----------------------- Start of variable list: ----------------------- Sample_ID: WT4 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 04:49:08 EDT 2019 Running on node : scc-ka1 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/07_CollectInsertSizeMetrics Current job ID : 5781861 Current job name : Step_07_WT4 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5781861.1.linga Loading required modules... Loading required modules... List files in scratch directory: total 261M drwx------ 3 kkarri waxmanlab 4.0K Apr 30 04:50 . drwxrwxrwt. 53 root root 124K Apr 30 04:46 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 30 04:50 CollectInsertSizeMetrics -rw-r--r-- 1 kkarri waxmanlab 261M Apr 30 04:50 WT4_primary_unique.bam Starting to run my commands Starting CollectInsertSizeMetrics command Printing command: CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/WT4'_hist.pdf' INPUT=WT4_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/WT4'_metrics' Finished CollectInsertSizeMetrics command Copy output to storage dir List files in scratch total 261M drwx------ 3 kkarri waxmanlab 4.0K Apr 30 04:50 . drwxrwxrwt. 52 root root 124K Apr 30 04:52 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 30 04:52 CollectInsertSizeMetrics -rw-r--r-- 1 kkarri waxmanlab 261M Apr 30 04:50 WT4_primary_unique.bam ========================================================== Finished on : Tue Apr 30 04:53:52 EDT 2019 0 hours, 4 minutes and 45 seconds elapsed. ==========================================================