-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M10
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun Jul 15 18:04:19 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/05_Read_Strandness
Current job ID : 6944785
Current job name : Step_05_G167_M10
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6944785.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 723M
drwx------    3 kkarri waxmanlab 4.0K Jul 15 18:05 .
drwxrwxrwt. 119 root   root      116K Jul 15 18:05 ..
-rw-r--r--    1 kkarri waxmanlab 718M Jul 15 18:05 G167_M10_primary_unique.bam
drwxr-xr-x    2 kkarri waxmanlab 4.0K Jul 15 18:05 Read_Strandness
-rwxr-xr-x    1 kkarri waxmanlab 5.0M Jul 15 18:05 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=G167_M10_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/G167_M10_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:


Copy output to storage dir


List files in scratch

total 723M
drwx------    3 kkarri waxmanlab 4.0K Jul 15 18:05 .
drwxrwxrwt. 118 root   root      116K Jul 15 18:05 ..
-rw-r--r--    1 kkarri waxmanlab 718M Jul 15 18:05 G167_M10_primary_unique.bam
drwxr-xr-x    2 kkarri waxmanlab 4.0K Jul 15 18:05 Read_Strandness
-rwxr-xr-x    1 kkarri waxmanlab 5.0M Jul 15 18:05 mm9.refseq.bed
==========================================================
Finished on : Sun Jul 15 18:05:52 EDT 2018
0 hours, 1 minutes and 33 seconds elapsed.
==========================================================