# See problematic frame for where to report the bug. # The crash happened outside the Java Virtual Machine in native code. # If you would like to submit a bug report, please visit: Default location: /cores/core or core.3931 # Java VM: Java HotSpot(TM) 64-Bit Server VM (25.161-b12 mixed mode bsd-amd64 ) The fatal error is: # A fatal error has been detected by the Java Runtime Environment: I had edited the fastq headers to the standard format prior using awk and tr. ![]() ![]() is derived from paired read fastq files converted to an unaligned bam using FastqToSam. I am encountering a fatal error when I run the PathSeqPipeline tool using GATK 4.1.4.1 and the following command: /Users/jude/gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar PathSeqPipelineSpark -I -filter-bwa-image //Users/jude/GRCh38.primary_ -kmer-file //Users/jude/GRCh38.hss -min-clipped-read-length 70 -microbe-fasta //Users/jude//gatk-4.1.4.1/pathseq_microbe.fa -microbe-bwa-image //Users/jude//gatk-4.1.4.1/pathseq_microbe.fa.img -taxonomy-file //Users/jude//gatk-4.1.4.1/pathseq_taxonomy.db -output //Users/jude/RNAseq/SplitNCigarReads/ -scores-output //Users/jude/RNAseq/SplitNCigarReads/
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