Xscrapert
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Latest activity by Xscrapert-
Xscrapert commented,
Dear Lee, Thank you for your advice. I found a suggestion to tune the env variables OMP_NUM_THREADS and MKL_NUM_THREADS in a legacy discussion post on the GATK forum. I tried to limit the number to...
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Xscrapert commented,
In addition, I found that the CPUs are occupied by the same temporary python script to perform determine_ploidy/denoising in DetermineGermlinePloidy/GermlineCNVCaller, as shown below: I wonder wha...
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Xscrapert commented,
I want to supplement some information here. I found out that the actual GATK version I'm using is 4.3.0.0 and I tried to use gatk binary directly downloaded from the official website instead of the...
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Xscrapert created a post,
GermlineCNVCaller in CASE mode using too many CPU for denoising
AnsweredREQUIRED for all errors and issues: Found the denoising process in GermlineCNVCaller CASE mode using a lot of CPUs. Which is quite odd because no parallelism parameters are set when commanding GATK...
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Xscrapert created a post,
GermlineCNVCaller Assertion Error: Some samples do not have read depth metadata
As stated in the subject, I encounter the no sample depth metadata error. I found a legacy discussion about this in GATK forum here: https://sites.google.com/a/broadinstitute.org/legacy-gatk-foru...