-----------------------
Start of variable list:
-----------------------
Sample_ID:
PB1
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Apr 29 09:48:22 EDT 2019
Running on node : scc-bc2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE77729_PB/ENA/Scripts/05_Read_Strandness
Current job ID : 5738902
Current job name : Step_05_PB1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5738902.1.b

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 2.7G
drwx------   3 kkarri waxmanlab 4.0K Apr 29 09:51 .
drwxrwxrwt. 32 root   root       20K Apr 29 09:48 ..
-rw-r--r--   1 kkarri waxmanlab 2.7G Apr 29 09:51 PB1_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 29 09:51 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Apr 29 09:51 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=PB1_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/PB1_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is PairEnd Data
Fraction of reads failed to determine: 0.0180
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0069
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9751

Copy output to storage dir


List files in scratch

total 2.7G
drwx------   3 kkarri waxmanlab 4.0K Apr 29 09:51 .
drwxrwxrwt. 32 root   root       20K Apr 29 09:48 ..
-rw-r--r--   1 kkarri waxmanlab 2.7G Apr 29 09:51 PB1_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 29 09:51 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Apr 29 09:51 mm9.refseq.bed
==========================================================
Finished on : Mon Apr 29 09:51:25 EDT 2019
0 hours, 3 minutes and 3 seconds elapsed.
==========================================================