-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M30
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 11:18:40 EDT 2019
Running on node : scc-kb5
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig
Current job ID : 9374135
Current job name : Step_11_G170_M30
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9374135.1.linga

Loading required modules...


INPUT_BAM:
G170_M30_primary_unique.bam


List files in scratch directory:

total 1.7G
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:24 .
drwxrwxrwt. 40 root   root      4.0K Sep 16 11:18 ..
-rw-r--r--   1 kkarri waxmanlab 1.7G Sep 16 11:24 G170_M30_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 11:24 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 11:24 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Sep 16 11:24 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_M30_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M30 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G170_M30.Forward.wig <==
variableStep chrom=chrY
978287	0.19
978288	0.19
978289	0.19
978290	0.19
978291	0.19
978292	0.19
978293	0.19
978294	0.19
978295	0.19

==> G170_M30.Reverse.wig <==
variableStep chrom=chrY
1525529	-0.19
1525530	-0.19
1525531	-0.19
1525532	-0.19
1525533	-0.19
1525534	-0.19
1525535	-0.19
1525536	-0.19
1525537	-0.19

#--------------------------------
G170_M30.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
139841089
Line count where 2nd column is only a negative sign:
0
Copy G170_M30.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G170_M30.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
137461724
Line count where 2nd column is only a negative sign:
0
Copy G170_M30.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 1998645467 Sep 16 13:07 ./UCSC_Tools/G170_M30.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 2102693826 Sep 16 13:13 ./UCSC_Tools/G170_M30.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Sep 16 13:13 ./UCSC_Tools/mm9.chrom.sizes
-rwx------ 1 kkarri waxmanlab    1012225 Sep 16 11:24 ./UCSC_Tools/wigToBigWig

Copy output to storage dir


List files in scratch

total 7.2G
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:42 .
drwxrwxrwt. 40 root   root      4.0K Sep 16 11:18 ..
-rw-r--r--   1 kkarri waxmanlab 1.9G Sep 16 13:04 G170_M30.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 2.0G Sep 16 13:04 G170_M30.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 1.7G Sep 16 11:24 G170_M30_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.7G Sep 16 11:37 G170_M30_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 5.4M Sep 16 11:38 G170_M30_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 13:14 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 13:13 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Sep 16 11:24 mm9.chrom.sizes
==========================================================
Finished on : Mon Sep 16 13:16:42 EDT 2019
1 hours, 58 minutes and 2 seconds elapsed.
==========================================================