Etchevers:Notebook/STRA6 in eye development/2009/07/16

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 * style="background-color: #EEE"|[[Image:C14.jpg|128px]] Genetics of human eye development
 * style="background-color: #F2F2F2" align="center"|  |Main project page
 * style="background-color: #F2F2F2" align="center"|  |Main project page


 * colspan="2"|
 * colspan="2"|

Findpeaks works - memory issues

 * oeil@cornee:~$ time java -Xms2G -Xmx4G -jar ~/trunk/jars/fp4/FindPeaks.jar -name RAX-PAX6-FP -input /home/oeil/Documents/Fasteris_7_2009/GDZ5_PAX6_bed/PAX6_Chr21.bed -output /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/ -aligner bed -dist_type 1 200 -minimum 2 -compare /home/oeil/Documents/Fasteris_7_2009/GDZ4_RAX_bed/RAX_Chr21.bed -alpha 0.05


 * Version: Initializing class Log_Buffer                       $Revision: 1145 $
 * Version: Initializing class FindPeaks                        $Revision: 1335 $
 * Info:   Note: all output now goes to log file.
 * Info:   Log file: /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/RAX-PAX6-FP.log
 * Version: Initializing class Parameters                       $Revision: 1298 $
 * Info:    * MC simulation        : Off
 * Info:    * Chr name prepend     : none
 * Info:    * Min. reported pk ht  : 2
 * Info:    * Minimum ht to process: Off
 * Info:    * Lander-Waterman FDR  : Off
 * Info:    * Output Sequence      : Off
 * Info:    * Output directory     : /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/
 * Info:    * Control files in use : Off
 * Info:    * Compare files in use : On
 * Info:    * Peak ht transform    : false
 * Info:    * Compare window size  : 100
 * Info:    * Auto-threshold       : Off
 * Info:    * Filter on PET flags  : Off
 * Info:    * Maximum PET frag size: Off
 * Info:    * Aligner              : bed
 * Info:    * Triangle dist.       : 100 low
 * Info:    * Triangle dist.       : 200 median
 * Info:    * Triangle dist.       : 300 high
 * Info:    * One file per chr.    : Off
 * Info:    * Naming files as      : RAX-PAX6-FP
 * Info:    * Sub-peaks            : Off
 * Info:    * Trim                 : Off
 * Info:    * Saturation Analysis  : Off
 * Info:    * Compare alpha value  : 0.05	(Confidence Interval: 95.0)
 * Info:    * Histogram length     : 30
 * Info:    * Histogram precision  : 1
 * Info:    * Peaks File Header    : On
 * Info:    * Bedgraph/Wigfile     : wig file
 * Info:    * R mode               : Off
 * Info:    * Filter Duplicates    : Off
 * Info:    * Filter quality       : Off
 * Version: Initializing class PeakWriter                       $Revision: 1299 $
 * Version: Initializing class Generic_AlignRead_Iterator       $Revision: 1318 $
 * Version: Initializing class BedIterator                      $Revision: 1317 $
 * Info:   Running Peak Processor
 * Version: Initializing class PeakDataSet Peak Locator         $Revision: 1335 $
 * Version: Initializing class PeakStore                        $Revision: 1335 $
 * Version: Initializing class MapStore                         $Revision: 1335 $
 * Info:   Current chromosome : chr21
 * Info:   Reads used: 39684
 * Version: Initializing class PeakStats                        $Revision: 1335 $
 * Version: Initializing class Histogram                        $Revision: 1197 $
 * Info:   Current chromosome : chr21
 * Info:   Reads used: 56661
 * Version: Initializing class ApplyCompare                     $Revision: 1332 $
 * Info:   Linear Regresion: Total:	11
 * Info:   Linear Regresion: Used:	0
 * Version: Initializing class LinearRegressionPerpendicular    $Revision: 1285 $
 * Warning: Can't run a Linear Regression calculation with zero points.
 * Warning: Can not apply filter. A valid slope was not obtained from the analysis.
 * Info:   Linear Regresion: Remaining:	11
 * Version: Initializing class RegionWriter                     $Revision: 1229 $
 * Info:   writing to : /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/RAX-PAX6-FP_triangle_standard_chr21.regions
 * Version: Initializing class Wigwriter                        $Revision: 1329 $
 * Info:   writing sample to:  /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/RAX-PAX6-FP_triangle_standard_chr21_filtered_sample.wig.gz
 * Info:   writing comtrol to: /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/RAX-PAX6-FP_triangle_standard_chr21_filtered_control.wig.gz
 * Info:   writing to: /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/RAX-PAX6-FP_triangle_standard_chr21.wig.gz
 * Info:   Wrote to:/home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/RAX-PAX6-FP_triangle_standard.wig.gz


 * real	2m49.149s
 * user	1m32.010s
 * sys	0m5.564s


 * Heather 09:36, 16 July 2009 (EDT):


 * }