-----------------------
Start of variable list:
-----------------------
Sample_ID:
ERaflox_male2
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/PRJNA395963_ERa
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/PRJNA395963_ERa/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/PRJNA395963_ERa/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 30 04:04:27 EDT 2019
Running on node : scc-kb1
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/PRJNA395963_ERa/Scripts/05_Read_Strandness
Current job ID : 5781618
Current job name : Step_05_ERaflox_male2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5781618.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 5.2M
drwx------   3 kkarri waxmanlab 4.0K Apr 30 04:05 .
drwxrwxrwt. 54 root   root      180K Apr 30 04:05 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 30 04:05 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Apr 30 04:05 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=ERaflox_male2_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/ERaflox_male2_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:


Copy output to storage dir


List files in scratch

total 5.2M
drwx------   3 kkarri waxmanlab 4.0K Apr 30 04:06 .
drwxrwxrwt. 62 root   root      180K Apr 30 04:06 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 30 04:06 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Apr 30 04:05 mm9.refseq.bed
==========================================================
Finished on : Tue Apr 30 04:07:00 EDT 2019
0 hours, 2 minutes and 47 seconds elapsed.
==========================================================