User: bioinformatics98

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Posts by bioinformatics98

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Failed to find GenomeAnalysisTKLite.jar file
... Hi everyone, I am trying to run the seqmule pipeline without GATKLite (I want the pipeline to use the full GATK instead) -- I have already removed any command asking for gatklite in the advanced config file of seqmule, however I keep getting this error: [ => SeqMule Execution Status: Runnin ...
seqmule gatklite gatk written 13 hours ago by bioinformatics980
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Comment: C: seqmule gatk vcfv4.2 error
... Here you go: JOBID=0 PID=1863 command=/home/CSTR/user/softwares/seqmule/bin/secondary/../../bin/secondary/worker /home/CSTR/user/data/sample/seqmule.02092020.57459.logs 31 "/home/CSTR/user/softwares/seqmule/bin/secondary/../../bin/seqmule stats -tmpdir /tmp -ref /home/FCAM/CSTR/user/softwares/seqmu ...
written 3 days ago by bioinformatics980
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Comment: A: seqmule gatk vcfv4.2 error
... The pipeline is requiring me to use GATKlite -- is there a way I can force it to use GATK instead? ...
written 3 days ago by bioinformatics980
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Comment: C: seqmule gatk vcfv4.2 error
... Ah! Thank you so much! The pipeline is requiring me to use GATKlite (v.2.3-9) -- is there a way I can force it to use GATK instead? ...
written 3 days ago by bioinformatics980
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seqmule gatk vcfv4.2 error
... Hi, I am getting this error -- and help will be much appreciated! Thank you! WARN 11:52:36,188 RestStorageService - Error Response: PUT '/GATK_Run_Reports/8Mxwpij5zPxCjkgJ3V61ne1iu4GHg824.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 837, Conten ...
vcf seqmule written 4 days ago by bioinformatics980
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Seqmule Error - Failed to find vcf stats
... Hi, I keep getting this issue in seqmule: ERROR: Failed to find vcf-stats. Please use 'cd /home/CLSTR/user/software/seqmule/bin/secondary/../..' and then './Build installexes' Progams in your PATH are NOT used by SeqMule. at /home/CLSTR/user/software/seqmule/bin/secondar ...
seqmule written 7 days ago by bioinformatics980 • updated 7 days ago by Pierre Lindenbaum126k

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