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/analysis2/MM0479/meta_maq/MM0479_5_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: 41949103
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 : chr1
Info:    Reads used: 1297279
Info:    Reads filtered by duplicate: 1165011
Info:    Reads filtered by iterator: 761776
Version: Initializing class PeakStats                         $Revision: 2532 $
Version: Initializing class Histogram                         $Revision: 2530 $
Info:    Number of background reads: 401391
Info:    Effective genome/chromosome length: 9.056483013677645E7
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_chr1.wig.gz
Info:    Running Peak Processor
Info:    Current chromosome : chr10
Info:    Reads used: 876249
Info:    Reads filtered by duplicate: 785167
Info:    Reads filtered by iterator: 1218074
Info:    Number of background reads: 272996
Info:    Effective genome/chromosome length: 6.002015266029595E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : chr11
Info:    Reads used: 863472
Info:    Reads filtered by duplicate: 789867
Info:    Reads filtered by iterator: 1555206
Info:    Number of background reads: 327370
Info:    Effective genome/chromosome length: 6.520085483002706E7
Info:    threshold for sample estimated (LW) at: 11.0
Info:    Running Peak Processor
Info:    Current chromosome : chr12
Info:    Reads used: 753582
Info:    Reads filtered by duplicate: 689573
Info:    Reads filtered by iterator: 2215832
Info:    Number of background reads: 217884
Info:    Effective genome/chromosome length: 5.321036899037908E7
Info:    threshold for sample estimated (LW) at: 9.0
Info:    Running Peak Processor
Info:    Current chromosome : chr13
Info:    Reads used: 788189
Info:    Reads filtered by duplicate: 718772
Info:    Reads filtered by iterator: 2773024
Info:    Number of background reads: 256344
Info:    Effective genome/chromosome length: 5.684533500175043E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : chr14
Info:    Reads used: 770191
Info:    Reads filtered by duplicate: 688345
Info:    Reads filtered by iterator: 3387840
Info:    Number of background reads: 217825
Info:    Effective genome/chromosome length: 5.316455557975585E7
Info:    threshold for sample estimated (LW) at: 9.0
Info:    Running Peak Processor
Info:    Current chromosome : chr15
Info:    Reads used: 679253
Info:    Reads filtered by duplicate: 609960
Info:    Reads filtered by iterator: 3730900
Info:    Number of background reads: 264614
Info:    Effective genome/chromosome length: 5.5048571262137875E7
Info:    threshold for sample estimated (LW) at: 11.0
Info:    Running Peak Processor
Info:    Current chromosome : chr16
Info:    Reads used: 645654
Info:    Reads filtered by duplicate: 577890
Info:    Reads filtered by iterator: 4061026
Info:    Number of background reads: 217118
Info:    Effective genome/chromosome length: 4.711769551955658E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : chr17
Info:    Reads used: 610248
Info:    Reads filtered by duplicate: 544939
Info:    Reads filtered by iterator: 4460052
Info:    Number of background reads: 213168
Info:    Effective genome/chromosome length: 4.717452866529001E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : chr18
Info:    Reads used: 603223
Info:    Reads filtered by duplicate: 547380
Info:    Reads filtered by iterator: 4756690
Info:    Number of background reads: 175177
Info:    Effective genome/chromosome length: 3.9906558112619355E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : chr19
Info:    Reads used: 419076
Info:    Reads filtered by duplicate: 384505
Info:    Reads filtered by iterator: 4939972
Info:    Number of background reads: 144102
Info:    Effective genome/chromosome length: 2.9894954572297227E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : chr2
Info:    Reads used: 1221555
Info:    Reads filtered by duplicate: 1759408
Info:    Reads filtered by iterator: 7540838
Info:    Number of background reads: 401240
Info:    Effective genome/chromosome length: 8.726271866907717E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : chr3
Info:    Reads used: 1053262
Info:    Reads filtered by duplicate: 935474
Info:    Reads filtered by iterator: 8189840
Info:    Number of background reads: 336931
Info:    Effective genome/chromosome length: 7.515078945840247E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : chr4
Info:    Reads used: 1003544
Info:    Reads filtered by duplicate: 898356
Info:    Reads filtered by iterator: 8906042
Info:    Number of background reads: 305654
Info:    Effective genome/chromosome length: 7.085583520646529E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : chr5
Info:    Reads used: 978882
Info:    Reads filtered by duplicate: 875323
Info:    Reads filtered by iterator: 9534650
Info:    Number of background reads: 326351
Info:    Effective genome/chromosome length: 7.314917382483064E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : chr6
Info:    Reads used: 993931
Info:    Reads filtered by duplicate: 912314
Info:    Reads filtered by iterator: 10203818
Info:    Number of background reads: 315267
Info:    Effective genome/chromosome length: 7.035073545098406E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : chr7
Info:    Reads used: 866799
Info:    Reads filtered by duplicate: 779222
Info:    Reads filtered by iterator: 10984844
Info:    Number of background reads: 281148
Info:    Effective genome/chromosome length: 6.801419835929985E7
Info:    threshold for sample estimated (LW) at: 9.0
Info:    Running Peak Processor
Info:    Current chromosome : chr8
Info:    Reads used: 838101
Info:    Reads filtered by duplicate: 754555
Info:    Reads filtered by iterator: 11474634
Info:    Number of background reads: 296777
Info:    Effective genome/chromosome length: 6.435001569470658E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : chr9
Info:    Reads used: 845746
Info:    Reads filtered by duplicate: 915860
Info:    Reads filtered by iterator: 16924466
Info:    Number of background reads: 339012
Info:    Effective genome/chromosome length: 6.810122861405487E7
Info:    threshold for sample estimated (LW) at: 11.0
Info:    Running Peak Processor
Info:    Current chromosome : chrX
Info:    Reads used: 726105
Info:    Reads filtered by duplicate: 615151
Info:    Reads filtered by iterator: 18155046
Info:    Number of background reads: 334855
Info:    Effective genome/chromosome length: 9.035171776821847E7
Info:    threshold for sample estimated (LW) at: 10.0
Info:    Running Peak Processor
Info:    Current chromosome : chrY
Info:    Reads used: 14777
Info:    Reads filtered by duplicate: 11999
Info:    Reads filtered by iterator: 18193290
Info:    Number of background reads: 2294
Info:    Effective genome/chromosome length: 1288911.542197371
Info:    threshold for sample estimated (LW) at: 6.0
Info:    Running Peak Processor
Info:    Current chromosome : chrM
Info:    Reads used: 10829
Info:    Reads filtered by duplicate: 21546
Info:    Reads filtered by iterator: 18216238
Info:    threshold for sample estimated (LW) at: 0.0
Info:    Wrote to:./MM0479_5_lanes_triangle_standard.wig.gz