-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M9
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/07_CollectInsertSizeMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun Jul 15 18:16:25 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/07_CollectInsertSizeMetrics
Current job ID : 6944810
Current job name : Step_07_G167_M9
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6944810.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 894M
drwx------   3 kkarri waxmanlab 4.0K Jul 15 18:16 .
drwxrwxrwt. 96 root   root      108K Jul 15 18:16 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 15 18:16 CollectInsertSizeMetrics
-rw-r--r--   1 kkarri waxmanlab 894M Jul 15 18:16 G167_M9_primary_unique.bam

Starting to run my commands


Starting CollectInsertSizeMetrics command

Printing command:
CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/G167_M9'_hist.pdf' INPUT=G167_M9_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/G167_M9'_metrics'


Finished CollectInsertSizeMetrics command


Copy output to storage dir


List files in scratch

total 894M
drwx------   3 kkarri waxmanlab 4.0K Jul 15 18:18 .
drwxrwxrwt. 93 root   root      108K Jul 15 18:18 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Jul 15 18:18 CollectInsertSizeMetrics
-rw-r--r--   1 kkarri waxmanlab 894M Jul 15 18:16 G167_M9_primary_unique.bam
==========================================================
Finished on : Sun Jul 15 18:18:53 EDT 2018
0 hours, 2 minutes and 28 seconds elapsed.
==========================================================