-----------------------
Start of variable list:
-----------------------
Sample_ID:
IC57-1169
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/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 : Mon Jun 24 22:47:43 EDT 2019
Running on node : scc-ca6
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/Scripts/04_TopHat_Paired_End
Current job ID : 7056812
Current job name : Step_04_IC57-1169
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7056812.1.c

Loading required modules...


Here is the Left_List:
SRR6833772_1.fastq.gz


Here is the Right_List:
SRR6833772_2.fastq.gz


List files in the scratch directory:

total 879M
drwx------  4 varsha97 waxmanlab 4.0K Jun 24 22:47 .
drwxrwxrwt. 7 root     root      4.0K Jun 24 22:47 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jun 24 22:47 Bowtie2Index
-rw-r--r--  1 varsha97 waxmanlab  72M Jun 24 22:47 RefSeq_GeneBody.gtf
-rw-r--r--  1 varsha97 waxmanlab 393M Jun 24 22:47 SRR6833772_1.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab 416M Jun 24 22:47 SRR6833772_2.fastq.gz
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jun 24 22:47 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/7056812.1.c/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-firststrand -r -86 --mate-std-dev 150 Bowtie2Index/genome SRR6833772_1.fastq.gz SRR6833772_2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 879M
drwx------  4 varsha97 waxmanlab  20K Jun 24 23:31 .
drwxrwxrwt. 7 root     root      4.0K Jun 24 22:47 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jun 24 22:47 Bowtie2Index
-rw-r--r--  1 varsha97 waxmanlab  72M Jun 24 22:47 RefSeq_GeneBody.gtf
-rw-r--r--  1 varsha97 waxmanlab 393M Jun 24 22:47 SRR6833772_1.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab 416M Jun 24 22:47 SRR6833772_2.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab    9 Jun 24 23:31 numunique_hits.txt
drwxr-xr-x  3 varsha97 waxmanlab 4.0K Jun 24 23:40 tophat2
==========================================================
Finished on : Mon Jun 24 23:40:55 EDT 2019
0 hours, 53 minutes and 12 seconds elapsed.
==========================================================