Version: Vancouver Short Read Analysis Package                4.0.16-dev.jars
Version: Initializing class FindPeaks                         $Revision: 3126 $
Version: Initializing class Parameters                        $Revision: 3117 $
Version: Initializing class Log_Buffer                        $Revision: 2530 $
Info:    Log File: ./MM0479_5_lanes.log
Info:     * Output directory     : ./
Info:     * Naming files as      : MM0479_5_lanes
Info:     * MC simulation        : Off
Info:     * Chr name prepend     : none
Info:     * Min. reported pk ht  : 3
Info:     * Min. cov. allowed    : 0.0010
Info:     * Minimum ht to process: Off
Info:     * Lander-Waterman FDR  : On (0.01)
Info:     * Output Sequence      : Off
Info:     * Control files in use : Off
Info:     * Compare files in use : Off
Info:     * Auto-threshold       : Off
Info:     * Filter on PET flags  : Off
Info:     * Maximum PET frag size: Off
Info:     * Aligner              : maq
Info:     * Triangle dist.       : 100 low
Info:     * Triangle dist.       : 200 median
Info:     * Triangle dist.       : 300 high
Info:     * Maq file format      : 128bit reads (default value.  use -maq_read_size to override)
Info:     * One file per chr.    : Off
Info:     * Sub-peaks            : Off
Info:     * Trim                 : Off
Info:     * Saturation Analysis  : Off
Info:     * Wig step size        : 1
Info:     * Histogram length     : 30
Info:     * Histogram precision  : 1
Info:     * Peaks File Header    : On
Info:     * Wig File Headers     : On
Info:     * Min readahead window : Off
Info:     * Bedgraph/Wigfile     : wig file
Info:     * R mode               : Off
Info:     * Filter Duplicates    : On
Info:     * Filter quality min.  : On (10)
Info:     * Input Files          : 
Info:          /archive/solexa1_4/analysis/MM0399/meta_maq/MM0399_3_lanes.map
Version: Initializing class PeakWriter                        $Revision: 2532 $
Version: Initializing class Generic_AlignRead_Iterator        $Revision: 3118 $
Version: Initializing class MAQmapIterator                    $Revision: 2726 $
Info:    number of mapped reads in header: 16585096
Info:    Running Peak Processor
Version: Initializing class PeakDataSet Peak Locator          $Revision: 2785 $
Version: Initializing class PeakStore                         $Revision: 2739 $
Version: Initializing class MapStore                          $Revision: 2738 $
Info:    Current chromosome : 1
Info:    Reads used: 932015
Info:    Reads filtered by duplicate: 31824
Info:    Reads filtered by iterator: 360952
Version: Initializing class PeakStats                         $Revision: 2532 $
Version: Initializing class Histogram                         $Revision: 2530 $
Info:    Number of background reads: 491647
Info:    Effective genome/chromosome length: 1.269371748163766E8
Version: Initializing class FileOut                           $Revision: 2530 $
Info:    threshold for sample estimated (LW) at: 10.0
Version: Initializing class WigwriterBuffered                 $Revision: 2530 $
Info:    writing to : ./MM0479_5_lanes_triangle_standard_1.wig.gz
Info:    Running Peak Processor
Info:    Current chromosome : 10
Info:    Reads used: 622123
Info:    Reads filtered by duplicate: 21079
Info:    Reads filtered by iterator: 580128
Info:    Number of background reads: 349613
Info:    Effective genome/chromosome length: 8.668685155342592E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 11
Info:    Reads used: 618846
Info:    Reads filtered by duplicate: 20776
Info:    Reads filtered by iterator: 746072
Info:    Number of background reads: 366725
Info:    Effective genome/chromosome length: 8.597500268506768E7
Info:    threshold for sample estimated (LW) at: 11.0
Info:    Running Peak Processor
Info:    Current chromosome : 12
Info:    Reads used: 545445
Info:    Reads filtered by duplicate: 21790
Info:    Reads filtered by iterator: 1039162
Info:    Number of background reads: 268844
Info:    Effective genome/chromosome length: 7.328119025535144E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 13
Info:    Reads used: 568870
Info:    Reads filtered by duplicate: 19196
Info:    Reads filtered by iterator: 1297780
Info:    Number of background reads: 294075
Info:    Effective genome/chromosome length: 7.533904475254638E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 14
Info:    Reads used: 551653
Info:    Reads filtered by duplicate: 18668
Info:    Reads filtered by iterator: 1587604
Info:    Number of background reads: 267977
Info:    Effective genome/chromosome length: 7.361986575995459E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 15
Info:    Reads used: 488437
Info:    Reads filtered by duplicate: 16566
Info:    Reads filtered by iterator: 1750712
Info:    Number of background reads: 264426
Info:    Effective genome/chromosome length: 6.75482222293428E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 16
Info:    Reads used: 461517
Info:    Reads filtered by duplicate: 15993
Info:    Reads filtered by iterator: 1908056
Info:    Number of background reads: 240446
Info:    Effective genome/chromosome length: 6.258553697279712E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 17
Info:    Reads used: 433275
Info:    Reads filtered by duplicate: 13994
Info:    Reads filtered by iterator: 2101424
Info:    Number of background reads: 231063
Info:    Effective genome/chromosome length: 6.118849595799418E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 18
Info:    Reads used: 438576
Info:    Reads filtered by duplicate: 15069
Info:    Reads filtered by iterator: 2244760
Info:    Number of background reads: 239553
Info:    Effective genome/chromosome length: 5.8903849483474165E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 19
Info:    Reads used: 299131
Info:    Reads filtered by duplicate: 9835
Info:    Reads filtered by iterator: 2333126
Info:    Number of background reads: 152633
Info:    Effective genome/chromosome length: 3.8188888405373625E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 2
Info:    Reads used: 878050
Info:    Reads filtered by duplicate: 195061
Info:    Reads filtered by iterator: 3403758
Info:    Number of background reads: 473559
Info:    Effective genome/chromosome length: 1.1852709145071505E8
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 3
Info:    Reads used: 747008
Info:    Reads filtered by duplicate: 26129
Info:    Reads filtered by iterator: 3708914
Info:    Number of background reads: 382232
Info:    Effective genome/chromosome length: 1.0137589441746429E8
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 4
Info:    Reads used: 713146
Info:    Reads filtered by duplicate: 24488
Info:    Reads filtered by iterator: 4048594
Info:    Number of background reads: 386885
Info:    Effective genome/chromosome length: 1.00078007335294E8
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 5
Info:    Reads used: 705772
Info:    Reads filtered by duplicate: 22755
Info:    Reads filtered by iterator: 4347764
Info:    Number of background reads: 368061
Info:    Effective genome/chromosome length: 9.644478476752803E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 6
Info:    Reads used: 710923
Info:    Reads filtered by duplicate: 24495
Info:    Reads filtered by iterator: 4649798
Info:    Number of background reads: 381936
Info:    Effective genome/chromosome length: 9.747219926233242E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 7
Info:    Reads used: 634619
Info:    Reads filtered by duplicate: 20059
Info:    Reads filtered by iterator: 5023360
Info:    Number of background reads: 314968
Info:    Effective genome/chromosome length: 8.699843691323145E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 8
Info:    Reads used: 611332
Info:    Reads filtered by duplicate: 20121
Info:    Reads filtered by iterator: 5255074
Info:    Number of background reads: 332551
Info:    Effective genome/chromosome length: 8.414244736168656E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : 9
Info:    Reads used: 612974
Info:    Reads filtered by duplicate: 59960
Info:    Reads filtered by iterator: 7213036
Info:    Number of background reads: 324152
Info:    Effective genome/chromosome length: 8.048804891629513E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : MT
Info:    Reads used: 117
Info:    Reads filtered by duplicate: 2
Info:    Reads filtered by iterator: 7213174
Info:    Number of background reads: 1
Info:    Effective genome/chromosome length: NaN
Info:    threshold for sample estimated (LW) at: 0.0
Info:    Running Peak Processor
Info:    Current chromosome : X
Info:    Reads used: 476580
Info:    Reads filtered by duplicate: 19462
Info:    Reads filtered by iterator: 7784644
Info:    Number of background reads: 315690
Info:    Effective genome/chromosome length: 1.1257133984528387E8
Info:    threshold for sample estimated (LW) at: 9.0
Info:    Running Peak Processor
Info:    Current chromosome : Y
Info:    Reads used: 11683
Info:    Reads filtered by duplicate: 1546
Info:    Reads filtered by iterator: 7808228
Info:    Number of background reads: 1625
Info:    Effective genome/chromosome length: 1548190.927767292
Info:    threshold for sample estimated (LW) at: 5.0
Info:    Wrote to:./MM0479_5_lanes_triangle_standard.wig.gz