Riad Hajdarevic
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Activity overview
Latest activity by Riad Hajdarevic-
Riad Hajdarevic commented,
Its me again, just adding info. So what I did I used the older version of the gnomAD data. The gnomADv2liftover to b38 instead of the gnomADv3 and it does around 7500 variants per minute.
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Riad Hajdarevic commented,
Hi Pamela, thank you for your time an effort. I run VariantAnnotator with a dbSnp file and it went quite fast. It seems that it only slows down when I use gnomAD vcf files for annotation. I hope t...
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Riad Hajdarevic commented,
Hi sorry that was a typo I didnt see. I put it on 16G now and It works very slow again. No error so far, but I can see on the generated output file that it goes very slow.
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Riad Hajdarevic commented,
Hi Pamela, thank you for your quick reply. Now it says I am out of memory. with this error message. The gnomAD annotation files are quite big is that maybe the reason? There is insufficient memory ...
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Riad Hajdarevic commented,
Hi Pamel there are 3 samples only (a family). I allocated 30G of memory to it ( I have 32 in total). here is the jstack output. Thank you! hreads class SMR info:_java_thread_list=0x00007fb878000c...
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Riad Hajdarevic commented,
Hi everyone I am having similar issues while trying to annotate my file with the gnomAD database. I am not using a bam file as additional input. It takes around 5 hours for one CHR. I am using GAT...