Louis Bergelson
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Activity overview
Latest activity by Louis Bergelson-
Louis Bergelson commented,
So we bundle snappy with Picard and it includes native code for a lot of different platforms. Do you know if your machines are x86/64 or if they're some sort of ARM machine? I don't think you'll ...
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Louis Bergelson commented,
Hello, I'm not sure what's causing this exactly. What sort of machines is your cluster using? I'm assuming they're not x64 machines since the intel libraries also aren't loading. I don't know ex...
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Louis Bergelson commented,
I would expect Hamsters have pretty standard mammalian diploid genomes. It looks like you're references have a lot of contigs. 250k/100k are many more than we usually use with a human genome. I...
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Louis Bergelson commented,
gabriele tosadori Based on the free stats you posted it looks like you're allocating more memory to java than you have available. I believe "available" is the amount of memory you are able to allo...
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Louis Bergelson commented,
Hi Salma H. Elaksher, I think you're saying that your output vcf is missing rsID tags for known variants? If you want those added to your file when doing GenotypeGvcfs, you have to include the --d...
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Louis Bergelson commented,
Hi Lindo Nkambule, Sorry you're running into problems. Generally I would expect to need around ~3x the size of the bam in disk space too do an operation that involves a sort. 1x to store the orig...
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Louis Bergelson commented,
This sort of sudden failure is often caused by running out of memory. It can result in the process being killed without any message. It's necessary to leave some memory for non-heap memory also. ...
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Louis Bergelson commented,
That sounds like a pretty normal process. It's not the one we use, but nothing particularly strange. I'm glad you have a good workaround.
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Louis Bergelson commented,
Disabling the indexing is a good idea. However, in this case I believe the problem is during the creation of the specialized spark splitting index which is disabled by this argument instead: --cr...
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Louis Bergelson commented,
Hello, We're not sure what this issue is, the main funcotator developer is currently out of the office with a new baby. We'll get this on his radar when he gets back if no one can diagnose it befo...