-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M5
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-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/07_CollectInsertSizeMetrics
Current job ID : 473929
Current job name : Step_07_G160_M5
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/473929.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 1.5G
drwxr-xr-x   3 kkarri pulmseq 4.0K Aug 30 20:37 .
drwxrwxrwt. 50 root   root    180K Aug 30 20:37 ..
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 20:37 CollectInsertSizeMetrics
-rw-r--r--   1 kkarri pulmseq 1.5G Aug 30 20:37 G160_M5_primary_unique.bam

Starting to run my commands


Starting CollectInsertSizeMetrics command

Printing command:
CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/G160_M5'_hist.pdf' INPUT=G160_M5_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/G160_M5'_metrics'


Finished CollectInsertSizeMetrics command


Copy output to storage dir


List files in scratch

total 1.5G
drwxr-xr-x   3 kkarri pulmseq 4.0K Aug 30 20:40 .
drwxrwxrwt. 47 root   root    180K Aug 30 20:40 ..
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 20:40 CollectInsertSizeMetrics
-rw-r--r--   1 kkarri pulmseq 1.5G Aug 30 20:37 G160_M5_primary_unique.bam
==========================================================
Finished on : Wed Aug 30 20:40:33 EDT 2017
0 hours, 3 minutes and 36 seconds elapsed.
==========================================================