-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M11
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-tm1
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig
Current job ID : 9374116
Current job name : Step_11_G170_M11
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9374116.1.linga

Loading required modules...


INPUT_BAM:
G170_M11_primary_unique.bam


List files in scratch directory:

total 2.2G
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:23 .
drwxrwxrwt. 14 root   root      4.0K Sep 16 11:18 ..
-rw-r--r--   1 kkarri waxmanlab 2.2G Sep 16 11:23 G170_M11_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_M11_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M11 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G170_M11.Forward.wig <==
variableStep chrom=chrY
1865610	0.14
1865611	0.14
1865612	0.14
1865613	0.14
1865614	0.14
1865615	0.14
1865616	0.14
1865617	0.14
1865618	0.14

==> G170_M11.Reverse.wig <==
variableStep chrom=chrY
945588	-0.14
945589	-0.14
945590	-0.14
945591	-0.14
945592	-0.14
945593	-0.14
945594	-0.14
945595	-0.14
945596	-0.14

#--------------------------------
G170_M11.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
111104179
Line count where 2nd column is only a negative sign:
0
Copy G170_M11.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G170_M11.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
110396401
Line count where 2nd column is only a negative sign:
0
Copy G170_M11.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 1593232589 Sep 16 12:21 ./UCSC_Tools/G170_M11.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1693954614 Sep 16 12:24 ./UCSC_Tools/G170_M11.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Sep 16 12:24 ./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 7.4G
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:38 .
drwxrwxrwt. 14 root   root      4.0K Sep 16 11:57 ..
-rw-r--r--   1 kkarri waxmanlab 1.5G Sep 16 12:20 G170_M11.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 1.6G Sep 16 12:20 G170_M11.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 2.2G Sep 16 11:23 G170_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.2G Sep 16 11:35 G170_M11_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 4.4M Sep 16 11:36 G170_M11_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 12:25 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 12:24 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Sep 16 11:23 mm9.chrom.sizes
==========================================================
Finished on : Mon Sep 16 12:26:45 EDT 2019
1 hours, 8 minutes and 8 seconds elapsed.
==========================================================