TCGA MC3 BAMs failing workflows
Hi,
I have been working with HG19 TCGA data held in various TCGA_{cancercode}_ControlledAccess_V1-0_DATA workspaces.
There are 209 MC3 bams that fail every workflow I run on them with an error code describing that the file is not found (attached picture). This has confused me because there is a path to a file in the workspace, but the path seems to lead to nowhere or is broken.
Here is a public google sheet of the sample ids, bam paths present in the data model(s), and workspace names that these failing samples came from.
All the best,
Sabrina
Comments
4 comments
Hi Sabrina,
Thank you for writing in, and thank you for creating that list of sample IDs. This is incredibly helpful for investigation of the issue. I will flag this up with project managers of the TCGA workspaces and get back to you as soon as I hear more from them on the status of these .bam files.
Kind regards,
Jason
Hi Sabrina,
Just to confirm, are these sample IDs distinct from the other list you've provided for investigation?
Kind regards,
Jason
Hi Jason,
Thank you for looking at this issue. These are distinct IDs from the other list I sent. However, when I looked at this list sent in this thread I did notice some with a missing bam path entirely. It appears that when I was making the list that I sent regarding samples with no paths present at all, I did not include the samples that had an "NA" entry in the data model.
Here is a revised list of the samples that have paths in the data model, but they are broken/ lead to no where. This reduces the list from 209 to 157 when I remove the "NA" bam paths.
I will update the ticket I submitted with the newly discovered "NA" bam path sample ids. Hopefully this makes sense! I attached a picture of the two different missing path scenarios that led to this mistake.
All the best,
Sabrina
Hi Sabrina,
Understood! Thank you for the explanation and revised list. I will keep an eye out for your next wave of sample IDs.
Kind regards,
Jason
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