-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M18
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Mar 12 12:00:38 EDT 2019
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/05_Read_Strandness
Current job ID : 3529859
Current job name : Step_05_G168_G169_M18
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/3529859.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 1.6G
drwx------   3 kkarri waxmanlab 4.0K Mar 12 12:01 .
drwxrwxrwt. 27 root   root      268K Mar 12 12:00 ..
-rw-r--r--   1 kkarri waxmanlab 1.6G Mar 12 12:01 G168_G169_M18_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 12 12:01 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Mar 12 12:01 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=G168_G169_M18_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/G168_G169_M18_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is PairEnd Data
Fraction of reads failed to determine: 0.0153
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0037
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9810

Copy output to storage dir


List files in scratch

total 1.6G
drwx------   3 kkarri waxmanlab 4.0K Mar 12 12:01 .
drwxrwxrwt. 27 root   root      268K Mar 12 12:00 ..
-rw-r--r--   1 kkarri waxmanlab 1.6G Mar 12 12:01 G168_G169_M18_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 12 12:01 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Mar 12 12:01 mm9.refseq.bed
==========================================================
Finished on : Tue Mar 12 12:01:19 EDT 2019
0 hours, 0 minutes and 41 seconds elapsed.
==========================================================