-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M10
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/00_Setup_Pipeline
STRAND_RULE:
1+-,1-+,2++,2--
BU_User:
kkarri
VM_DIR_UCSC:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G168_TCPO_Env
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/11_UCSC_BigWig
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Mar 13 10:53:08 EDT 2019
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/11_UCSC_BigWig
Current job ID : 3566207
Current job name : Step_11_G168_G169_M10
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/3566207.1.linga

Loading required modules...


INPUT_BAM:
G168_G169_M10_primary_unique.bam


List files in scratch directory:

total 1.9G
drwx------   4 kkarri waxmanlab 4.0K Mar 13 10:53 .
drwxrwxrwt. 31 root   root      164K Mar 13 10:52 ..
-rw-r--r--   1 kkarri waxmanlab 1.9G Mar 13 10:53 G168_G169_M10_primary_unique.bam
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 13 10:53 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 13 10:53 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Mar 13 10:53 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=G168_G169_M10_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G168_G169_M10 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G168_G169_M10.Forward.wig <==
variableStep chrom=chrY
223856	0.35
223857	0.35
223858	0.35
223859	0.35
223860	0.35
223861	0.35
223862	0.71
223863	0.71
223864	0.71

==> G168_G169_M10.Reverse.wig <==
variableStep chrom=chrY
430351	-0.18
430352	-0.18
430353	-0.18
430354	-0.18
430355	-0.18
430356	-0.18
430357	-0.18
430358	-0.18
430359	-0.18

#--------------------------------
G168_G169_M10.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
77471328
Line count where 2nd column is only a negative sign:
0
Copy G168_G169_M10.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G168_G169_M10.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
76013647
Line count where 2nd column is only a negative sign:
0
Copy G168_G169_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 1109937334 Mar 13 12:42 ./UCSC_Tools/G168_G169_M10.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1165567515 Mar 13 12:46 ./UCSC_Tools/G168_G169_M10.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Mar 13 12:46 ./UCSC_Tools/mm9.chrom.sizes
-rwx------ 1 kkarri waxmanlab    1012225 Mar 13 10:53 ./UCSC_Tools/wigToBigWig

Copy output to storage dir


List files in scratch

total 5.8G
drwx------   4 kkarri waxmanlab 4.0K Mar 13 11:12 .
drwxrwxrwt. 41 root   root      164K Mar 13 12:48 ..
-rw-r--r--   1 kkarri waxmanlab 1.1G Mar 13 12:40 G168_G169_M10.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 1.1G Mar 13 12:40 G168_G169_M10.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 1.9G Mar 13 10:53 G168_G169_M10_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.9G Mar 13 11:06 G168_G169_M10_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.1M Mar 13 11:07 G168_G169_M10_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 13 12:47 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 13 12:46 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Mar 13 10:53 mm9.chrom.sizes
==========================================================
Finished on : Wed Mar 13 12:48:53 EDT 2019
1 hours, 55 minutes and 45 seconds elapsed.
==========================================================