2016/11/06 11:52:12: DEBUG Enqueuing command:
#TASK tags=Sample_5
mkdir -p /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk && \
gatk -T IndelRealigner \
-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/picard/Sample_5_withrg.csorted.cleaned.aligned.bam \
-targetIntervals /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_realignment_targets.list \
-o /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/gatk/Sample_5_realigned.withrg.csorted.cleaned.aligned.bam
2016/11/06 11:53:46: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 01 minutes, 34 seconds