-----------------------
Start of variable list:
-----------------------
Sample_ID:
WT_3
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116_fullpipeline_run
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116_fullpipeline_run/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 18:56:43 EDT 2019
Running on node : scc-ka4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116_fullpipeline_run/Scripts/04_TopHat_Paired_End
Current job ID : 7775059
Current job name : Step_04_WT_3
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7775059.1.linga

Loading required modules...


Here is the Left_List:
SRR8261640_1.fastq.gz


Here is the Right_List:
SRR8261640_2.fastq.gz


List files in the scratch directory:

total 8.9G
drwx------   4 varsha97 waxmanlab 4.0K Jul 17 19:14 .
drwxrwxrwt. 15 root     root      4.0K Jul 17 18:56 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 17 19:13 Bowtie2Index
-rw-r--r--   1 varsha97 waxmanlab  72M Jul 17 19:14 RefSeq_GeneBody.gtf
-rw-r--r--   1 varsha97 waxmanlab 4.2G Jul 17 19:06 SRR8261640_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 4.7G Jul 17 19:12 SRR8261640_2.fastq.gz
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 17 19:14 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/7775059.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r -86 --mate-std-dev 150 Bowtie2Index/genome SRR8261640_1.fastq.gz SRR8261640_2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 8.9G
drwx------  4 varsha97 waxmanlab  36K Jul 19 04:22 .
drwxrwxrwt. 8 root     root      4.0K Jul 19 00:42 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul 17 19:13 Bowtie2Index
-rw-r--r--  1 varsha97 waxmanlab  72M Jul 17 19:14 RefSeq_GeneBody.gtf
-rw-r--r--  1 varsha97 waxmanlab 4.2G Jul 17 19:06 SRR8261640_1.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab 4.7G Jul 17 19:12 SRR8261640_2.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab    9 Jul 19 04:22 numunique_hits.txt
drwxr-xr-x  3 varsha97 waxmanlab 4.0K Jul 19 05:38 tophat2
==========================================================
Finished on : Fri Jul 19 05:38:46 EDT 2019
34 hours, 42 minutes and 4 seconds elapsed.
==========================================================