2016/11/06 09:51:23: DEBUG Enqueuing command:
#TASK tags=Sample_5
samtools mpileup -ugf /scratch/Reference_Genomes/Public/Vertebrate_mammalian/Homo_sapiens/ENSEMBL-release-81-GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa \
/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.sorted.bam | bcftools call -vmO z -o \
/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.sorted.vcf.gz
2016/11/06 09:55:06: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 03 minutes, 43 seconds
2016/11/06 09:51:18: INFO Starting Job: 5
Cmd is #TASK tags=Sample_5
rm -rf /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/Sample_5_aligned.sam
2016/11/06 09:51:18: INFO Finishing job 5 with ExitCode 0
2016/11/06 09:51:18: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 00 seconds
2016/11/06 09:51:18: INFO Starting Job: 3
Cmd is #TASK tags=Sample_5
mkdir -p /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard && \
picard -Xmx2g CleanSam \
INPUT=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.bam \
O=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_cleaned.aligned.bam \
TMP_DIR=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp
2016/11/06 09:51:30: ERROR [Sun Nov 06 09:51:30 GST 2016] picard.sam.CleanSam INPUT=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.bam OUTPUT=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_cleaned.aligned.bam TMP_DIR=[/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
2016/11/06 09:51:30: ERROR [Sun Nov 06 09:51:30 GST 2016] Executing as gencore@compute-21-1.local on Linux 3.10.0-327.10.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 2.5.0(2c370988aefe41f579920c8a6a678a201c5261c1_1466708365)
2016/11/06 09:51:38: ERROR [Sun Nov 06 09:51:38 GST 2016] picard.sam.CleanSam done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=1519386624
2016/11/06 09:51:38: INFO Finishing job 3 with ExitCode 0
2016/11/06 09:51:38: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 20 seconds
2016/11/06 09:51:18: DEBUG Enqueuing command:
#TASK tags=Sample_5
rm -rf /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/Sample_5_aligned.sam
2016/11/06 09:51:18: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 00 seconds
2016/11/06 09:51:18: DEBUG Enqueuing command:
#TASK tags=Sample_5
mkdir -p /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard && \
picard -Xmx2g CleanSam \
INPUT=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.bam \
O=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/picard/Sample_5_cleaned.aligned.bam \
TMP_DIR=/scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/tmp
2016/11/06 09:51:38: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 20 seconds
2016/11/06 09:51:13: INFO Starting Job: 6
Cmd is #TASK tags=Sample_5
samtools sort -@ 6 /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.bam \
> /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.sorted.bam && \
samtools index /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.sorted.bam
2016/11/06 09:51:16: INFO Finishing job 6 with ExitCode 0
2016/11/06 09:51:16: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 03 seconds
2016/11/06 09:51:13: DEBUG Enqueuing command:
#TASK tags=Sample_5
samtools sort -@ 6 /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.bam \
> /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.sorted.bam && \
samtools index /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.sorted.bam
2016/11/06 09:51:16: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 03 seconds
2016/11/06 09:51:02: DEBUG Enqueuing command:
#TASK tags=Sample_5
mkdir -p /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools && \
samtools view -b -S /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/Sample_5_aligned.sam \
> /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.bam
2016/11/06 09:51:11: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 09 seconds
2016/11/06 09:51:02: INFO Starting Job: 2
Cmd is #TASK tags=Sample_5
mkdir -p /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools && \
samtools view -b -S /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/Sample_5_aligned.sam \
> /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/samtools/Sample_5_aligned.bam
2016/11/06 09:51:11: INFO Finishing job 2 with ExitCode 0
2016/11/06 09:51:11: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 09 seconds
|Version| Scheduler Id | Jobname | Task Tags | ProcessID | ExitCode | Duration |
|0.05|24591|002_samtools_view|Sample_5|20703|0|0 years, 00 months, 0 days, 00 hours, 00 minutes, 09 seconds|
|0.05|24595|006_samtools_sort|Sample_5|14714|0|0 years, 00 months, 0 days, 00 hours, 00 minutes, 03 seconds|
|0.05|24594|005_remove_SAM|Sample_5|21714|0|0 years, 00 months, 0 days, 00 hours, 00 minutes, 00 seconds|
|0.05|24592|003_picard_cleansam|Sample_5|21713|0|0 years, 00 months, 0 days, 00 hours, 00 minutes, 20 seconds|
|0.05|24593|004_picard_sortsam|Sample_5|22037|-1|0 years, 00 months, 0 days, 00 hours, 00 minutes, 09 seconds|
|0.05|24596|007_picard_add_or_replace_groups|Sample_5|22362|0|0 years, 00 months, 0 days, 00 hours, 00 minutes, 11 seconds|
|0.05|24598|009_picard_collect_multiple_metrics|Sample_5|22360|0|0 years, 00 months, 0 days, 00 hours, 00 minutes, 19 seconds|
|0.05|24597|008_picard_bamindex|Sample_5|22979|0|0 years, 00 months, 0 days, 00 hours, 00 minutes, 06 seconds|
|0.05|24599|010_picard_markdups|Sample_5|22982|-1|0 years, 00 months, 0 days, 00 hours, 00 minutes, 16 seconds|
|0.05|24600|011_samtools_mpileup|Sample_5|21822|0|0 years, 00 months, 0 days, 00 hours, 03 minutes, 43 seconds|
|0.05|24601|012_tabix_index|Sample_5|23755|0|0 years, 00 months, 0 days, 00 hours, 00 minutes, 01 seconds|
|0.05|24602|013_bcftools_filter|Sample_5|24080|0|0 years, 00 months, 0 days, 00 hours, 00 minutes, 00 seconds|
|0.05|24603|014_bcftools_stats|Sample_5|24083|0|0 years, 00 months, 0 days, 00 hours, 00 minutes, 04 seconds|
|0.05|24604|015_gatk_realigner_target_creator|Sample_5|23338|0|0 years, 00 months, 0 days, 00 hours, 119 minutes, 27 seconds|
|0.05|24605|016_gatk_indel_realigner|Sample_5|30992|0|0 years, 00 months, 0 days, 00 hours, 01 minutes, 34 seconds|
|0.05|24606|017_freebayes_vcf_calling|Sample_5|31705|0|0 years, 00 months, 0 days, 00 hours, 16 minutes, 10 seconds|
|0.05|24607|018_freebayes_vcffilter|Sample_5|1026|0|0 years, 00 months, 0 days, 00 hours, 00 minutes, 01 seconds|
|0.05|24608|019_gatk_haplotypecaller|Sample_5|31706|-1|0 years, 00 months, 0 days, 00 hours, 183 minutes, 37 seconds|
|0.05|24609|020_gatk_variant_filtration|Sample_5|7774|-1|0 years, 00 months, 0 days, 00 hours, 00 minutes, 04 seconds|