----------------------- Start of variable list: ----------------------- Sample_ID: G170_M27 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 11:19:25 EDT 2019 Running on node : scc-ka8 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig Current job ID : 9374132 Current job name : Step_11_G170_M27 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9374132.1.linga Loading required modules... INPUT_BAM: G170_M27_primary_unique.bam List files in scratch directory: total 2.0G drwx------ 4 kkarri waxmanlab 4.0K Sep 16 11:26 . drwxrwxrwt. 49 root root 12K Sep 16 11:18 .. -rw-r--r-- 1 kkarri waxmanlab 2.0G Sep 16 11:26 G170_M27_primary_unique.bam drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 11:26 UCSC_BigWig drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 11:26 UCSC_Tools -rwxr-xr-x 1 kkarri waxmanlab 584 Sep 16 11:26 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_M27_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M27 --wigsum=1000000000 --strand=1+-,1-+,2++,2-- Skip multi-hits:False Finished bam2wig.py command Sample from wiggle files: ==> G170_M27.Forward.wig <== variableStep chrom=chrY 2894918 0.15 2894919 0.15 2894920 0.15 2894921 0.15 2894922 0.15 2894923 0.15 2894924 0.15 2894925 0.15 2894926 0.15 ==> G170_M27.Reverse.wig <== variableStep chrom=chrY 29923 -0.15 29924 -0.15 29925 -0.15 29926 -0.15 29927 -0.15 29928 -0.15 29929 -0.15 29930 -0.15 29931 -0.15 #-------------------------------- G170_M27.Forward.wig #-------------------------------- Line count where 2nd column does not equal "-": 92657869 Line count where 2nd column is only a negative sign: 0 Copy G170_M27.Forward.wig to UCSC_Tools folder Copy mm9.chrom.sizes to UCSC_Tools folder Start wigToBigWig End wigToBigWig #-------------------------------- G170_M27.Reverse.wig #-------------------------------- Line count where 2nd column does not equal "-": 89186166 Line count where 2nd column is only a negative sign: 0 Copy G170_M27.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 1328613002 Sep 16 13:18 ./UCSC_Tools/G170_M27.Forward.wig -rw-r--r-- 1 kkarri waxmanlab 1369133705 Sep 16 13:22 ./UCSC_Tools/G170_M27.Reverse.wig -rwxr-xr-x 1 kkarri waxmanlab 584 Sep 16 13:22 ./UCSC_Tools/mm9.chrom.sizes -rwx------ 1 kkarri waxmanlab 1012225 Sep 16 11:26 ./UCSC_Tools/wigToBigWig Copy output to storage dir List files in scratch total 6.6G drwx------ 4 kkarri waxmanlab 4.0K Sep 16 11:48 . drwxrwxrwt. 50 root root 12K Sep 16 13:23 .. -rw-r--r-- 1 kkarri waxmanlab 1.3G Sep 16 13:17 G170_M27.Forward.wig -rw-r--r-- 1 kkarri waxmanlab 1.3G Sep 16 13:17 G170_M27.Reverse.wig -rw-r--r-- 1 kkarri waxmanlab 2.0G Sep 16 11:26 G170_M27_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 2.0G Sep 16 11:42 G170_M27_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 3.7M Sep 16 11:42 G170_M27_sorted.bam.bai drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 13:23 UCSC_BigWig drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 13:22 UCSC_Tools -rwxr-xr-x 1 kkarri waxmanlab 584 Sep 16 11:26 mm9.chrom.sizes ========================================================== Finished on : Mon Sep 16 13:25:03 EDT 2019 2 hours, 5 minutes and 38 seconds elapsed. ==========================================================