rahelp
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Activity overview
Latest activity by rahelp-
rahelp commented,
Dear Samuel, Thank you for your reply. Could you send me a link on how to collect common variant sites? I was unable to find it from the link you provided before. I apologize if there is something ...
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rahelp commented,
Dear Genevieve,I checked the memory and both computer and docker have enough memory (over 200 GB). Also, the whole process is still VERY slow, creating a tmp folder did not help much.Thank you for ...
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rahelp commented,
Dear Genevieve,I have tried creating a tmp folder. It did not seem to help much. I am using the latest gatk version on docker. gatk --java-options "-Xmx200g" CollectAllelicCounts -L targets_C.p...
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rahelp commented,
Hi Genevieve!Thank you for these links. Increasing memory helped, now I can run it. However, the whole process is still extremely slow- it takes ca 20 hours to complete one sample. How long does it...
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rahelp created a post,
CollectAllelicCounts- Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
AnsweredDear GATK, I am working with the CNV pipeline. I am currently trying to get allelic counts for my samples. Here is part of the output (too long to paste the entire output): gatk) root@f64f5651979b:...
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rahelp commented,
I see now that NC_007605 is missing from the BAM file. I fixed this problem by using: java -jar picard.jar ReorderSam INPUT= test.bam OUTPUT=reordered.bam SEQUENCE_DIC...
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rahelp commented,
Dear Genevieve,Here it is with full stack trace: (gatk) root:/gatk/# gatk CollectReadCounts -I test.bam -L targets_C.preprocessed.interval_list --interval-merging-rule OVERLAPPING_ONLY ...
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rahelp commented,
Dear Genevieve, I updated the bai file with the BuildBamIndex. The warning is gone but the error remains: (gatk) root@f64f5651979b:/gatk# gatk CollectReadCounts -I test.bam -L targets_C.pre...
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rahelp created a post,
Badly formed genome unclippedLoc: Contig NC_007605 given as location, but this contig isn't present in the Fasta sequence dictionary
AnsweredHi! I'm using GATK version: broadinstitute/gatk:latest (docker). And I was trying to run CollectReadCounts for somatic CNV analysis: gatk CollectReadCounts -I 3-B.bam -L targets_C.preproces...
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rahelp commented,
Dear Genevieve, The issue was that CreateSequenceDictionary was not working properly. For it to work properly: google authentication completed Docker default memory is only 2 GB. This needs to be ...