-----------------------
Start of variable list:
-----------------------
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170
Dataset_Label:
G170
bin_mode:
Off
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/10_bamCorrelate
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/10_bamCorrelate/Output
JOB_COUNTER:
03
zMin:
0.6
zMax:
1.0
BED_file_name:
RefSeq_GeneBody
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Sep 16 11:14:38 EDT 2019
Running on node : scc-tl2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/10_bamCorrelate
Current job ID : 9374100
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/9374100.1.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 Sep 16 11:15 .
drwxrwxrwt. 12 root   root      4.0K Sep 16 11:14 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 11:15 Input
-rwxr-xr-x   1 kkarri waxmanlab  311 Sep 16 11:15 Input_Samples.txt
-rwxr-xr-x   1 kkarri waxmanlab  36M Sep 16 11:15 RefSeq_GeneBody.bed
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 11:15 RefSeq_GeneBody_mm9-blacklist_Output
-rwxr-xr-x   1 kkarri waxmanlab  71K Sep 16 11:14 mm9-blacklist.bed
-rwxr-xr-x   1 kkarri waxmanlab 7.6K Sep 16 11:14 overlap.R
-rwxr-xr-x   1 kkarri waxmanlab 6.0K Sep 16 11:14 overlap.sh
-rw-r--r--   1 kkarri waxmanlab  80K Sep 16 11:14 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 Sep 16 11:15 .
drwxrwxrwt. 12 root   root      4.0K Sep 16 11:14 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 11:15 Input
-rwxr-xr-x   1 kkarri waxmanlab  311 Sep 16 11:15 Input_Samples.txt
-rwxr-xr-x   1 kkarri waxmanlab  36M Sep 16 11:15 RefSeq_GeneBody.bed
drwxr-xr-x   2 kkarri waxmanlab 4.0K Sep 16 11:15 RefSeq_GeneBody_mm9-blacklist_Output
-rwxr-xr-x   1 kkarri waxmanlab  71K Sep 16 11:14 mm9-blacklist.bed
-rwxr-xr-x   1 kkarri waxmanlab 7.6K Sep 16 11:14 overlap.R
-rwxr-xr-x   1 kkarri waxmanlab 6.0K Sep 16 11:14 overlap.sh
-rw-r--r--   1 kkarri waxmanlab  80K Sep 16 11:14 peak1_dump.bed
==========================================================
Finished on : Mon Sep 16 11:15:19 EDT 2019
0 hours, 0 minutes and 41 seconds elapsed.
==========================================================