----------------------- Start of variable list: ----------------------- Sample_ID: WT5 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 04:47:39 EDT 2019 Running on node : scc-ka3 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/07_CollectInsertSizeMetrics Current job ID : 5781863 Current job name : Step_07_WT5 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5781863.1.linga Loading required modules... Loading required modules... List files in scratch directory: total 276M drwx------ 3 kkarri waxmanlab 4.0K Apr 30 04:48 . drwxrwxrwt. 64 root root 108K Apr 30 04:46 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 30 04:48 CollectInsertSizeMetrics -rw-r--r-- 1 kkarri waxmanlab 276M Apr 30 04:48 WT5_primary_unique.bam Starting to run my commands Starting CollectInsertSizeMetrics command Printing command: CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/WT5'_hist.pdf' INPUT=WT5_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/WT5'_metrics' Finished CollectInsertSizeMetrics command Copy output to storage dir List files in scratch total 276M drwx------ 3 kkarri waxmanlab 4.0K Apr 30 04:48 . drwxrwxrwt. 62 root root 108K Apr 30 04:53 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 30 04:49 CollectInsertSizeMetrics -rw-r--r-- 1 kkarri waxmanlab 276M Apr 30 04:48 WT5_primary_unique.bam ========================================================== Finished on : Tue Apr 30 04:54:17 EDT 2019 0 hours, 6 minutes and 40 seconds elapsed. ==========================================================