-----------------------
Start of variable list:
-----------------------
Sample_ID:
TA_IP3
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/00_Setup_Pipeline
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/07_CollectInsertSizeMetrics
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Jun 15 06:20:15 EDT 2017
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/samples/fastqfiles/IP_Saline/Scripts/07_CollectInsertSizeMetrics
Current job ID : 9332934
Current job name : Step_07_TA_IP3
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9332934.1.linga

Loading required modules...


Loading required modules...


List files in scratch directory:

total 2.3G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 15 06:20 .
drwxrwxrwt. 64 root   root       164K Jun 15 06:20 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 06:20 CollectInsertSizeMetrics
-rw-r--r--   1 kkarri montilab-p 2.3G Jun 15 06:20 TA_IP3_primary_unique.bam

Starting to run my commands


Starting CollectInsertSizeMetrics command

Printing command:
CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/TA_IP3'_hist.pdf' INPUT=TA_IP3_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/TA_IP3'_metrics'


Finished CollectInsertSizeMetrics command


Copy output to storage dir


List files in scratch

total 2.3G
drwxr-xr-x   3 kkarri montilab-p 4.0K Jun 15 06:23 .
drwxrwxrwt. 56 root   root       164K Jun 15 06:23 ..
drwxr-xr-x   2 kkarri montilab-p 4.0K Jun 15 06:23 CollectInsertSizeMetrics
-rw-r--r--   1 kkarri montilab-p 2.3G Jun 15 06:20 TA_IP3_primary_unique.bam
==========================================================
Finished on : Thu Jun 15 06:23:37 EDT 2017
0 hours, 3 minutes and 22 seconds elapsed.
==========================================================