-----------------------
Start of variable list:
-----------------------
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation
Dataset_Label:
LZ
bin_mode:
Off
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/09_bamCorrelate
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/09_bamCorrelate/Output
JOB_COUNTER:
04
zMin:
0.6
zMax:
1.0
BED_file_name:
genes
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed May  9 20:27:39 EDT 2018
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/09_bamCorrelate
Current job ID : 6139638
Current job name : Step_09_bamCor_04
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6139638.1.linga

Loading required modules...

Getting BED file line count...
Before ENCODE_Blacklist filter:
595632
Overlap BED file with mm9-blacklist.bed and filter out overlap
genes
mm9-blacklist
----------------------------------------------------------------------------
cleaning input
sorting input files
classify common or unique peaks
getting the union of the peak sets
getting the merged common peaks
getting distance of nearest peak
counting peaks
Running overlap.R script to get peak overlap, peak width, and peak proximity statistics ...
Creating summary file
Done!
----------------------------------------------------------------------------

Getting BED file line count...
After ENCODE_Blacklist filter:
591398

Copy input sample BAM files to Input folder


Save Input file lists to a variable

Input_List:

Labels_List:


List files in scratch directory:

total 27M
drwx------   4 kkarri waxmanlab 4.0K May  9 20:28 .
drwxrwxrwt. 48 root   root      168K May  9 20:27 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K May  9 20:28 Input
-rwxr-xr-x   1 kkarri waxmanlab  318 May  9 20:28 Input_Samples.txt
-rwxr-xr-x   1 kkarri waxmanlab  27M May  9 20:28 genes.bed
drwxr-xr-x   2 kkarri waxmanlab 4.0K May  9 20:28 genes_mm9-blacklist_Output
-rwxr-xr-x   1 kkarri waxmanlab  71K May  9 20:27 mm9-blacklist.bed
-rwxr-xr-x   1 kkarri waxmanlab 7.6K May  9 20:27 overlap.R
-rwxr-xr-x   1 kkarri waxmanlab 6.0K May  9 20:27 overlap.sh
-rw-r--r--   1 kkarri waxmanlab  66K May  9 20:27 peak1_dump.bed

Starting to run my commands


Starting bamCorrelate command


Ending bamCorrelate command


Starting plotCorrelation command


Ending plotCorrelation command


List files:

total 27M
drwx------   4 kkarri waxmanlab 4.0K May  9 20:28 .
drwxrwxrwt. 48 root   root      168K May  9 20:27 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K May  9 20:28 Input
-rwxr-xr-x   1 kkarri waxmanlab  318 May  9 20:28 Input_Samples.txt
-rwxr-xr-x   1 kkarri waxmanlab  27M May  9 20:28 genes.bed
drwxr-xr-x   2 kkarri waxmanlab 4.0K May  9 20:28 genes_mm9-blacklist_Output
-rwxr-xr-x   1 kkarri waxmanlab  71K May  9 20:27 mm9-blacklist.bed
-rwxr-xr-x   1 kkarri waxmanlab 7.6K May  9 20:27 overlap.R
-rwxr-xr-x   1 kkarri waxmanlab 6.0K May  9 20:27 overlap.sh
-rw-r--r--   1 kkarri waxmanlab  66K May  9 20:27 peak1_dump.bed
==========================================================
Finished on : Wed May  9 20:28:22 EDT 2018
0 hours, 0 minutes and 43 seconds elapsed.
==========================================================