-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M12
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Nov  4 10:52:00 EST 2019
Running on node : scc-tk3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/05_Read_Strandness
Current job ID : 294758
Current job name : Step_05_G170_M12
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/294758.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 2.1G
drwx------   3 kkarri waxmanlab 4.0K Nov  4 10:58 .
drwxrwxrwt. 19 root   root      4.0K Nov  4 10:56 ..
-rw-r--r--   1 kkarri waxmanlab 2.1G Nov  4 10:58 G170_M12_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Nov  4 10:58 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Nov  4 10:58 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=G170_M12_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/G170_M12_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is PairEnd Data
Fraction of reads failed to determine: 0.0110
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0067
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9824

Copy output to storage dir


List files in scratch

total 2.1G
drwx------   3 kkarri waxmanlab 4.0K Nov  4 10:59 .
drwxrwxrwt. 19 root   root      4.0K Nov  4 10:56 ..
-rw-r--r--   1 kkarri waxmanlab 2.1G Nov  4 10:58 G170_M12_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Nov  4 10:59 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Nov  4 10:58 mm9.refseq.bed
==========================================================
Finished on : Mon Nov  4 10:59:14 EST 2019
0 hours, 7 minutes and 14 seconds elapsed.
==========================================================