-----------------------
Start of variable list:
-----------------------
Sample_ID:
O_YgWT_3
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 20:10:59 EDT 2019
Running on node : scc-kb2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Scripts/04_TopHat_Paired_End
Current job ID : 7505710
Current job name : Step_04_O_YgWT_3
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7505710.1.linga

Loading required modules...


Here is the Left_List:
SRR8261630_1.fastq.gz


Here is the Right_List:
SRR8261630_2.fastq.gz


List files in the scratch directory:

total 4.8G
drwx------   4 varsha97 waxmanlab 4.0K Jul  3 20:12 .
drwxrwxrwt. 10 root     root      4.0K Jul  3 20:10 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 20:11 Bowtie2Index
-rw-r--r--   1 varsha97 waxmanlab  72M Jul  3 20:11 RefSeq_GeneBody.gtf
-rw-r--r--   1 varsha97 waxmanlab 2.2G Jul  3 20:11 SRR8261630_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 2.5G Jul  3 20:11 SRR8261630_2.fastq.gz
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 20:12 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/7505710.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r -86 --mate-std-dev 150 Bowtie2Index/genome SRR8261630_1.fastq.gz SRR8261630_2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 4.8G
drwx------  4 varsha97 waxmanlab  20K Jul  4 15:20 .
drwxrwxrwt. 8 root     root      4.0K Jul  4 15:46 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul  3 20:11 Bowtie2Index
-rw-r--r--  1 varsha97 waxmanlab  72M Jul  3 20:11 RefSeq_GeneBody.gtf
-rw-r--r--  1 varsha97 waxmanlab 2.2G Jul  3 20:11 SRR8261630_1.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab 2.5G Jul  3 20:11 SRR8261630_2.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab    9 Jul  4 15:20 numunique_hits.txt
drwxr-xr-x  3 varsha97 waxmanlab 4.0K Jul  4 15:56 tophat2
==========================================================
Finished on : Thu Jul  4 15:57:13 EDT 2019
19 hours, 46 minutes and 14 seconds elapsed.
==========================================================