----------------------- Start of variable list: ----------------------- Sample_ID: WT7 Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo Sample_Labels_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/00_Setup_Pipeline SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/07_CollectInsertSizeMetrics ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Apr 30 04:48:18 EDT 2019 Running on node : scc-ka4 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/07_CollectInsertSizeMetrics Current job ID : 5781865 Current job name : Step_07_WT7 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5781865.1.linga Loading required modules... Loading required modules... List files in scratch directory: total 282M drwx------ 3 kkarri waxmanlab 4.0K Apr 30 04:51 . drwxrwxrwt. 55 root root 84K Apr 30 04:49 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 30 04:51 CollectInsertSizeMetrics -rw-r--r-- 1 kkarri waxmanlab 281M Apr 30 04:51 WT7_primary_unique.bam Starting to run my commands Starting CollectInsertSizeMetrics command Printing command: CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/WT7'_hist.pdf' INPUT=WT7_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/WT7'_metrics' Finished CollectInsertSizeMetrics command Copy output to storage dir List files in scratch total 282M drwx------ 3 kkarri waxmanlab 4.0K Apr 30 04:51 . drwxrwxrwt. 55 root root 84K Apr 30 04:49 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 30 04:52 CollectInsertSizeMetrics -rw-r--r-- 1 kkarri waxmanlab 281M Apr 30 04:51 WT7_primary_unique.bam ========================================================== Finished on : Tue Apr 30 04:53:57 EDT 2019 0 hours, 5 minutes and 40 seconds elapsed. ==========================================================