-----------------------
Start of variable list:
-----------------------
Sample_ID:
1_Liver_High_20
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/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 14:34:18 EDT 2019
Running on node : scc-ka4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/04_TopHat_Paired_End
Current job ID : 7502953
Current job name : Step_04_1_Liver_High_20
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7502953.1.linga

Loading required modules...


Here is the Left_List:
SRR7585210_1.fastq.gz


Here is the Right_List:
SRR7585210_2.fastq.gz


List files in the scratch directory:

total 532M
drwx------  4 varsha97 waxmanlab 4.0K Jul  3 14:45 .
drwxrwxrwt. 8 root     root      4.0K Jul  3 14:34 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul  3 14:44 Bowtie2Index
-rw-r--r--  1 varsha97 waxmanlab  72M Jul  3 14:45 RefSeq_GeneBody.gtf
-rw-r--r--  1 varsha97 waxmanlab 239M Jul  3 14:34 SRR7585210_1.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab 222M Jul  3 14:35 SRR7585210_2.fastq.gz
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul  3 14:45 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/7502953.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r -86 --mate-std-dev 150 Bowtie2Index/genome SRR7585210_1.fastq.gz SRR7585210_2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 532M
drwx------  4 varsha97 waxmanlab 4.0K Jul  3 15:42 .
drwxrwxrwt. 8 root     root      4.0K Jul  3 15:38 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul  3 14:44 Bowtie2Index
-rw-r--r--  1 varsha97 waxmanlab  72M Jul  3 14:45 RefSeq_GeneBody.gtf
-rw-r--r--  1 varsha97 waxmanlab 239M Jul  3 14:34 SRR7585210_1.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab 222M Jul  3 14:35 SRR7585210_2.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab    8 Jul  3 15:42 numunique_hits.txt
drwxr-xr-x  3 varsha97 waxmanlab 4.0K Jul  3 15:47 tophat2
==========================================================
Finished on : Wed Jul  3 15:47:55 EDT 2019
1 hours, 13 minutes and 37 seconds elapsed.
==========================================================