----------------------- Start of variable list: ----------------------- Sample_ID: WT8 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 04:48:42 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 : 5781866 Current job name : Step_07_WT8 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5781866.1.linga Loading required modules... Loading required modules... List files in scratch directory: total 283M drwx------ 3 kkarri waxmanlab 4.0K Apr 30 04:52 . 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 283M Apr 30 04:52 WT8_primary_unique.bam Starting to run my commands Starting CollectInsertSizeMetrics command Printing command: CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/WT8'_hist.pdf' INPUT=WT8_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/WT8'_metrics' Finished CollectInsertSizeMetrics command Copy output to storage dir List files in scratch total 283M drwx------ 3 kkarri waxmanlab 4.0K Apr 30 04:52 . drwxrwxrwt. 54 root root 84K Apr 30 04:53 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 30 04:53 CollectInsertSizeMetrics -rw-r--r-- 1 kkarri waxmanlab 283M Apr 30 04:52 WT8_primary_unique.bam ========================================================== Finished on : Tue Apr 30 04:54:39 EDT 2019 0 hours, 5 minutes and 57 seconds elapsed. ==========================================================