----------------------- Start of variable list: ----------------------- Sample_ID: G170_M21 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 11:18:39 EDT 2019 Running on node : scc-kb3 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig Current job ID : 9374126 Current job name : Step_11_G170_M21 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9374126.1.linga Loading required modules... INPUT_BAM: G170_M21_primary_unique.bam List files in scratch directory: total 2.1G drwx------ 4 kkarri waxmanlab 4.0K Sep 16 11:23 . drwxrwxrwt. 24 root root 4.0K Sep 16 11:18 .. -rw-r--r-- 1 kkarri waxmanlab 2.1G Sep 16 11:23 G170_M21_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_M21_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M21 --wigsum=1000000000 --strand=1+-,1-+,2++,2-- Skip multi-hits:False Finished bam2wig.py command Sample from wiggle files: ==> G170_M21.Forward.wig <== variableStep chrom=chrY 1863801 0.15 1863802 0.15 1863803 0.15 1863804 0.15 1863805 0.15 1863806 0.15 1863807 0.15 1863808 0.15 1863809 0.15 ==> G170_M21.Reverse.wig <== variableStep chrom=chrY 23684 -0.15 23685 -0.15 23686 -0.15 23687 -0.15 23688 -0.15 23689 -0.15 23690 -0.15 23691 -0.15 23692 -0.15 #-------------------------------- G170_M21.Forward.wig #-------------------------------- Line count where 2nd column does not equal "-": 98890900 Line count where 2nd column is only a negative sign: 0 Copy G170_M21.Forward.wig to UCSC_Tools folder Copy mm9.chrom.sizes to UCSC_Tools folder Start wigToBigWig End wigToBigWig #-------------------------------- G170_M21.Reverse.wig #-------------------------------- Line count where 2nd column does not equal "-": 94778264 Line count where 2nd column is only a negative sign: 0 Copy G170_M21.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 1418125761 Sep 16 13:13 ./UCSC_Tools/G170_M21.Forward.wig -rw-r--r-- 1 kkarri waxmanlab 1455221671 Sep 16 13:17 ./UCSC_Tools/G170_M21.Reverse.wig -rwxr-xr-x 1 kkarri waxmanlab 584 Sep 16 13:17 ./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 6.9G drwx------ 4 kkarri waxmanlab 4.0K Sep 16 11:45 . drwxrwxrwt. 25 root root 4.0K Sep 16 12:39 .. -rw-r--r-- 1 kkarri waxmanlab 1.4G Sep 16 13:11 G170_M21.Forward.wig -rw-r--r-- 1 kkarri waxmanlab 1.4G Sep 16 13:11 G170_M21.Reverse.wig -rw-r--r-- 1 kkarri waxmanlab 2.1G Sep 16 11:23 G170_M21_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 2.1G Sep 16 11:39 G170_M21_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 3.6M Sep 16 11:40 G170_M21_sorted.bam.bai drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 13:18 UCSC_BigWig drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 13:17 UCSC_Tools -rwxr-xr-x 1 kkarri waxmanlab 584 Sep 16 11:23 mm9.chrom.sizes ========================================================== Finished on : Mon Sep 16 13:19:41 EDT 2019 2 hours, 1 minutes and 2 seconds elapsed. ==========================================================