----------------------- Start of variable list: ----------------------- Dataset_DIR: /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP Dataset_Label: G168_TCPO_Env bin_mode: Off SCRIPT_DIR: /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/10_bamCorrelate OUTPUT_DIR: /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/10_bamCorrelate/Output JOB_COUNTER: 02 zMin: 0.6 zMax: 1.0 BED_file_name: Intron_Only_Regions ----------------------- End of variable list ----------------------- ========================================================== Starting on : Wed Mar 13 10:46:19 EDT 2019 Running on node : scc-kb3 Current directory : /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/10_bamCorrelate Current job ID : 3566170 Current job name : Step_10_bamCor_02 Task index number : undefined Parameter for multiple cores : 16 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3566170.1.linga Loading required modules... Getting BED file line count... Before ENCODE_Blacklist filter: 193089 Overlap BED file with mm9-blacklist.bed and filter out overlap Intron_Only_Regions mm9-blacklist ---------------------------------------------------------------------------- cleaning input sorting input files classify common or unique peaks getting the union of the peak sets getting the merged common peaks getting distance of nearest peak counting peaks Running overlap.R script to get peak overlap, peak width, and peak proximity statistics ... Creating summary file Done! ---------------------------------------------------------------------------- Getting BED file line count... After ENCODE_Blacklist filter: 191105 Copy input sample BAM files to Input folder Save Input file lists to a variable Input_List: G168_G169_M10_primary_unique.bam G168_G169_M11_primary_unique.bam G168_G169_M12_primary_unique.bam G168_G169_M13_primary_unique.bam G168_G169_M14_primary_unique.bam G168_G169_M15_primary_unique.bam G168_G169_M16_primary_unique.bam G168_G169_M17_primary_unique.bam G168_G169_M18_primary_unique.bam G168_G169_M19_primary_unique.bam G168_G169_M1_primary_unique.bam G168_G169_M20_primary_unique.bam G168_G169_M21_primary_unique.bam G168_G169_M22_primary_unique.bam G168_G169_M2_primary_unique.bam G168_G169_M3_primary_unique.bam G168_G169_M4_primary_unique.bam G168_G169_M5_primary_unique.bam G168_G169_M6_primary_unique.bam G168_G169_M7_primary_unique.bam G168_G169_M8_primary_unique.bam G168_G169_M9_primary_unique.bam Labels_List: G168_G169_M10 G168_G169_M11 G168_G169_M12 G168_G169_M13 G168_G169_M14 G168_G169_M15 G168_G169_M16 G168_G169_M17 G168_G169_M18 G168_G169_M19 G168_G169_M1 G168_G169_M20 G168_G169_M21 G168_G169_M22 G168_G169_M2 G168_G169_M3 G168_G169_M4 G168_G169_M5 G168_G169_M6 G168_G169_M7 G168_G169_M8 G168_G169_M9 List files in scratch directory: total 41G drwx------ 4 kkarri waxmanlab 4.0K Mar 13 10:50 . drwxrwxrwt. 21 root root 112K Mar 13 10:46 .. -rw-r--r-- 1 kkarri waxmanlab 1.9G Mar 13 10:47 G168_G169_M10_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:47 G168_G169_M10_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.2G Mar 13 10:47 G168_G169_M11_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:47 G168_G169_M11_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.8G Mar 13 10:48 G168_G169_M12_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:48 G168_G169_M12_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.0G Mar 13 10:48 G168_G169_M13_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:48 G168_G169_M13_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.0G Mar 13 10:48 G168_G169_M14_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:48 G168_G169_M14_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.1G Mar 13 10:49 G168_G169_M15_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:49 G168_G169_M15_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.2G Mar 13 10:49 G168_G169_M16_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:49 G168_G169_M16_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.7G Mar 13 10:49 G168_G169_M17_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:49 G168_G169_M17_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.6G Mar 13 10:49 G168_G169_M18_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:49 G168_G169_M18_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.8G Mar 13 10:49 G168_G169_M19_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:49 G168_G169_M19_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.6G Mar 13 10:46 G168_G169_M1_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.0M Mar 13 10:46 G168_G169_M1_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.8G Mar 13 10:50 G168_G169_M20_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:50 G168_G169_M20_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.6G Mar 13 10:50 G168_G169_M21_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:50 G168_G169_M21_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.8G Mar 13 10:50 G168_G169_M22_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:50 G168_G169_M22_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.0G Mar 13 10:46 G168_G169_M2_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:46 G168_G169_M2_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.9G Mar 13 10:46 G168_G169_M3_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:46 G168_G169_M3_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.1G Mar 13 10:46 G168_G169_M4_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:46 G168_G169_M4_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.9G Mar 13 10:46 G168_G169_M5_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:46 G168_G169_M5_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.9G Mar 13 10:46 G168_G169_M6_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:46 G168_G169_M6_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.8G Mar 13 10:47 G168_G169_M7_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:47 G168_G169_M7_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.9G Mar 13 10:47 G168_G169_M8_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:47 G168_G169_M8_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.6G Mar 13 10:47 G168_G169_M9_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:47 G168_G169_M9_primary_unique.bam.bai drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 13 10:50 Input -rwxr-xr-x 1 kkarri waxmanlab 1.3K Mar 13 10:46 Input_Samples.txt -rwxr-xr-x 1 kkarri waxmanlab 12M Mar 13 10:46 Intron_Only_Regions.bed drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 13 10:46 Intron_Only_Regions_mm9-blacklist_Output -rwxr-xr-x 1 kkarri waxmanlab 71K Mar 13 10:46 mm9-blacklist.bed -rwxr-xr-x 1 kkarri waxmanlab 7.6K Mar 13 10:46 overlap.R -rwxr-xr-x 1 kkarri waxmanlab 6.0K Mar 13 10:46 overlap.sh -rw-r--r-- 1 kkarri waxmanlab 23K Mar 13 10:46 peak1_dump.bed Starting to run my commands Starting bamCorrelate command Ending bamCorrelate command Starting plotCorrelation command Ending plotCorrelation command List files: total 41G drwx------ 4 kkarri waxmanlab 4.0K Mar 13 10:50 . drwxrwxrwt. 21 root root 112K Mar 13 10:46 .. -rw-r--r-- 1 kkarri waxmanlab 1.9G Mar 13 10:47 G168_G169_M10_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:47 G168_G169_M10_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.2G Mar 13 10:47 G168_G169_M11_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:47 G168_G169_M11_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.8G Mar 13 10:48 G168_G169_M12_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:48 G168_G169_M12_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.0G Mar 13 10:48 G168_G169_M13_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:48 G168_G169_M13_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.0G Mar 13 10:48 G168_G169_M14_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:48 G168_G169_M14_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.1G Mar 13 10:49 G168_G169_M15_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:49 G168_G169_M15_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.2G Mar 13 10:49 G168_G169_M16_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:49 G168_G169_M16_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.7G Mar 13 10:49 G168_G169_M17_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:49 G168_G169_M17_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.6G Mar 13 10:49 G168_G169_M18_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:49 G168_G169_M18_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.8G Mar 13 10:49 G168_G169_M19_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:49 G168_G169_M19_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.6G Mar 13 10:46 G168_G169_M1_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.0M Mar 13 10:46 G168_G169_M1_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.8G Mar 13 10:50 G168_G169_M20_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:50 G168_G169_M20_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.6G Mar 13 10:50 G168_G169_M21_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:50 G168_G169_M21_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.8G Mar 13 10:50 G168_G169_M22_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:50 G168_G169_M22_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.0G Mar 13 10:46 G168_G169_M2_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:46 G168_G169_M2_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.9G Mar 13 10:46 G168_G169_M3_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:46 G168_G169_M3_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 2.1G Mar 13 10:46 G168_G169_M4_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:46 G168_G169_M4_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.9G Mar 13 10:46 G168_G169_M5_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:46 G168_G169_M5_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.9G Mar 13 10:46 G168_G169_M6_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:46 G168_G169_M6_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.8G Mar 13 10:47 G168_G169_M7_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:47 G168_G169_M7_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.9G Mar 13 10:47 G168_G169_M8_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.2M Mar 13 10:47 G168_G169_M8_primary_unique.bam.bai -rw-r--r-- 1 kkarri waxmanlab 1.6G Mar 13 10:47 G168_G169_M9_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 3.1M Mar 13 10:47 G168_G169_M9_primary_unique.bam.bai drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 13 10:50 Input -rwxr-xr-x 1 kkarri waxmanlab 1.3K Mar 13 10:46 Input_Samples.txt -rwxr-xr-x 1 kkarri waxmanlab 12M Mar 13 10:46 Intron_Only_Regions.bed drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 13 10:46 Intron_Only_Regions_mm9-blacklist_Output -rwxr-xr-x 1 kkarri waxmanlab 71K Mar 13 10:46 mm9-blacklist.bed -rwxr-xr-x 1 kkarri waxmanlab 7.6K Mar 13 10:46 overlap.R -rwxr-xr-x 1 kkarri waxmanlab 6.0K Mar 13 10:46 overlap.sh -rw-r--r-- 1 kkarri waxmanlab 23K Mar 13 10:46 peak1_dump.bed ========================================================== Finished on : Wed Mar 13 10:50:54 EDT 2019 0 hours, 4 minutes and 35 seconds elapsed. ==========================================================