----------------------- Start of variable list: ----------------------- Sample_ID: G166_M13 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 STRAND_RULE: 1+-,1-+,2++,2-- BU_User: kkarri VM_DIR_UCSC: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_Env SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/11_UCSC_BigWig ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Apr 23 13:29:54 EDT 2019 Running on node : scc-wl3 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/11_UCSC_BigWig Current job ID : 5544740 Current job name : Step_11_G166_M13 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/5544740.1.w Loading required modules... INPUT_BAM: G166_M13_primary_unique.bam List files in scratch directory: total 2.8G drwx------ 4 kkarri waxmanlab 4.0K Apr 23 13:31 . drwxrwxrwt. 36 root root 12K Apr 23 13:29 .. -rw-r--r-- 1 kkarri waxmanlab 2.8G Apr 23 13:31 G166_M13_primary_unique.bam drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 23 13:31 UCSC_BigWig drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 23 13:31 UCSC_Tools -rwxr-xr-x 1 kkarri waxmanlab 584 Apr 23 13:31 mm9.chrom.sizes Starting to run my commands Starting samtools sort and index Finished samtools sort and index Starting bam2wig.py command Printing command: bam2wig.py --input-file=G166_M13_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G166_M13 --wigsum=1000000000 --strand=1+-,1-+,2++,2-- Skip multi-hits:False Finished bam2wig.py command Sample from wiggle files: ==> G166_M13.Forward.wig <== variableStep chrom=chrY 184 0.26 185 0.26 186 0.26 187 0.26 188 0.26 189 0.26 190 0.26 191 0.26 192 0.26 ==> G166_M13.Reverse.wig <== variableStep chrom=chrY 287 -0.26 288 -0.26 289 -0.26 290 -0.26 291 -0.26 292 -0.26 293 -0.26 294 -0.26 295 -0.26 #-------------------------------- G166_M13.Forward.wig #-------------------------------- Line count where 2nd column does not equal "-": 968575012 Line count where 2nd column is only a negative sign: 0 Copy G166_M13.Forward.wig to UCSC_Tools folder Copy mm9.chrom.sizes to UCSC_Tools folder Start wigToBigWig End wigToBigWig #-------------------------------- G166_M13.Reverse.wig #-------------------------------- Line count where 2nd column does not equal "-": 967531479 Line count where 2nd column is only a negative sign: 0 Copy G166_M13.Reverse.wig to UCSC_Tools folder Copy mm9.chrom.sizes to UCSC_Tools folder Start wigToBigWig End wigToBigWig List of files in UCSC_Tools folder: -rw-r--r-- 1 kkarri waxmanlab 13781210207 Apr 23 15:26 ./UCSC_Tools/G166_M13.Forward.wig -rw-r--r-- 1 kkarri waxmanlab 14734174824 Apr 23 15:56 ./UCSC_Tools/G166_M13.Reverse.wig -rwxr-xr-x 1 kkarri waxmanlab 584 Apr 23 15:56 ./UCSC_Tools/mm9.chrom.sizes -rwx------ 1 kkarri waxmanlab 1012225 Apr 23 13:31 ./UCSC_Tools/wigToBigWig Copy output to storage dir List files in scratch total 33G drwx------ 4 kkarri waxmanlab 4.0K Apr 23 13:46 . drwxrwxrwt. 34 root root 12K Apr 23 16:04 .. -rw-r--r-- 1 kkarri waxmanlab 13G Apr 23 15:12 G166_M13.Forward.wig -rw-r--r-- 1 kkarri waxmanlab 14G Apr 23 15:12 G166_M13.Reverse.wig -rw-r--r-- 1 kkarri waxmanlab 2.8G Apr 23 13:31 G166_M13_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 2.8G Apr 23 13:42 G166_M13_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 6.5M Apr 23 13:43 G166_M13_sorted.bam.bai drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 23 16:02 UCSC_BigWig drwxr-xr-x 2 kkarri waxmanlab 4.0K Apr 23 15:56 UCSC_Tools -rwxr-xr-x 1 kkarri waxmanlab 584 Apr 23 13:31 mm9.chrom.sizes ========================================================== Finished on : Tue Apr 23 16:14:19 EDT 2019 2 hours, 44 minutes and 25 seconds elapsed. ==========================================================