-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M15
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 10:52:59 EDT 2019
Running on node : scc-ka5
Current directory : /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/11_UCSC_BigWig
Current job ID : 3566212
Current job name : Step_11_G168_G169_M15
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/3566212.1.linga

Loading required modules...


INPUT_BAM:
G168_G169_M15_primary_unique.bam


List files in scratch directory:

total 2.1G
drwx------   4 kkarri waxmanlab 4.0K Mar 13 10:53 .
drwxrwxrwt. 24 root   root      128K Mar 13 10:52 ..
-rw-r--r--   1 kkarri waxmanlab 2.1G Mar 13 10:53 G168_G169_M15_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_M15_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G168_G169_M15 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G168_G169_M15.Forward.wig <==
variableStep chrom=chrY
223860	0.15
223861	0.15
223862	0.15
223863	0.15
223864	0.15
223865	0.15
223866	0.15
223867	0.15
223868	0.15

==> G168_G169_M15.Reverse.wig <==
variableStep chrom=chrY
40618	-0.15
40619	-0.15
40620	-0.15
40621	-0.15
40622	-0.15
40623	-0.15
40624	-0.15
40625	-0.15
40626	-0.15

#--------------------------------
G168_G169_M15.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
86293666
Line count where 2nd column is only a negative sign:
0
Copy G168_G169_M15.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G168_G169_M15.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
84777684
Line count where 2nd column is only a negative sign:
0
Copy G168_G169_M15.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 1235489804 Mar 13 13:02 ./UCSC_Tools/G168_G169_M15.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1299058618 Mar 13 13:06 ./UCSC_Tools/G168_G169_M15.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Mar 13 13:06 ./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 6.6G
drwx------   4 kkarri waxmanlab 4.0K Mar 13 11:15 .
drwxrwxrwt. 37 root   root      128K Mar 13 12:57 ..
-rw-r--r--   1 kkarri waxmanlab 1.2G Mar 13 12:59 G168_G169_M15.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 1.3G Mar 13 12:59 G168_G169_M15.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 2.1G Mar 13 10:53 G168_G169_M15_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.1G Mar 13 11:08 G168_G169_M15_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.2M Mar 13 11:09 G168_G169_M15_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 13 13:07 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 13 13:06 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Mar 13 10:53 mm9.chrom.sizes
==========================================================
Finished on : Wed Mar 13 13:08:40 EDT 2019
2 hours, 15 minutes and 41 seconds elapsed.
==========================================================