GATK4-RNA-Germline-VariantCalling sample file failing

Post author
Maayan Baron

Hey,

I have been trying to use the GATK4-RNA-Germline-VariantCalling workspace. As a start, I am running the sample file provided (NA12878). For some reason I got the following error in the gtfToCallingIntervals task:

Using GATK jar /gatk/gatk-package-4.2.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-4.2.0.0-local.jar BedToIntervalList -I=exome.fixed.bed -O=star.gencode.v19.transcripts.patched_contigs.exons.interval_list -SD=/cromwell_root/gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict 2021/04/15 00:40:11 Starting delocalization. 2021/04/15 00:40:12 Delocalization script execution started... 2021/04/15 00:40:12 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-74e9b8c4-32bf-49aa-a087-e71336b97a7c/df52d2dc-dc0c-4e19-9772-bb37d69fa3c7/RNAseq/0bc024d3-a6e3-4f9a-9f01-b3754f320887/call-gtfToCallingIntervals/memory_retry_rc 2021/04/15 00:40:12 Delocalizing output /cromwell_root/rc -> gs://fc-74e9b8c4-32bf-49aa-a087-e71336b97a7c/df52d2dc-dc0c-4e19-9772-bb37d69fa3c7/RNAseq/0bc024d3-a6e3-4f9a-9f01-b3754f320887/call-gtfToCallingIntervals/rc 2021/04/15 00:40:14 Delocalizing output /cromwell_root/stdout -> gs://fc-74e9b8c4-32bf-49aa-a087-e71336b97a7c/df52d2dc-dc0c-4e19-9772-bb37d69fa3c7/RNAseq/0bc024d3-a6e3-4f9a-9f01-b3754f320887/call-gtfToCallingIntervals/stdout 2021/04/15 00:40:16 Delocalizing output /cromwell_root/stderr -> gs://fc-74e9b8c4-32bf-49aa-a087-e71336b97a7c/df52d2dc-dc0c-4e19-9772-bb37d69fa3c7/RNAseq/0bc024d3-a6e3-4f9a-9f01-b3754f320887/call-gtfToCallingIntervals/stderr 2021/04/15 00:40:17 Delocalizing output /cromwell_root/star.gencode.v19.transcripts.patched_contigs.exons.interval_list -> gs://fc-74e9b8c4-32bf-49aa-a087-e71336b97a7c/df52d2dc-dc0c-4e19-9772-bb37d69fa3c7/RNAseq/0bc024d3-a6e3-4f9a-9f01-b3754f320887/call-gtfToCallingIntervals/star.gencode.v19.transcripts.patched_contigs.exons.interval_list Required file output '/cromwell_root/star.gencode.v19.transcripts.patched_contigs.exons.interval_list' does not exist.

any idea what is this file output or how to solve this error?

Thank you!
Maayan.

Comments

6 comments

  • Comment author
    Samantha (she/her)

    Hi Maayan Baron,

     

    Thanks for writing in. Can you share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.

    1. Add GROUP_FireCloud-Support@firecloud.org to the User email field and press enter on your keyboard.
    2. Click Save.

    Let us know the workspace name, as well as the relevant submission and workflow IDs. We’ll be happy to take a closer look as soon as we can.

     

    Best,

    Samantha

    0
  • Comment author
    Maayan Baron

    Hi Samantha-she-her

    Thank you for the reply. I just shared the workspace as you requested. The name of my workspace is: GATK4-RNA-Germline-VariantCalling_test and the relevant submission is: 0ace9e79-f1a6-48e6-8194-2788c6c52948.

    Thanks again!
    Maayan

    0
  • Comment author
    Samantha (she/her)

    Hi Maayan Baron,

     

    Sorry for the delayed response. It looks like there is an issue with version 1.0.0 of the workflow you are running. Can you try setting the version to 1.1.0 and rerunning the workflow?

     

    Please let me know if you have any issues.

     

    Best,

    Samantha

    0
  • Comment author
    Maayan Baron

    Hello Samantha-she-her,

    Thanks for your reply! I have tried to change the version 1.1.0 but the job is still failing (submission id: 8f7ba7a2-484a-4798-b4c8-9ad751a2a947). 

    Any idea what is the problem?

    Thanks!
    Maayan.

     

    0
  • Comment author
    Samantha (she/her)

    Hi Maayan Baron,

     

    We were able to reproduce the issue on our end. Do you mind rerunning the workflow with the version named bs_debug_gt? It should be available in Terra as a workflow version after refreshing your page.

     

    Best,

    Samantha

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  • Comment author
    Maayan Baron

    Hi Samantha-she-her,

    Thank you for looking into this. I ran the new version and it does work with the sample provided.
    I am still having issues with running it on my own sample but I will try to see if the problem is on my side or not.

    Thanks!
    Maayan.

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