-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M2
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/07_CollectInsertSizeMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Aug 30 20:36:57 EDT 2017
Running on node : scc-tm4
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/07_CollectInsertSizeMetrics
Current job ID : 473923
Current job name : Step_07_G160_M2
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/473923.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 1.8G
drwxr-xr-x   3 kkarri pulmseq 4.0K Aug 30 20:37 .
drwxrwxrwt. 23 root   root     20K Aug 30 20:36 ..
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 20:37 CollectInsertSizeMetrics
-rw-r--r--   1 kkarri pulmseq 1.8G Aug 30 20:37 G160_M2_primary_unique.bam

Starting to run my commands


Starting CollectInsertSizeMetrics command

Printing command:
CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/G160_M2'_hist.pdf' INPUT=G160_M2_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/G160_M2'_metrics'


Finished CollectInsertSizeMetrics command


Copy output to storage dir


List files in scratch

total 1.8G
drwxr-xr-x   3 kkarri pulmseq 4.0K Aug 30 20:39 .
drwxrwxrwt. 21 root   root     20K Aug 30 20:38 ..
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 20:39 CollectInsertSizeMetrics
-rw-r--r--   1 kkarri pulmseq 1.8G Aug 30 20:37 G160_M2_primary_unique.bam
==========================================================
Finished on : Wed Aug 30 20:39:08 EDT 2017
0 hours, 2 minutes and 11 seconds elapsed.
==========================================================