020_gatk_variant_filtration CMD_020

DateTime: 2016-11-06T14:57:44

ProcessID: 7774

SchedulerID: 24609

2016/11/06 14:57:44: INFO Starting Job: 20
Cmd is #TASK tags=Sample_5
gatk -T VariantFiltration \
-R /scratch/Reference_Genomes/Public/Vertebrate_mammalian/Homo_sapiens/ENSEMBL-release-81-GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa \
-I /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_haplotype.realigned.withrg.csorted.cleaned.aligned.vcf \
–filterExpression “QD ‘<’ 2.0 || FS ‘>’ 60.0 || MQ ‘<’ 40.0 || MQRankSum ‘<’ -12.5 || ReadPosRankSum ‘<’ -8.0” \
–filterName “my_snp_filter” \
-o /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_my_snp_filter.haplotype.realigned.mdup.csorted.cleaned.aligned.vcf
2016/11/06 14:57:48: ERROR ##### ERROR ——————————————————————————————
2016/11/06 14:57:48: ERROR

ERROR A USER ERROR has occurred (version 3.5-0-g36282e4):

ERROR

ERROR This means that one or more arguments or inputs in your command are incorrect.

ERROR The error message below tells you what is the problem.

ERROR

ERROR If the problem is an invalid argument, please check the online documentation guide

ERROR (or rerun your command with –help) to view allowable command-line arguments for this tool.

ERROR

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions http://www.broadinstitute.org/gatk

ERROR

ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.

ERROR

ERROR MESSAGE: Invalid argument value ‘<’ at position 8.

ERROR Invalid argument value ‘2.0’ at position 9.

ERROR ——————————————————————————————

2016/11/06 14:57:48: ERROR /scratch/gencore/.local/easybuild/software/gencore_variant_detection/1.0/bin/gatk: line 67: FS: command not found
2016/11/06 14:57:48: ERROR /scratch/gencore/.local/easybuild/software/gencore_variant_detection/1.0/bin/gatk: line 67: MQ: command not found
2016/11/06 14:57:48: ERROR /scratch/gencore/.local/easybuild/software/gencore_variant_detection/1.0/bin/gatk: line 67: MQRankSum: command not found
2016/11/06 14:57:48: ERROR /scratch/gencore/.local/easybuild/software/gencore_variant_detection/1.0/bin/gatk: line 67: ReadPosRankSum: command not found
2016/11/06 14:57:48: INFO Finishing job 20 with ExitCode -1
2016/11/06 14:57:48: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 04 seconds