-----------------------
Start of variable list:
-----------------------
Sample_ID:
MM_M3
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sat Jun 17 04:48:53 EDT 2017
Running on node : scc-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/Water_Saline/Scripts/05_Read_Strandness
Current job ID : 9394787
Current job name : Step_05_MM_M3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9394787.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 2.5G
drwxr-xr-x    3 kkarri montilab-p 4.0K Jun 17 04:49 .
drwxrwxrwt. 208 root   root       124K Jun 17 04:48 ..
-rw-r--r--    1 kkarri montilab-p 2.5G Jun 17 04:49 MM_M3_primary_unique.bam
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 17 04:49 Read_Strandness
-rwx------    1 kkarri montilab-p 2.7M Jun 17 04:49 rn6.refSeq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=MM_M3_primary_unique.bam --refgene=rn6.refSeq.bed > Read_Strandness/MM_M3_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-+": 0.4991
Fraction of reads explained by "1+-,1-+,2++,2--": 0.5009
Fraction of reads explained by other combinations: 0.0000

Copy output to storage dir


List files in scratch

total 2.5G
drwxr-xr-x    3 kkarri montilab-p 4.0K Jun 17 04:49 .
drwxrwxrwt. 208 root   root       124K Jun 17 04:48 ..
-rw-r--r--    1 kkarri montilab-p 2.5G Jun 17 04:49 MM_M3_primary_unique.bam
drwxr-xr-x    2 kkarri montilab-p 4.0K Jun 17 04:49 Read_Strandness
-rwx------    1 kkarri montilab-p 2.7M Jun 17 04:49 rn6.refSeq.bed
==========================================================
Finished on : Sat Jun 17 04:49:44 EDT 2017
0 hours, 0 minutes and 51 seconds elapsed.
==========================================================