-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M13
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/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri May 11 15:02:45 EDT 2018
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/infusion/Scripts/05_Read_Strandness
Current job ID : 6178386
Current job name : Step_05_LZ_M13
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6178386.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 481M
drwx------   3 kkarri waxmanlab 4.0K May 11 15:02 .
drwxrwxrwt. 37 root   root      168K May 11 15:02 ..
-rw-r--r--   1 kkarri waxmanlab 475M May 11 15:02 LZ_M13_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 15:02 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M May 11 15:02 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=LZ_M13_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/LZ_M13_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is SingleEnd Data
Fraction of reads explained by "++,--": 0.0138
Fraction of reads explained by "+-,-+": 0.9862
Fraction of reads explained by other combinations: 0.0000

Copy output to storage dir


List files in scratch

total 481M
drwx------   3 kkarri waxmanlab 4.0K May 11 15:03 .
drwxrwxrwt. 37 root   root      168K May 11 15:02 ..
-rw-r--r--   1 kkarri waxmanlab 475M May 11 15:02 LZ_M13_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K May 11 15:03 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M May 11 15:02 mm9.refseq.bed
==========================================================
Finished on : Fri May 11 15:03:07 EDT 2018
0 hours, 0 minutes and 22 seconds elapsed.
==========================================================