-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M25
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 11:18:37 EDT 2019
Running on node : scc-kb2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig
Current job ID : 9374130
Current job name : Step_11_G170_M25
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9374130.1.linga

Loading required modules...


INPUT_BAM:
G170_M25_primary_unique.bam


List files in scratch directory:

total 1.8G
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:22 .
drwxrwxrwt. 18 root   root      4.0K Sep 16 11:18 ..
-rw-r--r--   1 kkarri waxmanlab 1.8G Sep 16 11:22 G170_M25_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 11:22 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 11:22 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Sep 16 11:22 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_M25_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M25 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G170_M25.Forward.wig <==
variableStep chrom=chrY
2037886	0.17
2037887	0.17
2037888	0.17
2037889	0.17
2037890	0.17
2037891	0.17
2037892	0.17
2037893	0.17
2037894	0.17

==> G170_M25.Reverse.wig <==
variableStep chrom=chrY
1835774	-0.17
1835775	-0.17
1835776	-0.17
1835777	-0.17
1835778	-0.17
1835779	-0.17
1835780	-0.17
1835781	-0.17
1835782	-0.17

#--------------------------------
G170_M25.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
85883733
Line count where 2nd column is only a negative sign:
0
Copy G170_M25.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G170_M25.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
82744984
Line count where 2nd column is only a negative sign:
0
Copy G170_M25.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 1232857409 Sep 16 13:12 ./UCSC_Tools/G170_M25.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1271578438 Sep 16 13:17 ./UCSC_Tools/G170_M25.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 11:22 ./UCSC_Tools/wigToBigWig

Copy output to storage dir


List files in scratch

total 5.8G
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:45 .
drwxrwxrwt. 18 root   root      4.0K Sep 16 11:18 ..
-rw-r--r--   1 kkarri waxmanlab 1.2G Sep 16 13:10 G170_M25.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 1.2G Sep 16 13:10 G170_M25.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 1.8G Sep 16 11:22 G170_M25_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.8G Sep 16 11:38 G170_M25_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.3M Sep 16 11:39 G170_M25_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 11:22 mm9.chrom.sizes
==========================================================
Finished on : Mon Sep 16 13:19:36 EDT 2019
2 hours, 0 minutes and 59 seconds elapsed.
==========================================================