-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Dec 18 18:40:33 EST 2018
Running on node : scc-tk2
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_Env/Scripts/05_Read_Strandness
Current job ID : 364916
Current job name : Step_05_G123_M1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/364916.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 1.3G
drwx------  3 kkarri waxmanlab 4.0K Dec 18 18:41 .
drwxrwxrwt. 9 root   root       36K Dec 18 18:40 ..
-rw-r--r--  1 kkarri waxmanlab 1.3G Dec 18 18:41 G123_M1_primary_unique.bam
drwxr-xr-x  2 kkarri waxmanlab 4.0K Dec 18 18:41 Read_Strandness
-rwxr-xr-x  1 kkarri waxmanlab 5.0M Dec 18 18:41 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=G123_M1_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/G123_M1_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is PairEnd Data
Fraction of reads failed to determine: 0.0229
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0359
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9413

Copy output to storage dir


List files in scratch

total 1.3G
drwx------  3 kkarri waxmanlab 4.0K Dec 18 18:41 .
drwxrwxrwt. 9 root   root       36K Dec 18 18:40 ..
-rw-r--r--  1 kkarri waxmanlab 1.3G Dec 18 18:41 G123_M1_primary_unique.bam
drwxr-xr-x  2 kkarri waxmanlab 4.0K Dec 18 18:41 Read_Strandness
-rwxr-xr-x  1 kkarri waxmanlab 5.0M Dec 18 18:41 mm9.refseq.bed
==========================================================
Finished on : Tue Dec 18 18:41:29 EST 2018
0 hours, 0 minutes and 56 seconds elapsed.
==========================================================