-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M26
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun May 13 14:02:26 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion_rerun/Scripts/05_Read_Strandness
Current job ID : 6184402
Current job name : Step_05_LZ_M26
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6184402.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 318M
drwx------   3 kkarri waxmanlab 4.0K May 13 14:02 .
drwxrwxrwt. 38 root   root      116K May 13 14:02 ..
-rw-r--r--   1 kkarri waxmanlab 313M May 13 14:02 LZ_M26_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 13 14:02 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M May 13 14:02 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=LZ_M26_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/LZ_M26_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is SingleEnd Data
Fraction of reads explained by "++,--": 0.0104
Fraction of reads explained by "+-,-+": 0.9896
Fraction of reads explained by other combinations: 0.0000

Copy output to storage dir


List files in scratch

total 318M
drwx------   3 kkarri waxmanlab 4.0K May 13 14:02 .
drwxrwxrwt. 38 root   root      116K May 13 14:02 ..
-rw-r--r--   1 kkarri waxmanlab 313M May 13 14:02 LZ_M26_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 13 14:02 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M May 13 14:02 mm9.refseq.bed
==========================================================
Finished on : Sun May 13 14:02:34 EDT 2018
0 hours, 0 minutes and 8 seconds elapsed.
==========================================================