-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M15
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 11:18:56 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 : 9374120
Current job name : Step_11_G170_M15
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9374120.1.linga

Loading required modules...


INPUT_BAM:
G170_M15_primary_unique.bam


List files in scratch directory:

total 2.1G
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 2.1G Sep 16 11:25 G170_M15_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_M15_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M15 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G170_M15.Forward.wig <==
variableStep chrom=chrY
1543715	0.15
1543716	0.15
1543717	0.15
1543718	0.29
1543719	0.29
1543720	0.29
1543721	0.29
1543722	0.29
1543723	0.29

==> G170_M15.Reverse.wig <==
variableStep chrom=chrY
598326	-0.44
598327	-0.44
598328	-0.44
598329	-0.44
598330	-0.44
598331	-0.44
598332	-0.44
598333	-0.44
598334	-0.44

#--------------------------------
G170_M15.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
108707821
Line count where 2nd column is only a negative sign:
0
Copy G170_M15.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G170_M15.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
107360920
Line count where 2nd column is only a negative sign:
0
Copy G170_M15.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 1559207955 Sep 16 13:25 ./UCSC_Tools/G170_M15.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1647802858 Sep 16 13:29 ./UCSC_Tools/G170_M15.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Sep 16 13:29 ./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 7.2G
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:48 .
drwxrwxrwt. 35 root   root      4.0K Sep 16 13:08 ..
-rw-r--r--   1 kkarri waxmanlab 1.5G Sep 16 13:22 G170_M15.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 1.6G Sep 16 13:22 G170_M15.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 2.1G Sep 16 11:25 G170_M15_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.1G Sep 16 11:41 G170_M15_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.7M Sep 16 11:42 G170_M15_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 13:30 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 13:29 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Sep 16 11:25 mm9.chrom.sizes
==========================================================
Finished on : Mon Sep 16 13:32:11 EDT 2019
2 hours, 13 minutes and 15 seconds elapsed.
==========================================================