-----------------------
Start of variable list:
-----------------------
Sample_ID:
MANFHet_4
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/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 : Sat Jul 13 02:46:20 EDT 2019
Running on node : scc-ph4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/Scripts/04_TopHat_Paired_End
Current job ID : 7682060
Current job name : Step_04_MANFHet_4
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7682060.1.p16

Loading required modules...


Here is the Left_List:
SRR8261645_1.fastq.gz


Here is the Right_List:
SRR8261645_2.fastq.gz


List files in the scratch directory:

total 12G
drwx------   4 varsha97 waxmanlab 4.0K Jul 13 02:49 .
drwxrwxrwt. 12 root     root      4.0K Jul 13 02:46 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 13 02:48 Bowtie2Index
-rw-r--r--   1 varsha97 waxmanlab  72M Jul 13 02:49 RefSeq_GeneBody.gtf
-rw-r--r--   1 varsha97 waxmanlab 5.4G Jul 13 02:47 SRR8261645_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 6.0G Jul 13 02:48 SRR8261645_2.fastq.gz
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 13 02:49 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/7682060.1.p16/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r -86 --mate-std-dev 150 Bowtie2Index/genome SRR8261645_1.fastq.gz SRR8261645_2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 12G
drwx------   4 varsha97 waxmanlab  40K Jul 13 20:04 .
drwxrwxrwt. 12 root     root      4.0K Jul 13 02:46 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 13 02:48 Bowtie2Index
-rw-r--r--   1 varsha97 waxmanlab  72M Jul 13 02:49 RefSeq_GeneBody.gtf
-rw-r--r--   1 varsha97 waxmanlab 5.4G Jul 13 02:47 SRR8261645_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 6.0G Jul 13 02:48 SRR8261645_2.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab    9 Jul 13 20:04 numunique_hits.txt
drwxr-xr-x   3 varsha97 waxmanlab 4.0K Jul 13 21:04 tophat2
==========================================================
Finished on : Sat Jul 13 21:05:32 EDT 2019
18 hours, 19 minutes and 12 seconds elapsed.
==========================================================