-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M31
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-kb4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig
Current job ID : 9374136
Current job name : Step_11_G170_M31
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9374136.1.linga

Loading required modules...


INPUT_BAM:
G170_M31_primary_unique.bam


List files in scratch directory:

total 854M
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:20 .
drwxrwxrwt. 41 root   root      4.0K Sep 16 11:18 ..
-rw-r--r--   1 kkarri waxmanlab 854M Sep 16 11:20 G170_M31_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 11:20 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 11:20 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Sep 16 11:20 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_M31_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M31 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G170_M31.Forward.wig <==
variableStep chrom=chrY
120160	1.78
120161	1.78
120162	1.78
120163	1.78
120164	1.78
120165	1.78
120166	1.78
120167	1.78
120168	1.78

==> G170_M31.Reverse.wig <==
variableStep chrom=chrY
113549	-0.36
113550	-0.36
113551	-0.36
113552	-0.36
113553	-0.36
113554	-0.36
113555	-0.36
113556	-0.36
113557	-0.36

#--------------------------------
G170_M31.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
79557386
Line count where 2nd column is only a negative sign:
0
Copy G170_M31.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G170_M31.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
77786505
Line count where 2nd column is only a negative sign:
0
Copy G170_M31.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 1139319026 Sep 16 12:10 ./UCSC_Tools/G170_M31.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1192235917 Sep 16 12:14 ./UCSC_Tools/G170_M31.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Sep 16 12:14 ./UCSC_Tools/mm9.chrom.sizes
-rwx------ 1 kkarri waxmanlab    1012225 Sep 16 11:20 ./UCSC_Tools/wigToBigWig

Copy output to storage dir


List files in scratch

total 3.9G
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:29 .
drwxrwxrwt. 41 root   root      4.0K Sep 16 11:18 ..
-rw-r--r--   1 kkarri waxmanlab 1.1G Sep 16 12:09 G170_M31.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 1.2G Sep 16 12:09 G170_M31.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 854M Sep 16 11:20 G170_M31_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 854M Sep 16 11:26 G170_M31_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 4.7M Sep 16 11:27 G170_M31_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 12:14 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 12:14 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Sep 16 11:20 mm9.chrom.sizes
==========================================================
Finished on : Mon Sep 16 12:16:00 EDT 2019
0 hours, 57 minutes and 22 seconds elapsed.
==========================================================