-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M3
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Dec  7 18:45:35 EST 2018
Running on node : scc-tm3
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/05_Read_Strandness
Current job ID : 27126
Current job name : Step_05_G123_M3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/27126.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 1.2G
drwx------   3 kkarri waxmanlab 4.0K Dec  7 18:45 .
drwxrwxrwt. 22 root   root       36K Dec  7 18:45 ..
-rw-r--r--   1 kkarri waxmanlab 1.2G Dec  7 18:45 G123_M3_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec  7 18:45 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Dec  7 18:45 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=G123_M3_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/G123_M3_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is PairEnd Data
Fraction of reads failed to determine: 0.0219
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0283
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9499

Copy output to storage dir


List files in scratch

total 1.2G
drwx------   3 kkarri waxmanlab 4.0K Dec  7 18:45 .
drwxrwxrwt. 22 root   root       36K Dec  7 18:45 ..
-rw-r--r--   1 kkarri waxmanlab 1.2G Dec  7 18:45 G123_M3_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec  7 18:45 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Dec  7 18:45 mm9.refseq.bed
==========================================================
Finished on : Fri Dec  7 18:45:51 EST 2018
0 hours, 0 minutes and 16 seconds elapsed.
==========================================================