-----------------------
Start of variable list:
-----------------------
Sample_ID:
16wk_PBS1
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE122243_asparaginase
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE122243_asparaginase/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE122243_asparaginase/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Mar  9 06:24:02 EDT 2020
Running on node : scc-bb3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE122243_asparaginase/Scripts/05_Read_Strandness
Current job ID : 3763558
Current job name : Step_05_16wk_PBS1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/3763558.1.b

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 767M
drwx------   3 kkarri waxmanlab 4.0K Mar  9 06:24 .
drwxrwxrwt. 20 root   root      4.0K Mar  9 06:24 ..
-rwxr-xr-x   1 kkarri waxmanlab 762M Mar  9 06:24 16wk_PBS1_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar  9 06:24 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Mar  9 06:24 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=16wk_PBS1_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/16wk_PBS1_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is SingleEnd Data
Fraction of reads failed to determine: 0.0123
Fraction of reads explained by "++,--": 0.4958
Fraction of reads explained by "+-,-+": 0.4919

Copy output to storage dir


List files in scratch

total 767M
drwx------   3 kkarri waxmanlab 4.0K Mar  9 06:24 .
drwxrwxrwt. 20 root   root      4.0K Mar  9 06:24 ..
-rwxr-xr-x   1 kkarri waxmanlab 762M Mar  9 06:24 16wk_PBS1_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar  9 06:24 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Mar  9 06:24 mm9.refseq.bed
==========================================================
Finished on : Mon Mar  9 06:25:13 EDT 2020
0 hours, 1 minutes and 12 seconds elapsed.
==========================================================