon of your workspace in the workspace list or inside the workspace dashboard (see the icon with the three dots). Let us know the workspace name, as well as the submission and workflow ids for both the previously successful run and the recent failure. We'll be happy to take a closer look.

    Many thanks,

    Jason

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    Matthew Miller

    Jason:  I'm totally new to Terra. The workspace is "test".  There are three submissions. All failed. But take a look at 157ddecb-0614-4458-8769-79a2a5d13290, because that one used the intervals from Picard.  The submission 993f343b-4476-4fbe-aabf-f4a4bd4e1a48 was with a handmade GATK style interval list.

     

    Thanks!

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    lck

    Jason Cerrato, the workspace has bam files that can't be shared -- is there some other option by any chance, or a way I can share without sharing the workspace data? Thanks.

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    lck

    (Also, Matthew Miller, I think you meant to leave your comment on your thread instead...)

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    Jason Cerrato

    Hi Ick,

    Are the files unable to be shared due to an authorization domain? If so, even if the workspace is shared with the GROUP, only members who are part of the authorization domain will be able to access the workspace. If the workspace is under an authorization domain, please let me know which.

    Kind regards,

    Jason

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    lck

    Hi Jason Cerrato, it's a regulatory/data security issue for the project -- we're not supposed to share the files with people outside of my institution, although we have permission to upload them to Terra. If necessary I could delete the bam files and then share the workspace? I just hate to delete them then have to reupload later... Or is there any other way I could share troubleshooting information with you?

    Thanks! 

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    GE

    Hello, I'm having the same error. For a pipeline that previously worked perfectly fine. So it must be a bug in Terra. Please fix it.

     

    Validation errors: Extra inputs: WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.CollectRawWgsMetrics.memory_multiplier,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.BaseRecalibrator.gatk_docker,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.ApplyBQSR.gatk_docker,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectAggregationMetrics.collect_gc_bias_metrics,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.MarkDuplicates.read_name_regex,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.ApplyBQSR.memory_multiplier,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.GatherBqsrReports.gatk_docker,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.BamToGvcf.make_bamout,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.MarkDuplicates.memory_multiplier,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.BamToGvcf.make_gvcf,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.BamToGvcf.VariantCalling.HaplotypeCallerGATK4.gatk_docker,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.AggregatedBamQC.AggregatedBamQC.CollectReadgroupBamQualityMetrics.collect_gc_bias_metrics,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.CheckContamination.disable_sanity_check,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.BamToCram.BamToCram.ValidateCram.memory_multiplier,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.BamToGvcf.VariantCalling.ValidateVCF.gatk_docker,WholeGenomeGermlineSingleSample.WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.UnmappedBamToAlignedBam.SplitRG.reads_per_file

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    lck

    GE, I ended up getting it to run by switching the version to 2.7 -- whatever new was introduced in Cromwell v48 was handled appropriately by version 2.7 of the workflow. My previous runs used version 2.6, and this was still selected by default when the Cromwell version was updated. So you might try that. (I also confirmed that my results using 2.6 and 2.7 were identical.)

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    Jason Cerrato

    Hi Ick,

    Thank you for reporting that using the newer version worked. Gilad, please see if Ick's suggestion resolves your issue. If you run into any further difficulties, please let us know.

    KInd regards,

    Jason

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