Rachael Bay
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Activity overview
Latest activity by Rachael Bay-
Rachael Bay commented,
Hi Andrius, Sorry, this is really frustrating and I'm not sure I have a good answer for you. I did finally get it to work, but only because our lab switched to a new cluster. It then ran without an...
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Rachael Bay commented,
Genevieve Brandt (she/her) thanks, that make sense. When I run SelectVariants for Chr01:200000-201000 it stalls with no variants output.
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Rachael Bay commented,
Also, I guess I'm confused about how running SelectVariants would see anything different since it would just return a subset of the raw vcf file, right?
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Rachael Bay commented,
Genevieve Brandt (she/her) Sorry, it was a typo sort of. Just looking right now. The last position recorded for Chr01 is 199988 and for Chr03 is 199998, so not EXACTLY the same position. Let me kno...
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Rachael Bay commented,
Hi Genevieve Brandt (she/her). When I look at that region, it actually looks like the last position is 1999988. This is exactly the same across multiple chromosomes (I have tried three of six). I a...
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Rachael Bay commented,
Hi Genevieve Brandt (she/her), *I tried writing to a .gz file - same issue *The genomicsDB directory is large - looks like 793G. We have 471 individuals. *I am running on the Bridges cluster throug...
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Rachael Bay commented,
Genevieve Brandt (she/her) I have only tried the first 2 chromosomes, but they both stalled at position 200000. The jobs do not actually fail, they just stall. They reach 200000 quickly (an hour or...
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Rachael Bay commented,
Hi Genevieve Brandt (she/her), I don't think it's the location, since we stall at the exact same position (200000) when we try a different chromosome. I've also tried updating my GATK version and s...
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Rachael Bay commented,
Hi Genevieve Brandt (she/her) - thanks for the response! We've tried with up to 96G for java and both with and without the --tmp-dir option. Any other ideas?
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Rachael Bay created a post,
GenotypeGVCFs stalls while using --all-sites
AnsweredHello, I am using GATK4.1.0.0 and trying to combine GVCFs using GenotypeGVCFs. I need to genotype at all sites (not just SNPs) for popgen measures (pi, dxy). When I run without --all-sites, it runs...