----------------------- Start of variable list: ----------------------- Sample_ID: G168_G169_M13 Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP Sample_Labels_DIR: /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/00_Setup_Pipeline SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/07_CollectInsertSizeMetrics ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 12 12:10:07 EDT 2019 Running on node : scc-kb7 Current directory : /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/07_CollectInsertSizeMetrics Current job ID : 3529986 Current job name : Step_07_G168_G169_M13 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3529986.1.linga Loading required modules... Loading required modules... List files in scratch directory: total 2.0G drwx------ 3 kkarri waxmanlab 4.0K Mar 12 12:10 . drwxrwxrwt. 23 root root 168K Mar 12 12:10 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 12 12:10 CollectInsertSizeMetrics -rw-r--r-- 1 kkarri waxmanlab 2.0G Mar 12 12:10 G168_G169_M13_primary_unique.bam Starting to run my commands Starting CollectInsertSizeMetrics command Printing command: CollectInsertSizeMetrics HISTOGRAM_FILE=CollectInsertSizeMetrics/G168_G169_M13'_hist.pdf' INPUT=G168_G169_M13_primary_unique.bam OUTPUT=CollectInsertSizeMetrics/G168_G169_M13'_metrics' Finished CollectInsertSizeMetrics command Copy output to storage dir List files in scratch total 2.0G drwx------ 3 kkarri waxmanlab 4.0K Mar 12 12:10 . drwxrwxrwt. 23 root root 168K Mar 12 12:10 .. drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 12 12:10 CollectInsertSizeMetrics -rw-r--r-- 1 kkarri waxmanlab 2.0G Mar 12 12:10 G168_G169_M13_primary_unique.bam ========================================================== Finished on : Tue Mar 12 12:10:23 EDT 2019 0 hours, 0 minutes and 16 seconds elapsed. ==========================================================