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
|
Genetics of human eye development
Main project page
Previous entry Next entry
