-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M13
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-tm3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig
Current job ID : 9374118
Current job name : Step_11_G170_M13
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9374118.1.linga

Loading required modules...


INPUT_BAM:
G170_M13_primary_unique.bam


List files in scratch directory:

total 2.0G
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:23 .
drwxrwxrwt. 12 root   root      4.0K Sep 16 11:18 ..
-rw-r--r--   1 kkarri waxmanlab 2.0G Sep 16 11:23 G170_M13_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_M13_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M13 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G170_M13.Forward.wig <==
variableStep chrom=chrY
279766	0.32
279767	0.32
279768	0.32
279769	0.32
279770	0.32
279771	0.32
279772	0.32
279773	0.32
279774	0.32

==> G170_M13.Reverse.wig <==
variableStep chrom=chrY
433871	-0.16
433872	-0.16
433873	-0.16
433874	-0.16
433875	-0.16
433876	-0.16
433877	-0.16
433878	-0.16
433879	-0.16

#--------------------------------
G170_M13.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
108714918
Line count where 2nd column is only a negative sign:
0
Copy G170_M13.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G170_M13.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
107645847
Line count where 2nd column is only a negative sign:
0
Copy G170_M13.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 1559754330 Sep 16 12:16 ./UCSC_Tools/G170_M13.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1652457305 Sep 16 12:19 ./UCSC_Tools/G170_M13.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Sep 16 12:19 ./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 11:38 .
drwxrwxrwt. 12 root   root      4.0K Sep 16 11:56 ..
-rw-r--r--   1 kkarri waxmanlab 1.5G Sep 16 12:15 G170_M13.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 1.6G Sep 16 12:15 G170_M13.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 2.0G Sep 16 11:23 G170_M13_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.0G Sep 16 11:35 G170_M13_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.7M Sep 16 11:35 G170_M13_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 12:20 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 12:19 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Sep 16 11:23 mm9.chrom.sizes
==========================================================
Finished on : Mon Sep 16 12:21:57 EDT 2019
1 hours, 3 minutes and 20 seconds elapsed.
==========================================================