-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M1
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 18:16:24 EDT 2018
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/07_CollectInsertSizeMetrics
Current job ID : 6944802
Current job name : Step_07_G167_M1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6944802.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 960M
drwx------    3 kkarri waxmanlab 4.0K Jul 15 18:16 .
drwxrwxrwt. 144 root   root      168K Jul 15 18:16 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Jul 15 18:16 CollectInsertSizeMetrics
-rw-r--r--    1 kkarri waxmanlab 960M Jul 15 18:16 G167_M1_primary_unique.bam

Starting to run my commands


Starting CollectInsertSizeMetrics command

Printing command:
CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/G167_M1'_hist.pdf' INPUT=G167_M1_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/G167_M1'_metrics'


Finished CollectInsertSizeMetrics command


Copy output to storage dir


List files in scratch

total 960M
drwx------    3 kkarri waxmanlab 4.0K Jul 15 18:18 .
drwxrwxrwt. 142 root   root      168K Jul 15 18:18 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Jul 15 18:18 CollectInsertSizeMetrics
-rw-r--r--    1 kkarri waxmanlab 960M Jul 15 18:16 G167_M1_primary_unique.bam
==========================================================
Finished on : Sun Jul 15 18:18:49 EDT 2018
0 hours, 2 minutes and 25 seconds elapsed.
==========================================================