gabriele tosadori
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Latest activity by gabriele tosadori-
gabriele tosadori commented,
Louis Bergelson, thanks for your replies and thanks for the reference. however, i am not sure whether we can actually use that genome, or others that are available, for the task. i am working with ...
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gabriele tosadori commented,
Louis Bergelson, the organism is actually the hamster (cho cells). I dont think it is a complex genome, but i may be wrong. Not sure if it is connected but the files provided by ncbi have some issu...
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gabriele tosadori commented,
i am running it in a local machine. this is the output you requested: total used free shared buff/cache availableMem: 78Gi 20Gi ...
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gabriele tosadori commented,
Gökalp Çelik fun fact: even if i use the gatk container provided by gatk itself...it is not working. i had the same error, again:> [March 16, 2024 8:48:47 AM UTC] org.broadinstitute.hellbender.tool...
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gabriele tosadori commented,
Gökalp Çelik, i am afraid it doesn't help much. if i set it to 4gb it explodes in no time. even with 32gb it is unable to finish. i also tried 64gb same problem. the machine i am working with has 7...
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gabriele tosadori commented,
Louis Bergelson, i am trying to make mutect2 work. i am running an analysis for somatic mutation with tumor and normal genome (see first post here). I changed the call to mutect to: ./gatk --java-o...
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gabriele tosadori commented,
Can Kockan, yes it worked indeed. Well, at least i think it did. Is it correct if the last line mutect2 prints is something like this: 10:13:08.683 INFO ProgressMeter - NW_003613915.1:1166429 ...
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gabriele tosadori commented,
I am having a very similar problem, except it takes more than 2hs to show up. If needed, i am running the script using: openjdk 17.0.9 2023-10-17OpenJDK Runtime Environment (build 17.0.9+9-Ubuntu-...