-----------------------
Start of variable list:
-----------------------
Sample_ID:
O_YgWT_1
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Scripts/00_Setup_Pipeline
Bowtie2Index_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/
GTF_Files_DIR:
/unprotected/projects/waxmanlab/routines/GTF_Files
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
STRANDEDNESS:
fr-firststrand
DISTANCE_BT_READ_PAIR:
-86
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Jul  3 18:58:51 EDT 2019
Running on node : scc-kb4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Scripts/04_TopHat_Paired_End
Current job ID : 7505708
Current job name : Step_04_O_YgWT_1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7505708.1.linga

Loading required modules...


Here is the Left_List:
SRR8261628_1.fastq.gz


Here is the Right_List:
SRR8261628_2.fastq.gz


List files in the scratch directory:

total 4.6G
drwx------   4 varsha97 waxmanlab 4.0K Jul  3 18:59 .
drwxrwxrwt. 11 root     root      4.0K Jul  3 18:58 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 18:59 Bowtie2Index
-rw-r--r--   1 varsha97 waxmanlab  72M Jul  3 18:59 RefSeq_GeneBody.gtf
-rw-r--r--   1 varsha97 waxmanlab 2.2G Jul  3 18:59 SRR8261628_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 2.4G Jul  3 18:59 SRR8261628_2.fastq.gz
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 18:59 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/7505708.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r -86 --mate-std-dev 150 Bowtie2Index/genome SRR8261628_1.fastq.gz SRR8261628_2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 4.6G
drwx------  4 varsha97 waxmanlab  20K Jul  4 18:07 .
drwxrwxrwt. 9 root     root      4.0K Jul  4 17:45 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul  3 18:59 Bowtie2Index
-rw-r--r--  1 varsha97 waxmanlab  72M Jul  3 18:59 RefSeq_GeneBody.gtf
-rw-r--r--  1 varsha97 waxmanlab 2.2G Jul  3 18:59 SRR8261628_1.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab 2.4G Jul  3 18:59 SRR8261628_2.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab    9 Jul  4 18:07 numunique_hits.txt
drwxr-xr-x  3 varsha97 waxmanlab 4.0K Jul  4 18:37 tophat2
==========================================================
Finished on : Thu Jul  4 18:37:39 EDT 2019
23 hours, 38 minutes and 48 seconds elapsed.
==========================================================