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joint discovery error in 3 samples of WGS

jin0008jin0008 Seoul, South KoreaMember

When I ran this execution in fire cloud. I got the error message.
message: Task JointGenotyping.ImportGVCFs:23:1 failed. JES error code 5. Message: 10: Failed to delocalize files: failed to copy the following files: "/mnt/local-disk/genomicsdb.tar -> gs://fc-675a604c-d4aa-4520-81c1-48ede8300786/4c9747b9-a69f-4270-834d-9f6e3472ab8e/JointGenotyping/cf4bcaaf-d2c2-4436-b814-2d1c3d8f29d2/call-ImportGVCFs/shard-23/genomicsdb.tar (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/genomicsdb.tar gs://fc-675a604c-d4aa-4520-81c1-48ede8300786/4c9747b9-a69f-4270-834d-9f6e3472ab8e/JointGenotyping/cf4bcaaf-d2c2-4436-b814-2d1c3d8f29d2/call-ImportGVCFs/shard-23/genomicsdb.tar, command failed: CommandException: No URLs matched: /mnt/local-disk/genomicsdb.tar\nCommandException: 1 file/object could not be transferred.\n)"
Can you help me?

Best Answer

  • KateNKateN Cambridge, MAMember, Broadie, Moderator
    Accepted Answer

    Usually the Failed to localize files error doesn't mean that your files were unable to be localized, but that something prevented the system from finding the files. This can range from something as simple as your workflow not running properly (and thus the files not being generated), to a more complicated bug. The latter is not very common.

    Could you please share the workspace you encountered this error in with GROUP_support@firecloud.org so I can take a look? I will also need the name of the workspace itself (found in the top right when you are in your workspace), and the Submission ID (found in the Monitor tab when you go to click on the specific submission where you encountered this error).

Answers

  • KateNKateN Cambridge, MAMember, Broadie, Moderator
    Accepted Answer

    Usually the Failed to localize files error doesn't mean that your files were unable to be localized, but that something prevented the system from finding the files. This can range from something as simple as your workflow not running properly (and thus the files not being generated), to a more complicated bug. The latter is not very common.

    Could you please share the workspace you encountered this error in with GROUP_support@firecloud.org so I can take a look? I will also need the name of the workspace itself (found in the top right when you are in your workspace), and the Submission ID (found in the Monitor tab when you go to click on the specific submission where you encountered this error).

  • jin0008jin0008 Seoul, South KoreaMember

    I shared my project. Unfortunately, I deleted my original workspace due to above errors.
    I thought that my problems might be caused by initial pre-process of data.
    I don't know what flowcell_unmapped_bam_list file is, so I attached Unaligned bam list of NA12878.
    How can I produce flowcell-unmapped-bam-list file?
    I shared my workspace with group_support@firecloud.org.

  • KateNKateN Cambridge, MAMember, Broadie, Moderator

    Ah, unfortunately I won't be able to diagnose the error without being able to look at the error message itself. If you encounter it again, please do let me know and I can take a look.

    For the any file that you don't know what it should be, if the author of the method should have some documentation telling you what they expect to be there. You can usually find this in the Documentation section on the Summary page. If there is no documentation, or if the documentation doesn't describe the input you have a question on (in this case flowcell_unmapped_bam_list), you can try looking in the method configuration.

    When an author of a method publishes, they can also choose to include a method configuration. A method configuration is simply all of the inputs and outputs filled out how they expect them to be for a workspace they ran on. If there is a published method configuration for a method, you would find it under the Method Configurations tab when looking at the method you want to use in the Method Repository.

    If neither of these options have information for you, and the method is one published by us, please let me know the name of the method and I will be sure to fix any lapses in our documentation and find the answer for you.

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