-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M29
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-ka6
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig
Current job ID : 9374134
Current job name : Step_11_G170_M29
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9374134.1.linga

Loading required modules...


INPUT_BAM:
G170_M29_primary_unique.bam


List files in scratch directory:

total 2.0G
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:25 .
drwxrwxrwt. 55 root   root      4.0K Sep 16 11:18 ..
-rw-r--r--   1 kkarri waxmanlab 2.0G Sep 16 11:25 G170_M29_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 11:25 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 11:25 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Sep 16 11:25 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_M29_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M29 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G170_M29.Forward.wig <==
variableStep chrom=chrY
2036648	0.16
2036649	0.16
2036650	0.16
2036651	0.16
2036652	0.16
2036653	0.16
2036654	0.16
2036655	0.16
2036656	0.16

==> G170_M29.Reverse.wig <==
variableStep chrom=chrY
476137	-0.16
476138	-0.16
476139	-0.16
476140	-0.16
476141	-0.16
476142	-0.16
476143	-0.16
476144	-0.16
476145	-0.16

#--------------------------------
G170_M29.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
93468709
Line count where 2nd column is only a negative sign:
0
Copy G170_M29.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G170_M29.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
90369984
Line count where 2nd column is only a negative sign:
0
Copy G170_M29.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 1341176878 Sep 16 13:13 ./UCSC_Tools/G170_M29.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1388325684 Sep 16 13:17 ./UCSC_Tools/G170_M29.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Sep 16 13:17 ./UCSC_Tools/mm9.chrom.sizes
-rwx------ 1 kkarri waxmanlab    1012225 Sep 16 11:25 ./UCSC_Tools/wigToBigWig

Copy output to storage dir


List files in scratch

total 6.5G
drwx------   4 kkarri waxmanlab 4.0K Sep 16 11:47 .
drwxrwxrwt. 55 root   root      4.0K Sep 16 11:18 ..
-rw-r--r--   1 kkarri waxmanlab 1.3G Sep 16 13:11 G170_M29.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 1.3G Sep 16 13:11 G170_M29.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 2.0G Sep 16 11:25 G170_M29_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.0G Sep 16 11:40 G170_M29_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.5M Sep 16 11:41 G170_M29_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 13:18 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 13:17 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Sep 16 11:25 mm9.chrom.sizes
==========================================================
Finished on : Mon Sep 16 13:19:18 EDT 2019
2 hours, 0 minutes and 38 seconds elapsed.
==========================================================