----------------------- Start of variable list: ----------------------- Sample_ID: G170_M24 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 11:19:16 EDT 2019 Running on node : scc-ka3 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig Current job ID : 9374129 Current job name : Step_11_G170_M24 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9374129.1.linga Loading required modules... INPUT_BAM: G170_M24_primary_unique.bam List files in scratch directory: total 1.6G drwx------ 4 kkarri waxmanlab 4.0K Sep 16 11:25 . drwxrwxrwt. 37 root root 4.0K Sep 16 11:18 .. -rw-r--r-- 1 kkarri waxmanlab 1.6G Sep 16 11:25 G170_M24_primary_unique.bam drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 11:25 UCSC_BigWig drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 11:25 UCSC_Tools -rwxr-xr-x 1 kkarri waxmanlab 584 Sep 16 11:25 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_M24_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M24 --wigsum=1000000000 --strand=1+-,1-+,2++,2-- Skip multi-hits:False Finished bam2wig.py command Sample from wiggle files: ==> G170_M24.Forward.wig <== variableStep chrom=chrY variableStep chrom=chrX 3017888 0.20 3017889 0.20 3017890 0.20 3017891 0.20 3017892 0.20 3017893 0.20 3017894 0.20 3017895 0.20 ==> G170_M24.Reverse.wig <== variableStep chrom=chrY 29923 -0.20 29924 -0.20 29925 -0.20 29926 -0.20 29927 -0.20 29928 -0.20 29929 -0.20 29930 -0.20 29931 -0.20 #-------------------------------- G170_M24.Forward.wig #-------------------------------- Line count where 2nd column does not equal "-": 76506492 Line count where 2nd column is only a negative sign: 0 Copy G170_M24.Forward.wig to UCSC_Tools folder Copy mm9.chrom.sizes to UCSC_Tools folder Start wigToBigWig End wigToBigWig #-------------------------------- G170_M24.Reverse.wig #-------------------------------- Line count where 2nd column does not equal "-": 73510189 Line count where 2nd column is only a negative sign: 0 Copy G170_M24.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 1097398599 Sep 16 12:52 ./UCSC_Tools/G170_M24.Forward.wig -rw-r--r-- 1 kkarri waxmanlab 1128787617 Sep 16 12:55 ./UCSC_Tools/G170_M24.Reverse.wig -rwxr-xr-x 1 kkarri waxmanlab 584 Sep 16 12:55 ./UCSC_Tools/mm9.chrom.sizes -rwx------ 1 kkarri waxmanlab 1012225 Sep 16 11:25 ./UCSC_Tools/wigToBigWig Copy output to storage dir List files in scratch total 5.2G drwx------ 4 kkarri waxmanlab 4.0K Sep 16 11:43 . drwxrwxrwt. 37 root root 4.0K Sep 16 11:18 .. -rw-r--r-- 1 kkarri waxmanlab 1.1G Sep 16 12:50 G170_M24.Forward.wig -rw-r--r-- 1 kkarri waxmanlab 1.1G Sep 16 12:50 G170_M24.Reverse.wig -rw-r--r-- 1 kkarri waxmanlab 1.6G Sep 16 11:25 G170_M24_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 1.6G Sep 16 11:38 G170_M24_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 3.5M Sep 16 11:38 G170_M24_sorted.bam.bai drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 12:56 UCSC_BigWig drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 12:55 UCSC_Tools -rwxr-xr-x 1 kkarri waxmanlab 584 Sep 16 11:25 mm9.chrom.sizes ========================================================== Finished on : Mon Sep 16 12:57:13 EDT 2019 1 hours, 37 minutes and 58 seconds elapsed. ==========================================================