Jenny Xu
- Total activity 17
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Activity overview
Latest activity by Jenny Xu-
Jenny Xu commented,
Hi Bob, thank you for the suggestion. By increasing the -h_vmem within jobNative parameter the job completes. The ticket can be closed now.
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Jenny Xu commented,
Hi Bob, Here's the extracted related log file (number 13). I'd appreciate if you can help diagnosis of cause of error. Thank you.ERROR 11:27:49,881 FunctionEdge - Error: 'java' '-Xmx3072m' '-XX:+Us...
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Jenny Xu commented,
Hi Bob, thanks for the detailed explanation and it makes total sense. Besides these suggestion, could you help troubleshoot - I am stuck (tried multiple times) at stage10 and the error message is u...
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Jenny Xu commented,
Hi Bob, I have found out the invalid interval error is caused because in the previous SVPreprocess step I specified only a small region using -L chrXX:start_end, yet CNV -intervalList can only acce...
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Jenny Xu commented,
HI Bob, After I added both -jobRunner and -gatkJobrunner Drmaa, it solves the lsf error. However, there are new errors complaining "invalid intervals", though I think those intervals are legitimate...
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Jenny Xu created a post,
GenomeSTRiP CNVDiscoveryPipeline failed
AnsweredI am running the CVN pipeline commands on our HPC clusters, got error around lsf library - not sure if this is something I can solve since our clusters use sge and I don't have cluster admin permis...
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Jenny Xu commented,
Thanks Bob. Adding the LB tag in the header solves the issue.
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Jenny Xu created a post,
GenomeSTRiP SVPreprocess failed
AnsweredDear Forum member I downloaded latest version of GenomeStrip (Release 2.00.1982) and trying to run SVPreprocess on my genome files samples. I kept getting error about "Cannot determine library iden...
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Jenny Xu commented,
Sure, command line like this: /path/to/gatk GenotypeConcordance --TRUTH_VCF truth.vcf.gz --CALL_VCF call.vcf.gz --OUTPUT test.out --TRUTH_SAMPLE truth_id --CALL_SAMPLE call_id --INTERVALS target.in...
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Jenny Xu created a post,
[BUG] genotypceConcordance output details hom_ref:hom_ref combination of status is wrong
Hi, using gatk 4.1.2.0 genotypeconcordance tool, I found in the output details file, the hom_ref, hom_ref state count is always 0, which is incorrect. My input are array-based genotyping converted...