-----------------------
Start of variable list:
-----------------------
Sample_ID:
48h_Act4
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE111828_actiminophen
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE111828_actiminophen/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE111828_actiminophen/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Apr 26 12:35:29 EDT 2019
Running on node : scc-ka1
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE111828_actiminophen/Scripts/05_Read_Strandness
Current job ID : 5607807
Current job name : Step_05_48h_Act4
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5607807.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 578M
drwx------   3 kkarri waxmanlab 4.0K Apr 26 12:37 .
drwxrwxrwt. 85 root   root      124K Apr 26 12:35 ..
-rw-r--r--   1 kkarri waxmanlab 573M Apr 26 12:36 48h_Act4_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 26 12:37 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Apr 26 12:37 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=48h_Act4_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/48h_Act4_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is PairEnd Data
Fraction of reads failed to determine: 0.0121
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0074
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9805

Copy output to storage dir


List files in scratch

total 578M
drwx------   3 kkarri waxmanlab 4.0K Apr 26 12:37 .
drwxrwxrwt. 85 root   root      124K Apr 26 12:35 ..
-rw-r--r--   1 kkarri waxmanlab 573M Apr 26 12:36 48h_Act4_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 26 12:37 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Apr 26 12:37 mm9.refseq.bed
==========================================================
Finished on : Fri Apr 26 12:37:16 EDT 2019
0 hours, 1 minutes and 47 seconds elapsed.
==========================================================