-----------------------
Start of variable list:
-----------------------
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples
Dataset_Label:
G160
bin_mode:
Off
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/10_bamCorrelate
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/10_bamCorrelate/Output
JOB_COUNTER:
02
zMin:
0.6
zMax:
1.0
BED_file_name:
Intron_Only_Regions
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Aug 24 07:44:48 EDT 2017
Running on node : scc-ph4
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/10_bamCorrelate
Current job ID : 383584
Current job name : Step_10_bamCor_02
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/383584.1.p16

Loading required modules...

Getting BED file line count...
Before ENCODE_Blacklist filter:
193089
Overlap BED file with mm9-blacklist.bed and filter out overlap
Intron_Only_Regions
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:
191105

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 12M
drwxr-xr-x   4 kkarri pulmseq 4.0K Aug 24 07:44 .
drwxrwxrwt. 38 root   root     20K Aug 24 07:44 ..
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 24 07:44 Input
-rwxr-xr-x   1 kkarri pulmseq  205 Aug 24 07:44 Input_Samples.txt
-rwxr-xr-x   1 kkarri pulmseq  12M Aug 24 07:44 Intron_Only_Regions.bed
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 24 07:44 Intron_Only_Regions_mm9-blacklist_Output
-rwxr-xr-x   1 kkarri pulmseq  71K Aug 24 07:44 mm9-blacklist.bed
-rwxr-xr-x   1 kkarri pulmseq 7.6K Aug 24 07:44 overlap.R
-rwxr-xr-x   1 kkarri pulmseq 6.0K Aug 24 07:44 overlap.sh
-rw-r--r--   1 kkarri pulmseq  23K Aug 24 07:44 peak1_dump.bed

Starting to run my commands


Starting bamCorrelate command


Ending bamCorrelate command


Starting plotCorrelation command


Ending plotCorrelation command


List files:

total 12M
drwxr-xr-x   4 kkarri pulmseq 4.0K Aug 24 07:44 .
drwxrwxrwt. 38 root   root     20K Aug 24 07:44 ..
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 24 07:44 Input
-rwxr-xr-x   1 kkarri pulmseq  205 Aug 24 07:44 Input_Samples.txt
-rwxr-xr-x   1 kkarri pulmseq  12M Aug 24 07:44 Intron_Only_Regions.bed
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 24 07:44 Intron_Only_Regions_mm9-blacklist_Output
-rwxr-xr-x   1 kkarri pulmseq  71K Aug 24 07:44 mm9-blacklist.bed
-rwxr-xr-x   1 kkarri pulmseq 7.6K Aug 24 07:44 overlap.R
-rwxr-xr-x   1 kkarri pulmseq 6.0K Aug 24 07:44 overlap.sh
-rw-r--r--   1 kkarri pulmseq  23K Aug 24 07:44 peak1_dump.bed
==========================================================
Finished on : Thu Aug 24 07:45:01 EDT 2017
0 hours, 0 minutes and 13 seconds elapsed.
==========================================================