-----------------------
Start of variable list:
-----------------------
Sample_ID:
TA_IP2
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Jun 15 06:14:15 EDT 2017
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/05_Read_Strandness
Current job ID : 9332895
Current job name : Step_05_TA_IP2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9332895.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 2.3G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 15 06:15 .
drwxrwxrwt. 93 root   root       168K Jun 15 06:14 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 06:15 Read_Strandness
-rw-r--r--   1 kkarri montilab-p 2.3G Jun 15 06:15 TA_IP2_primary_unique.bam
-rwx------   1 kkarri montilab-p 2.7M Jun 15 06:15 rn6.refSeq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=TA_IP2_primary_unique.bam --refgene=rn6.refSeq.bed > Read_Strandness/TA_IP2_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-+": 0.5013
Fraction of reads explained by "1+-,1-+,2++,2--": 0.4987
Fraction of reads explained by other combinations: 0.0000

Copy output to storage dir


List files in scratch

total 2.3G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 15 06:15 .
drwxrwxrwt. 93 root   root       168K Jun 15 06:14 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 06:15 Read_Strandness
-rw-r--r--   1 kkarri montilab-p 2.3G Jun 15 06:15 TA_IP2_primary_unique.bam
-rwx------   1 kkarri montilab-p 2.7M Jun 15 06:15 rn6.refSeq.bed
==========================================================
Finished on : Thu Jun 15 06:15:32 EDT 2017
0 hours, 1 minutes and 17 seconds elapsed.
==========================================================