-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M22
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-ka5
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig
Current job ID : 9374127
Current job name : Step_11_G170_M22
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9374127.1.linga

Loading required modules...


INPUT_BAM:
G170_M22_primary_unique.bam


List files in scratch directory:

total 2.1G
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:23 .
drwxrwxrwt. 36 root   root      4.0K Sep 16 11:18 ..
-rw-r--r--   1 kkarri waxmanlab 2.1G Sep 16 11:23 G170_M22_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_M22_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M22 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G170_M22.Forward.wig <==
variableStep chrom=chrY
1477245	0.15
1477246	0.15
1477247	0.15
1477248	0.15
1477249	0.15
1477250	0.15
1477251	0.15
1477252	0.15
1477253	0.15

==> G170_M22.Reverse.wig <==
variableStep chrom=chrY
317842	-0.15
317843	-0.15
317844	-0.15
317845	-0.15
317846	-0.15
317848	-0.15
317849	-0.15
317850	-0.15
317851	-0.15

#--------------------------------
G170_M22.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
101263659
Line count where 2nd column is only a negative sign:
0
Copy G170_M22.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G170_M22.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
97195737
Line count where 2nd column is only a negative sign:
0
Copy G170_M22.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 1452567965 Sep 16 13:08 ./UCSC_Tools/G170_M22.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1492403473 Sep 16 13:12 ./UCSC_Tools/G170_M22.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Sep 16 13:12 ./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 6.9G
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:45 .
drwxrwxrwt. 36 root   root      4.0K Sep 16 11:18 ..
-rw-r--r--   1 kkarri waxmanlab 1.4G Sep 16 13:06 G170_M22.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 1.4G Sep 16 13:06 G170_M22.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 2.1G Sep 16 11:23 G170_M22_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.1G Sep 16 11:38 G170_M22_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.6M Sep 16 11:39 G170_M22_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 13:13 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 13:12 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Sep 16 11:23 mm9.chrom.sizes
==========================================================
Finished on : Mon Sep 16 13:15:18 EDT 2019
1 hours, 56 minutes and 40 seconds elapsed.
==========================================================