-----------------------
Start of variable list:
-----------------------
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New
Dataset_Label:
G123
bin_mode:
Off
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/10_bamCorrelate
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/10_bamCorrelate/Output
JOB_COUNTER:
03
zMin:
0.6
zMax:
1.0
BED_file_name:
RefSeq_GeneBody
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sat Dec  8 01:33:01 EST 2018
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/G123_New/Scripts/10_bamCorrelate
Current job ID : 29299
Current job name : Step_10_bamCor_03
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/29299.1.linga

Loading required modules...

Getting BED file line count...
Before ENCODE_Blacklist filter:
665744
Overlap BED file with mm9-blacklist.bed and filter out overlap
RefSeq_GeneBody
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:
660786

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 37M
drwx------   4 kkarri waxmanlab 4.0K Dec  8 01:33 .
drwxrwxrwt. 29 root   root      268K Dec  8 01:33 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec  8 01:33 Input
-rwxr-xr-x   1 kkarri waxmanlab 1.3K Dec  8 01:33 Input_Samples.txt
-rwxr-xr-x   1 kkarri waxmanlab  36M Dec  8 01:33 RefSeq_GeneBody.bed
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec  8 01:33 RefSeq_GeneBody_mm9-blacklist_Output
-rwxr-xr-x   1 kkarri waxmanlab  71K Dec  8 01:33 mm9-blacklist.bed
-rwxr-xr-x   1 kkarri waxmanlab 7.6K Dec  8 01:33 overlap.R
-rwxr-xr-x   1 kkarri waxmanlab 6.0K Dec  8 01:33 overlap.sh
-rw-r--r--   1 kkarri waxmanlab  80K Dec  8 01:33 peak1_dump.bed

Starting to run my commands


Starting bamCorrelate command


Ending bamCorrelate command


Starting plotCorrelation command


Ending plotCorrelation command


List files:

total 37M
drwx------   4 kkarri waxmanlab 4.0K Dec  8 01:33 .
drwxrwxrwt. 29 root   root      268K Dec  8 01:33 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec  8 01:33 Input
-rwxr-xr-x   1 kkarri waxmanlab 1.3K Dec  8 01:33 Input_Samples.txt
-rwxr-xr-x   1 kkarri waxmanlab  36M Dec  8 01:33 RefSeq_GeneBody.bed
drwxr-xr-x   2 kkarri waxmanlab 4.0K Dec  8 01:33 RefSeq_GeneBody_mm9-blacklist_Output
-rwxr-xr-x   1 kkarri waxmanlab  71K Dec  8 01:33 mm9-blacklist.bed
-rwxr-xr-x   1 kkarri waxmanlab 7.6K Dec  8 01:33 overlap.R
-rwxr-xr-x   1 kkarri waxmanlab 6.0K Dec  8 01:33 overlap.sh
-rw-r--r--   1 kkarri waxmanlab  80K Dec  8 01:33 peak1_dump.bed
==========================================================
Finished on : Sat Dec  8 01:33:38 EST 2018
0 hours, 0 minutes and 37 seconds elapsed.
==========================================================