-----------------------
Start of variable list:
-----------------------
Sample_ID:
3_Liver_Low_3h
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
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Jul  9 11:50:40 EDT 2019
Running on node : scc-tk2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/05_Read_Strandness
Current job ID : 7623049
Current job name : Step_05_3_Liver_Low_3h
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7623049.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 322M
drwx------  3 varsha97 waxmanlab 4.0K Jul  9 11:51 .
drwxrwxrwt. 5 root     root      4.0K Jul  9 11:50 ..
-rw-r--r--  1 varsha97 waxmanlab 317M Jul  9 11:51 3_Liver_Low_3h_primary_unique.bam
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul  9 11:51 Read_Strandness
-rwxr-xr-x  1 varsha97 waxmanlab 5.0M Jul  9 11:51 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=3_Liver_Low_3h_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/3_Liver_Low_3h_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is PairEnd Data
Fraction of reads failed to determine: 0.0105
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0045
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9850

Copy output to storage dir


List files in scratch

total 322M
drwx------  3 varsha97 waxmanlab 4.0K Jul  9 11:51 .
drwxrwxrwt. 5 root     root      4.0K Jul  9 11:50 ..
-rw-r--r--  1 varsha97 waxmanlab 317M Jul  9 11:51 3_Liver_Low_3h_primary_unique.bam
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul  9 11:51 Read_Strandness
-rwxr-xr-x  1 varsha97 waxmanlab 5.0M Jul  9 11:51 mm9.refseq.bed
==========================================================
Finished on : Tue Jul  9 11:51:26 EDT 2019
0 hours, 0 minutes and 47 seconds elapsed.
==========================================================