-----------------------
Start of variable list:
-----------------------
Sample_ID:
G168_G169_M1
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-tl3
Current directory : /restricted/projectnb/waxmanlab/kkarri/G168_G169/G168/TCPOBOP_frStrand_Env/TCPOBOP/Scripts/11_UCSC_BigWig
Current job ID : 3566197
Current job name : Step_11_G168_G169_M1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/3566197.1.linga

Loading required modules...


INPUT_BAM:
G168_G169_M1_primary_unique.bam


List files in scratch directory:

total 1.6G
drwx------   4 kkarri waxmanlab 4.0K Mar 13 10:53 .
drwxrwxrwt. 14 root   root      132K Mar 13 10:52 ..
-rw-r--r--   1 kkarri waxmanlab 1.6G Mar 13 10:53 G168_G169_M1_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_M1_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G168_G169_M1 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G168_G169_M1.Forward.wig <==
variableStep chrom=chrY
223817	0.65
223818	0.65
223819	0.65
223820	0.65
223821	0.65
223822	0.65
223823	0.65
223824	0.65
223825	0.65

==> G168_G169_M1.Reverse.wig <==
variableStep chrom=chrY
426883	-0.22
426884	-0.22
426885	-0.22
426886	-0.22
426887	-0.22
426888	-0.22
426889	-0.22
426890	-0.22
426891	-0.22

#--------------------------------
G168_G169_M1.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
68038656
Line count where 2nd column is only a negative sign:
0
Copy G168_G169_M1.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G168_G169_M1.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
66767124
Line count where 2nd column is only a negative sign:
0
Copy G168_G169_M1.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  975166374 Mar 13 11:35 ./UCSC_Tools/G168_G169_M1.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1024191791 Mar 13 11:37 ./UCSC_Tools/G168_G169_M1.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Mar 13 11:37 ./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 4.9G
drwx------   4 kkarri waxmanlab 4.0K Mar 13 11:04 .
drwxrwxrwt. 15 root   root      132K Mar 13 11:33 ..
-rw-r--r--   1 kkarri waxmanlab 930M Mar 13 11:34 G168_G169_M1.Forward.wig
-rw-r--r--   1 kkarri waxmanlab 977M Mar 13 11:34 G168_G169_M1.Reverse.wig
-rw-r--r--   1 kkarri waxmanlab 1.6G Mar 13 10:53 G168_G169_M1_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.6G Mar 13 11:01 G168_G169_M1_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 3.0M Mar 13 11:01 G168_G169_M1_sorted.bam.bai
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 13 11:38 UCSC_BigWig
drwxr-xr-x   2 kkarri waxmanlab 4.0K Mar 13 11:37 UCSC_Tools
-rwxr-xr-x   1 kkarri waxmanlab  584 Mar 13 10:53 mm9.chrom.sizes
==========================================================
Finished on : Wed Mar 13 11:38:47 EDT 2019
0 hours, 45 minutes and 48 seconds elapsed.
==========================================================