-----------------------
Start of variable list:
-----------------------
Sample_ID:
CHOW3
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/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 Jun 26 15:01:58 EDT 2019
Running on node : scc-ka4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/Scripts/04_TopHat_Paired_End
Current job ID : 7076170
Current job name : Step_04_CHOW3
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7076170.1.linga

Loading required modules...


Here is the Left_List:
SRR8543821_1.fastq.gz


Here is the Right_List:
SRR8543821_2.fastq.gz


List files in the scratch directory:

total 2.3G
drwx------   4 varsha97 waxmanlab 4.0K Jun 26 15:03 .
drwxrwxrwt. 11 root     root      4.0K Jun 26 15:01 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 26 15:03 Bowtie2Index
-rw-r--r--   1 varsha97 waxmanlab  72M Jun 26 15:03 RefSeq_GeneBody.gtf
-rw-r--r--   1 varsha97 waxmanlab 1.1G Jun 26 15:02 SRR8543821_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 1.2G Jun 26 15:02 SRR8543821_2.fastq.gz
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 26 15:03 tophat2

Starting to run my commands


Starting tophat

tophat --no-coverage-search -o /scratch/7076170.1.linga/tophat2 -G RefSeq_GeneBody.gtf -p 16 --library-type fr-secondstrand -r -86 --mate-std-dev 150 Bowtie2Index/genome SRR8543821_1.fastq.gz SRR8543821_2.fastq.gz

Ending tophat


Starting samtools commands


Ending samtools commands


Starting spliced_read_counts


Ending spliced_read_counts


List files in scratch

total 2.3G
drwx------   4 varsha97 waxmanlab  28K Jun 26 23:06 .
drwxrwxrwt. 11 root     root      4.0K Jun 26 23:38 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 26 15:03 Bowtie2Index
-rw-r--r--   1 varsha97 waxmanlab  72M Jun 26 15:03 RefSeq_GeneBody.gtf
-rw-r--r--   1 varsha97 waxmanlab 1.1G Jun 26 15:02 SRR8543821_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 1.2G Jun 26 15:02 SRR8543821_2.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab    9 Jun 26 23:06 numunique_hits.txt
drwxr-xr-x   3 varsha97 waxmanlab 4.0K Jun 26 23:39 tophat2
==========================================================
Finished on : Wed Jun 26 23:40:12 EDT 2019
8 hours, 38 minutes and 14 seconds elapsed.
==========================================================