-----------------------
Start of variable list:
-----------------------
Sample_ID:
G166_M12
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-we3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/11_UCSC_BigWig
Current job ID : 5544739
Current job name : Step_11_G166_M12
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5544739.1.w

Loading required modules...


INPUT_BAM:
G166_M12_primary_unique.bam


List files in scratch directory:

total 786M
drwx------   4 kkarri waxmanlab 4.0K Apr 23 13:30 .
drwxrwxrwt. 38 root   root       64K Apr 23 13:29 ..
-rw-r--r--   1 kkarri waxmanlab 786M Apr 23 13:30 G166_M12_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_M12_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G166_M12 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G166_M12.Forward.wig <==
variableStep chrom=chrY
78154	0.62
78155	0.62
78156	0.62
78157	0.62
78158	0.62
78159	0.62
78160	0.62
78161	0.62
78162	0.62

==> G166_M12.Reverse.wig <==
variableStep chrom=chrY
29908	-0.62
29909	-0.62
29910	-0.62
29911	-0.62
29912	-0.62
29913	-0.62
29914	-0.62
29915	-0.62
29916	-0.62

#--------------------------------
G166_M12.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
120455351
Line count where 2nd column is only a negative sign:
0
Copy G166_M12.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G166_M12.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
116482232
Line count where 2nd column is only a negative sign:
0
Copy G166_M12.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 1718563537 Apr 23 13:55 ./UCSC_Tools/G166_M12.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1778857247 Apr 23 13:59 ./UCSC_Tools/G166_M12.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Apr 23 13:59 ./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 4.8G
drwx------   4 kkarri waxmanlab 4.0K Apr 23 13:36 .
drwxrwxrwt. 38 root   root       64K Apr 23 13:52 ..
-rw-r--r--   1 kkarri waxmanlab 1.7G Apr 23 13:54 G166_M12.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 1.7G Apr 23 13:54 G166_M12.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 786M Apr 23 13:30 G166_M12_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 786M Apr 23 13:34 G166_M12_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 4.9M Apr 23 13:34 G166_M12_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 23 14:00 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 23 13:59 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Apr 23 13:30 mm9.chrom.sizes
==========================================================
Finished on : Tue Apr 23 14:01:48 EDT 2019
0 hours, 31 minutes and 55 seconds elapsed.
==========================================================