----------------------- Start of variable list: ----------------------- Sample_ID: G166_M1 Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV Sample_Labels_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/00_Setup_Pipeline SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/07_CollectInsertSizeMetrics ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Apr 23 04:56:27 EDT 2019 Running on node : scc-kb3 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/07_CollectInsertSizeMetrics Current job ID : 5533282 Current job name : Step_07_G166_M1 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5533282.1.linga Loading required modules... Loading required modules... List files in scratch directory: total 267M drwx------ 3 kkarri waxmanlab 4.0K Apr 23 04:56 . drwxrwxrwt. 59 root root 112K Apr 23 04:56 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 23 04:56 CollectInsertSizeMetrics -rw-r--r-- 1 kkarri waxmanlab 267M Apr 23 04:56 G166_M1_primary_unique.bam Starting to run my commands Starting CollectInsertSizeMetrics command Printing command: CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/G166_M1'_hist.pdf' INPUT=G166_M1_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/G166_M1'_metrics' Finished CollectInsertSizeMetrics command Copy output to storage dir List files in scratch total 267M drwx------ 3 kkarri waxmanlab 4.0K Apr 23 04:56 . drwxrwxrwt. 59 root root 112K Apr 23 04:56 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 23 04:56 CollectInsertSizeMetrics -rw-r--r-- 1 kkarri waxmanlab 267M Apr 23 04:56 G166_M1_primary_unique.bam ========================================================== Finished on : Tue Apr 23 04:56:38 EDT 2019 0 hours, 0 minutes and 12 seconds elapsed. ==========================================================