-----------------------
Start of variable list:
-----------------------
Sample_ID:
LRH-APAPL3
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/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 17 22:25:34 EDT 2019
Running on node : scc-kb4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/Scripts/04_TopHat_Paired_End
Current job ID : 7776706
Current job name : Step_04_LRH-APAPL3
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7776706.1.linga

Loading required modules...


Here is the Left_List:
SRR6080073_1.fastq.gz


Here is the Right_List:
SRR6080073_2.fastq.gz


List files in the scratch directory:

total 4.0G
drwx------   4 varsha97 waxmanlab 4.0K Jul 17 22:28 .
drwxrwxrwt. 10 root     root      4.0K Jul 17 22:27 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 17 22:27 Bowtie2Index
-rw-r--r--   1 varsha97 waxmanlab  72M Jul 17 22:28 RefSeq_GeneBody.gtf
-rwxr-xr-x   1 varsha97 waxmanlab 2.5G Jul 17 22:26 SRR6080073_1.fastq.gz
-rwxr-xr-x   1 varsha97 waxmanlab 1.4G Jul 17 22:26 SRR6080073_2.fastq.gz
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 17 22:28 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/7776706.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r -86 --mate-std-dev 150 Bowtie2Index/genome SRR6080073_1.fastq.gz SRR6080073_2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 4.0G
drwx------   4 varsha97 waxmanlab  20K Jul 18 02:23 .
drwxrwxrwt. 10 root     root      4.0K Jul 18 01:59 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 17 22:27 Bowtie2Index
-rw-r--r--   1 varsha97 waxmanlab  72M Jul 17 22:28 RefSeq_GeneBody.gtf
-rwxr-xr-x   1 varsha97 waxmanlab 2.5G Jul 17 22:26 SRR6080073_1.fastq.gz
-rwxr-xr-x   1 varsha97 waxmanlab 1.4G Jul 17 22:26 SRR6080073_2.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab    9 Jul 18 02:23 numunique_hits.txt
drwxr-xr-x   3 varsha97 waxmanlab 4.0K Jul 18 03:04 tophat2
==========================================================
Finished on : Thu Jul 18 03:05:30 EDT 2019
4 hours, 39 minutes and 56 seconds elapsed.
==========================================================