----------------------- Start of variable list: ----------------------- Sample_ID: G170_M23 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 11:18:38 EDT 2019 Running on node : scc-ka2 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig Current job ID : 9374128 Current job name : Step_11_G170_M23 Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/9374128.1.linga Loading required modules... INPUT_BAM: G170_M23_primary_unique.bam List files in scratch directory: total 2.2G drwx------ 4 kkarri waxmanlab 4.0K Sep 16 11:23 . drwxrwxrwt. 34 root root 4.0K Sep 16 11:18 .. -rw-r--r-- 1 kkarri waxmanlab 2.2G Sep 16 11:23 G170_M23_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_M23_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M23 --wigsum=1000000000 --strand=1+-,1-+,2++,2-- Skip multi-hits:False Finished bam2wig.py command Sample from wiggle files: ==> G170_M23.Forward.wig <== variableStep chrom=chrY 383600 0.29 383601 0.29 383602 0.29 383603 0.29 383604 0.29 383605 0.29 383606 0.29 383607 0.29 383608 0.29 ==> G170_M23.Reverse.wig <== variableStep chrom=chrY 29897 -0.14 29898 -0.14 29899 -0.14 29900 -0.14 29901 -0.14 29902 -0.14 29903 -0.14 29904 -0.14 29905 -0.14 #-------------------------------- G170_M23.Forward.wig #-------------------------------- Line count where 2nd column does not equal "-": 106792366 Line count where 2nd column is only a negative sign: 0 Copy G170_M23.Forward.wig to UCSC_Tools folder Copy mm9.chrom.sizes to UCSC_Tools folder Start wigToBigWig End wigToBigWig #-------------------------------- G170_M23.Reverse.wig #-------------------------------- Line count where 2nd column does not equal "-": 102553867 Line count where 2nd column is only a negative sign: 0 Copy G170_M23.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 1531593097 Sep 16 13:22 ./UCSC_Tools/G170_M23.Forward.wig -rw-r--r-- 1 kkarri waxmanlab 1574532753 Sep 16 13:26 ./UCSC_Tools/G170_M23.Reverse.wig -rwxr-xr-x 1 kkarri waxmanlab 584 Sep 16 13:26 ./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 7.2G drwx------ 4 kkarri waxmanlab 4.0K Sep 16 11:46 . drwxrwxrwt. 34 root root 4.0K Sep 16 11:18 .. -rw-r--r-- 1 kkarri waxmanlab 1.5G Sep 16 13:20 G170_M23.Forward.wig -rw-r--r-- 1 kkarri waxmanlab 1.5G Sep 16 13:20 G170_M23.Reverse.wig -rw-r--r-- 1 kkarri waxmanlab 2.2G Sep 16 11:23 G170_M23_primary_unique.bam -rw-r--r-- 1 kkarri waxmanlab 2.2G Sep 16 11:39 G170_M23_sorted.bam -rw-r--r-- 1 kkarri waxmanlab 3.7M Sep 16 11:40 G170_M23_sorted.bam.bai drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 13:27 UCSC_BigWig drwxr-xr-x 2 kkarri waxmanlab 4.0K Sep 16 13:26 UCSC_Tools -rwxr-xr-x 1 kkarri waxmanlab 584 Sep 16 11:23 mm9.chrom.sizes ========================================================== Finished on : Mon Sep 16 13:29:17 EDT 2019 2 hours, 10 minutes and 39 seconds elapsed. ==========================================================