-----------------------
Start of variable list:
-----------------------
Sample_ID:
G166_M11
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/00_Setup_Pipeline
STRAND_RULE:
1+-,1-+,2++,2--
BU_User:
kkarri
VM_DIR_UCSC:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_Env
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/11_UCSC_BigWig
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 23 13:29:54 EDT 2019
Running on node : scc-we4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/11_UCSC_BigWig
Current job ID : 5544738
Current job name : Step_11_G166_M11
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5544738.1.w

Loading required modules...


INPUT_BAM:
G166_M11_primary_unique.bam


List files in scratch directory:

total 742M
drwx------   4 kkarri waxmanlab 4.0K Apr 23 13:30 .
drwxrwxrwt. 35 root   root       72K Apr 23 13:29 ..
-rw-r--r--   1 kkarri waxmanlab 742M Apr 23 13:30 G166_M11_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 23 13:30 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 23 13:30 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Apr 23 13:30 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=G166_M11_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G166_M11 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G166_M11.Forward.wig <==
variableStep chrom=chrY
61781	0.72
61782	0.72
61783	0.72
61784	0.72
61785	0.72
61786	0.72
61787	0.72
61788	0.72
61789	0.72

==> G166_M11.Reverse.wig <==
variableStep chrom=chrY
34786	-0.72
34787	-0.72
34788	-0.72
34789	-0.72
34790	-0.72
34791	-0.72
34792	-0.72
34793	-0.72
34794	-0.72

#--------------------------------
G166_M11.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
132421582
Line count where 2nd column is only a negative sign:
0
Copy G166_M11.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G166_M11.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
127682002
Line count where 2nd column is only a negative sign:
0
Copy G166_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 1892435787 Apr 23 13:54 ./UCSC_Tools/G166_M11.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1952879215 Apr 23 13:58 ./UCSC_Tools/G166_M11.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Apr 23 13:58 ./UCSC_Tools/mm9.chrom.sizes
-rwx------ 1 kkarri waxmanlab    1012225 Apr 23 13:30 ./UCSC_Tools/wigToBigWig

Copy output to storage dir


List files in scratch

total 5.1G
drwx------   4 kkarri waxmanlab 4.0K Apr 23 13:35 .
drwxrwxrwt. 35 root   root       72K Apr 23 13:40 ..
-rw-r--r--   1 kkarri waxmanlab 1.8G Apr 23 13:52 G166_M11.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 1.9G Apr 23 13:52 G166_M11.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 742M Apr 23 13:30 G166_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 742M Apr 23 13:33 G166_M11_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.9M Apr 23 13:34 G166_M11_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 23 13:59 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 23 13:58 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Apr 23 13:30 mm9.chrom.sizes
==========================================================
Finished on : Tue Apr 23 14:00:52 EDT 2019
0 hours, 30 minutes and 59 seconds elapsed.
==========================================================