-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M16
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 10:53:09 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 : 3566213
Current job name : Step_11_G168_G169_M16
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/3566213.1.linga

Loading required modules...


INPUT_BAM:
G168_G169_M16_primary_unique.bam


List files in scratch directory:

total 2.2G
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 2.2G Mar 13 10:53 G168_G169_M16_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_M16_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G168_G169_M16 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G168_G169_M16.Forward.wig <==
variableStep chrom=chrY
28563	0.15
28564	0.15
28565	0.15
28566	0.15
28567	0.15
28568	0.15
28569	0.15
28570	0.15
28571	0.15

==> G168_G169_M16.Reverse.wig <==
variableStep chrom=chrY
434744	-0.15
434745	-0.15
434746	-0.15
434747	-0.15
434748	-0.15
434749	-0.15
434750	-0.15
434751	-0.15
434752	-0.15

#--------------------------------
G168_G169_M16.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
92522730
Line count where 2nd column is only a negative sign:
0
Copy G168_G169_M16.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G168_G169_M16.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
90712253
Line count where 2nd column is only a negative sign:
0
Copy G168_G169_M16.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 1324058393 Mar 13 13:00 ./UCSC_Tools/G168_G169_M16.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1389234304 Mar 13 13:04 ./UCSC_Tools/G168_G169_M16.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Mar 13 13:04 ./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 6.8G
drwx------   4 kkarri waxmanlab 4.0K Mar 13 11:16 .
drwxrwxrwt. 36 root   root      164K Mar 13 12:59 ..
-rw-r--r--   1 kkarri waxmanlab 1.3G Mar 13 12:57 G168_G169_M16.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 1.3G Mar 13 12:57 G168_G169_M16.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 2.2G Mar 13 10:53 G168_G169_M16_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 2.2G Mar 13 11:09 G168_G169_M16_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.2M Mar 13 11:10 G168_G169_M16_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 13 13:05 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 13 13:04 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Mar 13 10:53 mm9.chrom.sizes
==========================================================
Finished on : Wed Mar 13 13:06:48 EDT 2019
2 hours, 13 minutes and 39 seconds elapsed.
==========================================================