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CRG-CNAG / CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow
Mozilla Public License 2.0
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Error: Unable to access jarfile /scratch/oknjav001/transcriptomics/proteogenomics/variabtcalling/gatk/gatk3.7/GenomeAnalysisTK.jar #18

Closed Jokendo-collab closed 4 years ago

Jokendo-collab commented 4 years ago

I am getting the following error. Can you please help with this Error executing process > '3_rnaseq_gatk_splitNcigar (rep1)'

Caused by: Process 3_rnaseq_gatk_splitNcigar (rep1) terminated with an error exit status (1)

Command executed:

SplitNCigarReads and reassign mapping qualities

java -jar /scratch/oknjav001/transcriptomics/proteogenomics/variabtcalling/gatk/gatk3.7/GenomeAnalysisTK.jar -T SplitNCigarReads -R genome.fa -I Aligned.sortedByCoord.out.bam -o spli t.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS --fix_misencoded_quality_scores

Command exit status: 1

Command output: (empty)

Command error: Error: Unable to access jarfile /scratch/oknjav001/transcriptomics/proteogenomics/variabtcalling/gatk/gatk3.7/GenomeAnalysisTK.jar

Work dir: /scratch/oknjav001/transcriptomics/proteogenomics/analscripts/work/84/39ebb85b80c6ec21edc450c6f70222

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

pditommaso commented 4 years ago

In the latest version GATK (4.1) binary is included in the container. Therefore this error should not happen anymore.