-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M9
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 : 3566206
Current job name : Step_11_G168_G169_M9
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/3566206.1.linga

Loading required modules...


INPUT_BAM:
G168_G169_M9_primary_unique.bam


List files in scratch directory:

total 1.6G
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 1.6G Mar 13 10:53 G168_G169_M9_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_M9_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G168_G169_M9 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G168_G169_M9.Forward.wig <==
variableStep chrom=chrY
253412	0.20
253413	0.20
253414	0.20
253415	0.20
253416	0.20
253417	0.20
253418	0.20
253419	0.20
253420	0.20

==> G168_G169_M9.Reverse.wig <==
variableStep chrom=chrY
421685	-0.20
421686	-0.20
421687	-0.20
421688	-0.20
421689	-0.20
421690	-0.20
421691	-0.20
421692	-0.20
421693	-0.20

#--------------------------------
G168_G169_M9.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
67984288
Line count where 2nd column is only a negative sign:
0
Copy G168_G169_M9.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G168_G169_M9.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
66700246
Line count where 2nd column is only a negative sign:
0
Copy G168_G169_M9.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  974311031 Mar 13 12:29 ./UCSC_Tools/G168_G169_M9.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1023396619 Mar 13 12:33 ./UCSC_Tools/G168_G169_M9.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Mar 13 12:33 ./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 5.1G
drwx------   4 kkarri waxmanlab 4.0K Mar 13 11:10 .
drwxrwxrwt. 41 root   root      128K Mar 13 11:31 ..
-rw-r--r--   1 kkarri waxmanlab 930M Mar 13 12:28 G168_G169_M9.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 976M Mar 13 12:28 G168_G169_M9.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 1.6G Mar 13 10:53 G168_G169_M9_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.6G Mar 13 11:05 G168_G169_M9_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.1M Mar 13 11:05 G168_G169_M9_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 13 12:34 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 13 12:33 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Mar 13 10:53 mm9.chrom.sizes
==========================================================
Finished on : Wed Mar 13 12:35:22 EDT 2019
1 hours, 42 minutes and 23 seconds elapsed.
==========================================================