-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M66
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Aug 30 20:22:51 EDT 2017
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/05_Read_Strandness
Current job ID : 473665
Current job name : Step_05_G160_M66
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/473665.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 819M
drwxr-xr-x   3 kkarri pulmseq 4.0K Aug 30 20:22 .
drwxrwxrwt. 56 root   root     92K Aug 30 20:22 ..
-rw-r--r--   1 kkarri pulmseq 814M Aug 30 20:22 G160_M66_primary_unique.bam
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 20:22 Read_Strandness
-rwxr-xr-x   1 kkarri pulmseq 5.0M Aug 30 20:22 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=G160_M66_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/G160_M66_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is PairEnd Data
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0322
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9678
Fraction of reads explained by other combinations: 0.0000

Copy output to storage dir


List files in scratch

total 819M
drwxr-xr-x   3 kkarri pulmseq 4.0K Aug 30 20:23 .
drwxrwxrwt. 56 root   root     92K Aug 30 20:22 ..
-rw-r--r--   1 kkarri pulmseq 814M Aug 30 20:22 G160_M66_primary_unique.bam
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 20:23 Read_Strandness
-rwxr-xr-x   1 kkarri pulmseq 5.0M Aug 30 20:22 mm9.refseq.bed
==========================================================
Finished on : Wed Aug 30 20:23:05 EDT 2017
0 hours, 0 minutes and 14 seconds elapsed.
==========================================================