----------------------- Start of variable list: ----------------------- Sample_ID: WT2 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 04:46:24 EDT 2019 Running on node : scc-ka6 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/07_CollectInsertSizeMetrics Current job ID : 5781857 Current job name : Step_07_WT2 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5781857.1.linga Loading required modules... Loading required modules... List files in scratch directory: total 257M drwx------ 3 kkarri waxmanlab 4.0K Apr 30 04:46 . drwxrwxrwt. 51 root root 92K Apr 30 04:46 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 30 04:46 CollectInsertSizeMetrics -rw-r--r-- 1 kkarri waxmanlab 257M Apr 30 04:46 WT2_primary_unique.bam Starting to run my commands Starting CollectInsertSizeMetrics command Printing command: CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/WT2'_hist.pdf' INPUT=WT2_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/WT2'_metrics' Finished CollectInsertSizeMetrics command Copy output to storage dir List files in scratch total 257M drwx------ 3 kkarri waxmanlab 4.0K Apr 30 04:46 . drwxrwxrwt. 51 root root 92K Apr 30 04:46 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 30 04:47 CollectInsertSizeMetrics -rw-r--r-- 1 kkarri waxmanlab 257M Apr 30 04:46 WT2_primary_unique.bam ========================================================== Finished on : Tue Apr 30 04:48:54 EDT 2019 0 hours, 2 minutes and 30 seconds elapsed. ==========================================================