-----------------------
Start of variable list:
-----------------------
Sample_ID:
WT_2
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Jul 16 15:39:28 EDT 2019
Running on node : scc-ka6
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/Scripts/05_Read_Strandness
Current job ID : 7740360
Current job name : Step_05_WT_2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7740360.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 3.1G
drwx------   3 varsha97 waxmanlab 4.0K Jul 16 15:41 .
drwxrwxrwt. 10 root     root      4.0K Jul 16 15:39 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul 16 15:41 Read_Strandness
-rw-r--r--   1 varsha97 waxmanlab 3.1G Jul 16 15:41 WT_2_primary_unique.bam
-rwxr-xr-x   1 varsha97 waxmanlab 5.0M Jul 16 15:41 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=WT_2_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/WT_2_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is PairEnd Data
Fraction of reads failed to determine: 0.0193
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0079
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9729

Copy output to storage dir


List files in scratch

total 3.1G
drwx------  3 varsha97 waxmanlab 4.0K Jul 16 15:41 .
drwxrwxrwt. 9 root     root      4.0K Jul 16 15:41 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul 16 15:41 Read_Strandness
-rw-r--r--  1 varsha97 waxmanlab 3.1G Jul 16 15:41 WT_2_primary_unique.bam
-rwxr-xr-x  1 varsha97 waxmanlab 5.0M Jul 16 15:41 mm9.refseq.bed
==========================================================
Finished on : Tue Jul 16 15:41:33 EDT 2019
0 hours, 2 minutes and 5 seconds elapsed.
==========================================================