Etchevers:Notebook/STRA6 in eye development/2009/07/20

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Chr 17 comparison

Launched the following comparisons between Chr 17 RAX and PAX6, which gave a fair number of peaks each in the Fasteris analysis. Many fewer were found not to be common between the two, and again there was no filtering (bold).

time java -Xms2G -Xmx11G -jar ~/trunk/jars/fp4/FindPeaks.jar -name PAX6-RAX-FP-Chr17 -input /home/oeil/Documents/Fasteris_7_2009/GDZ5_PAX6_bed/PAX6_Chr17.bed -output /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/17-7_PAX6-RAX_chr17 -aligner bed -dist_type 1 200 -minimum 20 -compare /home/oeil/Documents/Fasteris_7_2009/GDZ4_RAX_bed/RAX_Chr17.bed -alpha 0.05

  • Version: Initializing class Parameters $Revision: 1298 $
  • Info: * MC simulation  : Off
  • Info: * Chr name prepend  : none
  • Info: * Min. reported pk ht  : 20
  • 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/17-7_PAX6-RAX_chr17/
  • 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  : PAX6-RAX-FP-Chr17
  • 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 : chr17

*Info: Reads used: 103765

  • Version: Initializing class PeakStats $Revision: 1335 $
  • Version: Initializing class Histogram $Revision: 1197 $
  • Info: Current chromosome : chr17

*Info: Reads used: 161243

  • Version: Initializing class ApplyCompare $Revision: 1332 $

*Info: Linear Regresion: Total: 12 *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: 12
  • Version: Initializing class RegionWriter $Revision: 1229 $
  • Info: writing to : /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/17-7_PAX6-RAX_chr17/PAX6-RAX-FP-Chr17_triangle_standard_chr17.regions
  • Version: Initializing class Wigwriter $Revision: 1329 $
  • Info: writing sample to: /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/17-7_PAX6-RAX_chr17/PAX6-RAX-FP-Chr17_triangle_standard_chr17_filtered_sample.wig.gz
  • Info: writing comtrol to: /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/17-7_PAX6-RAX_chr17/PAX6-RAX-FP-Chr17_triangle_standard_chr17_filtered_control.wig.gz
  • Info: writing to: /home/oeil/Documents/Fasteris_7_2009/FindPeaks4_Results/17-7_PAX6-RAX_chr17/PAX6-RAX-FP-Chr17_triangle_standard_chr17.wig.gz

The end of the file was marked "Killed" and the time was at some 647 minutes in real time, just under 10 for the CPU and something like 6 for the user (or vice-versa; they closed the terminal window before I could copy it in). We really need more memory but it will only accommodate to 8 Mb.