-----------------------
Start of variable list:
-----------------------
Sample_ID:
CV_CO2
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE101650_GermFree
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE101650_GermFree/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE101650_GermFree/Scripts/05_Read_Strandness
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 30 04:04:21 EDT 2019
Running on node : scc-tl2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE101650_GermFree/Scripts/05_Read_Strandness
Current job ID : 5781595
Current job name : Step_05_CV_CO2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5781595.1.linga

Loading required modules...


Loading required modules...


Unzip files:


Finished unzipping


List files in scratch directory:

total 3.6G
drwx------   3 kkarri waxmanlab 4.0K Apr 30 04:14 .
drwxrwxrwt. 19 root   root       36K Apr 30 04:13 ..
-rw-r--r--   1 kkarri waxmanlab 3.6G Apr 30 04:14 CV_CO2_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 30 04:14 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Apr 30 04:14 mm9.refseq.bed

Starting to run my commands


Starting infer_experiment.py command

Printing command:
infer_experiment.py --input-file=CV_CO2_primary_unique.bam --refgene=mm9.refseq.bed > Read_Strandness/CV_CO2_Read_Strandness.txt


Finished infer_experiment.py command


Output file from infer_experiment.py:

This is PairEnd Data
Fraction of reads failed to determine: 0.0272
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0116
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9612

Copy output to storage dir


List files in scratch

total 3.6G
drwx------   3 kkarri waxmanlab 4.0K Apr 30 04:15 .
drwxrwxrwt. 19 root   root       36K Apr 30 04:13 ..
-rw-r--r--   1 kkarri waxmanlab 3.6G Apr 30 04:14 CV_CO2_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 30 04:15 Read_Strandness
-rwxr-xr-x   1 kkarri waxmanlab 5.0M Apr 30 04:14 mm9.refseq.bed
==========================================================
Finished on : Tue Apr 30 04:15:15 EDT 2019
0 hours, 10 minutes and 54 seconds elapsed.
==========================================================