TCGA RNA-Seq counts workflow -- fails for all or most samples
I've run the 'gdc_file_downloader__RNAseq__HTSeqCounts__gene_expression_quantification__txt__cfg' workflow several times on the 1015 samples available in the "TCGA Brain Lower Grade Glioma Open-Access Data Workspace", and the result is either 1) all the samples fail to be processed through the job, or 2) only a subset (15) of them are processed.
Is this a bug or is there something I should be doing differently to get the RNASeq count data for these LGG samples?
Thanks!
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9 comments
Hi Rebecca Eliscu,
Thanks for writing in—we're happy to take a closer look here!
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 IDs. We’ll get back to you as soon as we can.
Kind regards,
Jason
Hi Jason, thanks for your response.
I shared the workspace, as instructed.
These are the relevant submission IDs for the 'gdc_file_downloader__RNAseq__HTSeqCounts__gene_expression_quantification__txt__cfg' using my workspace: `TCGA Brain Lower Grade Glioma Open-Access Data Workspace copy`:
- 7ee24f2e-9087-4b4e-bc19-8d43dd8a3750
- 810194c8-b4bf-47d9-a29c-0c644e1a00af
- cb7ed454-154c-42ed-95fa-3232a0394ae4
- 30b3fe23-508b-41bd-8383-9be7af51870b
I should also mention that I was having trouble getting all of the samples from this same workspace to be processed using the 'gdc_file_downloader__WXS__SomSnipAggrMask__masked_somatic_mutation__maf__cfg' workflow. In this case, 6-7 samples would repeatedly fail:
- 854deac6-a274-4ea5-9948-94b61071bb52
- 3025b379-8d78-4062-a12b-a8fefb41d4f1
Thanks for your help!
Hi Rebecca,
Can you confirm GROUP_FireCloud-Support@firecloud.org is in the list of users the workspace is shared with? I am unable to find the workspace in a search.
If it isn't, can you add GROUP_FireCloud-Support@firecloud.org to the User email field and press Enter before clicking Save?
Many thanks,
Jason
Hi Jason,
Apologies, I thought I successfully added the user earlier.
Link to workspace: https://app.terra.bio/#workspaces/thisnameistotallyunique/TCGA_LGG_hg38_OpenAccess_GDCDR-12-0_DATA%20copy
Hi Rebecca,
Thanks for that! I'll take a look and get back to you as soon as I can.
Kind regards,
Jason
Hi Rebecca,
Since this workflow you're using isn't a Terra-maintained workflow, you may need to reach out to its authors if you determine anything about it is not functioning correctly. I'm happy to help you determine what's going wrong for your submissions as far as Terra is concerned.
For submission 854deac6-a274-4ea5-9948-94b61071bb52 I can see the following error message in Job Manager: https://app.terra.bio/#workspaces/thisnameistotallyunique/TCGA_LGG_hg38_OpenAccess_GDCDR-12-0_DATA%20copy/job_history/854deac6-a274-4ea5-9948-94b61071bb52
It looks like the workflow expects a value for uuid_and_filename but this sample doesn't have one. Looking at the method configuration, I see the workflow uses the sample's WXS__SomSnipAggrMask__masked_somatic_mutation__maf__uuid_and_filename value.
Looking at your Data tab and sample table, searching for that sample in question, I indeed see that this sample has no value for this column.
This is why the workflow failed for this sample. Those 6-7 samples that repeatedly fail may be failing for the same reason.
Kind regards,
Jason
Hi Rebecca,
For submission 30b3fe23-508b-41bd-8383-9be7af51870b I'm seeing similar types of error messages in Job Manager.
https://app.terra.bio/#workspaces/thisnameistotallyunique/TCGA_LGG_hg38_OpenAccess_GDCDR-12-0_DATA%20copy/job_history/30b3fe23-508b-41bd-8383-9be7af51870b
The method configuration shows that it's trying to pull the value of the sample's RNAseq__HTSeqFPKM__gene_expression_quantification__txt__uuid_and_filename.
Looking at the samples table I can see this value is missing for sample 00466b6b-9fd8-4cdb-aa73-f6179d874f39 which failed.
And it's present for sample 1b2f2768-883d-46fd-80b2-bfc416584c66 which succeeded.
Most of the workflow failures for these samples are likely due to the samples not having a value in this column.
Kind regards,
Jason
Hi Jason,
Is there a fix I can implement for this?
And how might I go about tracking down the authors of this workflow?
Thanks,
Rebecca
Hi Rebecca,
To resolve this issue, the column data will have to be added or restored to the workspace. Let me speak to some colleagues to see if there's a way we can do this - I'll get back to you as soon as I can.
Kind regards,
Jason
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