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