Aspen Neuro
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Latest activity by Aspen Neuro
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Aspen Neuro commented,
Hi Sushma, I've solved my issue when thinking about your suggestion that the last shard was computationally intensive. I looked back at a previous Mutect2 PON workflow I ran last year, and reali...
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Aspen Neuro created a post,
shard-9 consistently failing on Mutect2 PON creation
Hello, I've been trying to run the recommended Mutect2-PON workflow on 10 WGS samples, and the job is failing ONLY on the last shard (shard-9) of every M2 call, for all 10 M2 calls spawned from ...
- Aspen Neuro
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Aspen Neuro commented,
Hello Tiffany, I fixed the issue. It turns out the stderr file was truncated for many of the jobs, and the full stderr file can be found in some of the later failed runs. <...>INFO 2019-07-04 1...
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Aspen Neuro commented,
Hello Tiffany, That submission ID works, you can also look at 32928054-6abf-4275-ae63-c1f84fca4f51 as well. I ran a diff on the newest version of the tool, and the WDL file is identical to the o...
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Aspen Neuro created a post,
IO Error while running MergeBamAlignment on Terra
Hello, I'm currently running a sample through snapshot 8 of the "processing-for-variant-discovery-gatk4" workflow on Terra, and I'm consistently hitting the following error on the MergeBamAlignment...
- Aspen Neuro
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- 6 comments
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Aspen Neuro commented,
Thank you! That fix worked for me.
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Aspen Neuro commented,
Woops, forgot to include it. It is "pd-wgs-workspace", in the project "pd-wgs-project".
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Aspen Neuro created a post,
SortAndFixTags FileTruncatedException error
I've been running WGS samples through the "processing-for-variant-discovery-gatk4" workflow (snapshot 8). I've noticed that my samples consistently fail at the SortAndFixTags step, with the same er...
- Aspen Neuro
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- 4 comments
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