-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed May  9 18:37:21 EDT 2018
Running on node : scc-tm3
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/05_Read_Strandness
Current job ID : 6138045
Current job name : Step_05_LZ_M1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6138045.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 356M
drwx------   3 kkarri waxmanlab 4.0K May  9 18:37 .
drwxrwxrwt. 16 root   root       36K May  9 18:37 ..
-rw-r--r--   1 kkarri waxmanlab 351M May  9 18:37 LZ_M1_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K May  9 18:37 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M May  9 18:37 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=LZ_M1_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/LZ_M1_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is SingleEnd Data
Fraction of reads explained by "++,--": 0.0142
Fraction of reads explained by "+-,-+": 0.9858
Fraction of reads explained by other combinations: 0.0000

Copy output to storage dir


List files in scratch

total 356M
drwx------   3 kkarri waxmanlab 4.0K May  9 18:37 .
drwxrwxrwt. 16 root   root       36K May  9 18:37 ..
-rw-r--r--   1 kkarri waxmanlab 351M May  9 18:37 LZ_M1_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K May  9 18:37 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M May  9 18:37 mm9.refseq.bed
==========================================================
Finished on : Wed May  9 18:37:29 EDT 2018
0 hours, 0 minutes and 8 seconds elapsed.
==========================================================