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

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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