-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M6
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 : 473931
Current job name : Step_07_G160_M6
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/473931.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 814M
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 814M Aug 30 20:37 G160_M6_primary_unique.bam

Starting to run my commands


Starting CollectInsertSizeMetrics command

Printing command:
CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/G160_M6'_hist.pdf' INPUT=G160_M6_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/G160_M6'_metrics'


Finished CollectInsertSizeMetrics command


Copy output to storage dir


List files in scratch

total 814M
drwxr-xr-x   3 kkarri pulmseq 4.0K Aug 30 20:39 .
drwxrwxrwt. 49 root   root    180K Aug 30 20:37 ..
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 20:39 CollectInsertSizeMetrics
-rw-r--r--   1 kkarri pulmseq 814M Aug 30 20:37 G160_M6_primary_unique.bam
==========================================================
Finished on : Wed Aug 30 20:39:28 EDT 2017
0 hours, 2 minutes and 31 seconds elapsed.
==========================================================