-----------------------
Start of variable list:
-----------------------
Sample_ID:
G123_M5
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/07_CollectInsertSizeMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Dec  7 19:00:36 EST 2018
Running on node : scc-tm3
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/07_CollectInsertSizeMetrics
Current job ID : 27168
Current job name : Step_07_G123_M5
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/27168.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 1.2G
drwx------   3 kkarri waxmanlab 4.0K Dec  7 19:00 .
drwxrwxrwt. 15 root   root       36K Dec  7 19:00 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec  7 19:00 CollectInsertSizeMetrics
-rw-r--r--   1 kkarri waxmanlab 1.2G Dec  7 19:00 G123_M5_primary_unique.bam

Starting to run my commands


Starting CollectInsertSizeMetrics command

Printing command:
CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/G123_M5'_hist.pdf' INPUT=G123_M5_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/G123_M5'_metrics'


Finished CollectInsertSizeMetrics command


Copy output to storage dir


List files in scratch

total 1.2G
drwx------   3 kkarri waxmanlab 4.0K Dec  7 19:02 .
drwxrwxrwt. 15 root   root       36K Dec  7 19:00 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec  7 19:02 CollectInsertSizeMetrics
-rw-r--r--   1 kkarri waxmanlab 1.2G Dec  7 19:00 G123_M5_primary_unique.bam
==========================================================
Finished on : Fri Dec  7 19:02:08 EST 2018
0 hours, 1 minutes and 32 seconds elapsed.
==========================================================