----------------------- Start of variable list: ----------------------- Sample_ID: G170_M12 Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170 Sample_Labels_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/00_Setup_Pipeline STRAND_RULE: 1+-,1-+,2++,2-- BU_User: kkarri VM_DIR_UCSC: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170 SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig ----------------------- End of variable list ----------------------- ========================================================== Starting on : Mon Sep 16 11:18:37 EDT 2019 Running on node : scc-tk3 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig Current job ID : 9374117 Current job name : Step_11_G170_M12 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9374117.1.linga Loading required modules... INPUT_BAM: G170_M12_primary_unique.bam List files in scratch directory: total 2.1G drwx------ 4 kkarri waxmanlab 4.0K Sep 16 11:23 . drwxrwxrwt. 9 root root 4.0K Sep 16 11:18 .. -rw-r--r-- 1 kkarri waxmanlab 2.1G Sep 16 11:23 G170_M12_primary_unique.bam drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 11:23 UCSC_BigWig drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 11:23 UCSC_Tools -rwxr-xr-x 1 kkarri waxmanlab 584 Sep 16 11:23 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=G170_M12_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M12 --wigsum=1000000000 --strand=1+-,1-+,2++,2-- Skip multi-hits:False Finished bam2wig.py command Sample from wiggle files: ==> G170_M12.Forward.wig <== variableStep chrom=chrY 27387 0.14 27388 0.14 27389 0.14 27390 0.14 27391 0.14 27392 0.14 27393 0.14 27394 0.14 27395 0.14 ==> G170_M12.Reverse.wig <== variableStep chrom=chrY 1477249 -0.14 1477250 -0.14 1477251 -0.14 1477252 -0.14 1477253 -0.14 1477254 -0.14 1477255 -0.14 1477256 -0.14 1477257 -0.14 #-------------------------------- G170_M12.Forward.wig #-------------------------------- Line count where 2nd column does not equal "-": 116541401 Line count where 2nd column is only a negative sign: 0 Copy G170_M12.Forward.wig to UCSC_Tools folder Copy mm9.chrom.sizes to UCSC_Tools folder Start wigToBigWig End wigToBigWig #-------------------------------- G170_M12.Reverse.wig #-------------------------------- Line count where 2nd column does not equal "-": 115498131 Line count where 2nd column is only a negative sign: 0 Copy G170_M12.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 1671035068 Sep 16 12:20 ./UCSC_Tools/G170_M12.Forward.wig -rw-r--r-- 1 kkarri waxmanlab 1772283165 Sep 16 12:24 ./UCSC_Tools/G170_M12.Reverse.wig -rwxr-xr-x 1 kkarri waxmanlab 584 Sep 16 12:24 ./UCSC_Tools/mm9.chrom.sizes -rwx------ 1 kkarri waxmanlab 1012225 Sep 16 11:23 ./UCSC_Tools/wigToBigWig Copy output to storage dir List files in scratch total 7.4G drwx------ 4 kkarri waxmanlab 4.0K Sep 16 11:39 . drwxrwxrwt. 9 root root 4.0K Sep 16 11:57 .. -rw-r--r-- 1 kkarri waxmanlab 1.6G Sep 16 12:19 G170_M12.Forward.wig -rw-r--r-- 1 kkarri waxmanlab 1.7G Sep 16 12:19 G170_M12.Reverse.wig -rw-r--r-- 1 kkarri waxmanlab 2.1G Sep 16 11:23 G170_M12_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 2.1G Sep 16 11:36 G170_M12_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 4.0M Sep 16 11:36 G170_M12_sorted.bam.bai drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 12:24 UCSC_BigWig drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 12:24 UCSC_Tools -rwxr-xr-x 1 kkarri waxmanlab 584 Sep 16 11:23 mm9.chrom.sizes ========================================================== Finished on : Mon Sep 16 12:26:13 EDT 2019 1 hours, 7 minutes and 36 seconds elapsed. ==========================================================