-----------------------
Start of variable list:
-----------------------
Sample_ID:
GFP_1343
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/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-secondstrand
DISTANCE_BT_READ_PAIR:
-86
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Jul 17 22:14:47 EDT 2019
Running on node : scc-ka3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/Scripts/04_TopHat_Paired_End
Current job ID : 7776691
Current job name : Step_04_GFP_1343
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7776691.1.linga

Loading required modules...


Here is the Left_List:
SRR8450746_1.fastq.gz


Here is the Right_List:
SRR8450746_2.fastq.gz


List files in the scratch directory:

total 1.3G
drwx------   4 varsha97 waxmanlab 4.0K Jul 17 22:17 .
drwxrwxrwt. 15 root     root      4.0K Jul 17 22:14 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 17 22:16 Bowtie2Index
-rw-r--r--   1 varsha97 waxmanlab  72M Jul 17 22:17 RefSeq_GeneBody.gtf
-rw-r--r--   1 varsha97 waxmanlab 592M Jul 17 22:15 SRR8450746_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 607M Jul 17 22:15 SRR8450746_2.fastq.gz
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 17 22:17 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/7776691.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-secondstrand -r -86 --mate-std-dev 150 Bowtie2Index/genome SRR8450746_1.fastq.gz SRR8450746_2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 1.3G
drwx------   4 varsha97 waxmanlab  20K Jul 18 01:41 .
drwxrwxrwt. 13 root     root      4.0K Jul 18 01:58 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 17 22:16 Bowtie2Index
-rw-r--r--   1 varsha97 waxmanlab  72M Jul 17 22:17 RefSeq_GeneBody.gtf
-rw-r--r--   1 varsha97 waxmanlab 592M Jul 17 22:15 SRR8450746_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 607M Jul 17 22:15 SRR8450746_2.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab    9 Jul 18 01:41 numunique_hits.txt
drwxr-xr-x   3 varsha97 waxmanlab 4.0K Jul 18 02:04 tophat2
==========================================================
Finished on : Thu Jul 18 02:04:20 EDT 2019
3 hours, 49 minutes and 33 seconds elapsed.
==========================================================