Environment

Modules

1

NYUAD/3.0:gencore/1:gencore_dev/1.0:gencore_variant_detection/1.0

Path

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/scratch/gencore/.local/easybuild/software/gencore_variant_detection/1.0/sbin
/scratch/gencore/.local/easybuild/software/gencore_variant_detection/1.0/bin
/scratch/gencore/.local/easybuild/software/gencore_dev/1.0/bin
/scratch/gencore/.local/environment-modules/Modules/3.2.10/bin
/home/gencore/bin
/usr/local/bin
/usr/bin
/usr/local/sbin
/usr/sbin
/opt/ibutils/bin
/opt/slurm/default/bin
/opt/slurm/default/sbin
/scratch/gencore/software/MOCAT/src
/scratch/gencore/software/MOCAT/src

Git Things

Current branch: master
Current version: 0.05

DateTime: 2016-11-06T09:50:42

ProcessID: 14452

SchedulerID: 24590

2016/11/06 09:50:42: INFO Starting Job: 1
Cmd is #TASK tags=Sample_5
mkdir -p /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2 && \
bowtie2 -p 12 -x /scratch/Reference_Genomes/Public/Vertebrate_mammalian/Homo_sapiens/ENSEMBL-release-81-GRCh38/Homo_sapiens.GRCh38.dna.toplevel \
-1 /scratch/gencore/nov_dalma_training/resequencing/data/processed/Sample_5/trimmomatic/Sample_5_read1_trimmomatic_1PE.gz \
-2 /scratch/gencore/nov_dalma_training/resequencing/data/processed/Sample_5/trimmomatic/Sample_5_read2_trimmomatic_2PE.gz \
-S /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/Sample_5_aligned.sam
2016/11/06 09:50:55: ERROR 120078 reads; of these:
120078 (100.00%) were paired; of these:
9461 (7.88%) aligned concordantly 0 times
92428 (76.97%) aligned concordantly exactly 1 time

18189 (15.15%) aligned concordantly >1 times
----
9461 pairs aligned concordantly 0 times; of these:
  6684 (70.65%) aligned discordantly 1 time
----
2777 pairs aligned 0 times concordantly or discordantly; of these:
  5554 mates make up the pairs; of these:
    1743 (31.38%) aligned 0 times
    893 (16.08%) aligned exactly 1 time
    2918 (52.54%) aligned >1 times

99.27% overall alignment rate
2016/11/06 09:50:55: INFO Finishing job 1 with ExitCode 0
2016/11/06 09:50:55: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 13 seconds

DateTime: 2016-11-06T09:50:42

SchedulerID: 24590

2016/11/06 09:50:42: DEBUG Enqueuing command:

#TASK tags=Sample_5

mkdir -p /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2 && \
bowtie2 -p 12 -x /scratch/Reference_Genomes/Public/Vertebrate_mammalian/Homo_sapiens/ENSEMBL-release-81-GRCh38/Homo_sapiens.GRCh38.dna.toplevel \
-1 /scratch/gencore/nov_dalma_training/resequencing/data/processed/Sample_5/trimmomatic/Sample_5_read1_trimmomatic_1PE.gz \
-2 /scratch/gencore/nov_dalma_training/resequencing/data/processed/Sample_5/trimmomatic/Sample_5_read2_trimmomatic_2PE.gz \
-S /scratch/gencore/nov_dalma_training/resequencing/data/analysis/Sample_5/bowtie2/Sample_5_aligned.sam
2016/11/06 09:50:55: INFO Total execution time 0 years, 00 months, 0 days, 00 hours, 00 minutes, 13 seconds