-----------------------
Start of variable list:
-----------------------
Sample_ID:
G166_M10
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 : 5544737
Current job name : Step_11_G166_M10
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5544737.1.w

Loading required modules...


INPUT_BAM:
G166_M10_primary_unique.bam


List files in scratch directory:

total 439M
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 438M Apr 23 13:30 G166_M10_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_M10_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G166_M10 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G166_M10.Forward.wig <==
variableStep chrom=chrY
180234	1.15
180235	1.15
180236	1.15
180237	1.15
180238	1.15
180239	1.15
180240	1.15
180241	1.15
180242	1.15

==> G166_M10.Reverse.wig <==
variableStep chrom=chrY
45070	-2.30
45071	-2.30
45072	-2.30
45073	-2.30
45074	-2.30
45075	-2.30
45076	-2.30
45077	-2.30
45078	-2.30

#--------------------------------
G166_M10.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
77140492
Line count where 2nd column is only a negative sign:
0
Copy G166_M10.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G166_M10.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
73982748
Line count where 2nd column is only a negative sign:
0
Copy G166_M10.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 1101241988 Apr 23 13:45 ./UCSC_Tools/G166_M10.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1130827273 Apr 23 13:48 ./UCSC_Tools/G166_M10.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Apr 23 13:48 ./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 3.0G
drwx------   4 kkarri waxmanlab 4.0K Apr 23 13:34 .
drwxrwxrwt. 37 root   root       64K Apr 23 13:44 ..
-rw-r--r--   1 kkarri waxmanlab 1.1G Apr 23 13:44 G166_M10.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 1.1G Apr 23 13:44 G166_M10.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 438M Apr 23 13:30 G166_M10_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 438M Apr 23 13:33 G166_M10_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 4.4M Apr 23 13:33 G166_M10_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 23 13:48 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 23 13:48 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Apr 23 13:30 mm9.chrom.sizes
==========================================================
Finished on : Tue Apr 23 13:49:36 EDT 2019
0 hours, 19 minutes and 42 seconds elapsed.
==========================================================