Info: Log File: /projects/remc_bigdata/Karsan/HS1235_wt/saturation/HS1235_wt_hg18_noDups_ht3.log Info: * Output directory : /projects/remc_bigdata/Karsan/HS1235_wt/saturation/ Info: * Naming files as : HS1235_wt_hg18_noDups_ht3 Info: * MC Iterations : 5 Info: * Chr name prepend : chr Info: * Min. reported pk ht : 3 Info: * Min. cov. allowed : 0.0010 Info: * Minimum ht to process: Off Info: * Lander-Waterman FDR : Off Info: * Output Sequence : Off Info: * Eff. fraction : 0.7 Info: * Control files in use : Off Info: * Compare files in use : Off Info: * Auto-threshold : On 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 : 0.2 Info: * Trim-peaks : 0.2 Info: * Saturation Analysis : Off Info: * Wig step size : 1 Info: * Histogram length : 40 Info: * Histogram precision : 1 Info: * Peaks File Header : 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_5/analysis/HS1235/42F10AAXX_1/maq/42F10AAXX_1.map Version: Initializing class PeakWriter $Revision: 1498 $ Version: Initializing class Generic_AlignRead_Iterator $Revision: 1600 $ Version: Initializing class MAQmapIterator $Revision: 1790 $ Info: number of mapped reads in header: 21753664 Info: Running Peak Processor Version: Initializing class PeakDataSet Peak Locator $Revision: 2226 $ Version: Initializing class PeakStore $Revision: 1335 $ Version: Initializing class MapStore $Revision: 1335 $ Info: Current chromosome : 1 Info: Reads used: 1700099 Info: Reads filtered by duplicate: 94449 Info: Reads filtered by iterator: 408248 Version: Initializing class PeakStats $Revision: 1335 $ Version: Initializing class Histogram $Revision: 1197 $ Version: Initializing class MC_Simulation $Revision: 1548 $ Info: Info: ------------------------------------------------------------------------ Info: Chromosome 1 Statistics Info: Estimated Chromosome Size : 247,199,384 Info: Using Effective chr size of 0.7 * estimated size : 173,039,568 Info: Observed Coverage : 164,201,298 Info: Generating random reads in batches of : 164,201 Info: ------------------------------------------------------------------------ Info: Performing Simulations. Info: 1 Version: Initializing class RandomAlignedReadGenerator $Revision: 1831 $ Info: Reads used: 164157 Info: Reads filtered by duplicate: 44 Info: Reads used: 328252 Info: Reads filtered by duplicate: 150 Info: Reads used: 492260 Info: Reads filtered by duplicate: 343 Info: Reads used: 656166 Info: Reads filtered by duplicate: 638 Info: Reads used: 820008 Info: Reads filtered by duplicate: 997 Info: Reads used: 983772 Info: Reads filtered by duplicate: 1434 Info: Reads used: 1147439 Info: Reads filtered by duplicate: 1968 Info: Reads used: 1311069 Info: Reads filtered by duplicate: 2539 Info: Reads used: 1474624 Info: Reads filtered by duplicate: 3185 Info: Reads used: 1638082 Info: Reads filtered by duplicate: 3928 Info: Reads used: 1801478 Info: Reads filtered by duplicate: 4733 Info: 2 Info: Reads used: 164149 Info: Reads filtered by duplicate: 52 Info: Reads used: 328240 Info: Reads filtered by duplicate: 162 Info: Reads used: 492259 Info: Reads filtered by duplicate: 344 Info: Reads used: 656194 Info: Reads filtered by duplicate: 610 Info: Reads used: 820068 Info: Reads filtered by duplicate: 937 Info: Reads used: 983813 Info: Reads filtered by duplicate: 1393 Info: Reads used: 1147506 Info: Reads filtered by duplicate: 1901 Info: Reads used: 1311166 Info: Reads filtered by duplicate: 2442 Info: Reads used: 1474704 Info: Reads filtered by duplicate: 3105 Info: Reads used: 1638166 Info: Reads filtered by duplicate: 3844 Info: Reads used: 1801587 Info: Reads filtered by duplicate: 4624 Info: 3 Info: Reads used: 164156 Info: Reads filtered by duplicate: 45 Info: Reads used: 328239 Info: Reads filtered by duplicate: 163 Info: Reads used: 492237 Info: Reads filtered by duplicate: 366 Info: Reads used: 656166 Info: Reads filtered by duplicate: 638 Info: Reads used: 820030 Info: Reads filtered by duplicate: 975 Info: Reads used: 983762 Info: Reads filtered by duplicate: 1444 Info: Reads used: 1147482 Info: Reads filtered by duplicate: 1925 Info: Reads used: 1311081 Info: Reads filtered by duplicate: 2527 Info: Reads used: 1474618 Info: Reads filtered by duplicate: 3191 Info: Reads used: 1638069 Info: Reads filtered by duplicate: 3941 Info: Reads used: 1801449 Info: Reads filtered by duplicate: 4762 Info: 4 Info: Reads used: 164164 Info: Reads filtered by duplicate: 37 Info: Reads used: 328246 Info: Reads filtered by duplicate: 156 Info: Reads used: 492246 Info: Reads filtered by duplicate: 357 Info: Reads used: 656174 Info: Reads filtered by duplicate: 630 Info: Reads used: 820013 Info: Reads filtered by duplicate: 992 Info: Reads used: 983771 Info: Reads filtered by duplicate: 1435 Info: Reads used: 1147459 Info: Reads filtered by duplicate: 1948 Info: Reads used: 1311064 Info: Reads filtered by duplicate: 2544 Info: Reads used: 1474605 Info: Reads filtered by duplicate: 3204 Info: Reads used: 1638052 Info: Reads filtered by duplicate: 3958 Info: Reads used: 1801386 Info: Reads filtered by duplicate: 4825 Info: 5 Info: Reads used: 164160 Info: Reads filtered by duplicate: 41 Info: Reads used: 328243 Info: Reads filtered by duplicate: 159 Info: Reads used: 492257 Info: Reads filtered by duplicate: 346 Info: Reads used: 656194 Info: Reads filtered by duplicate: 610 Info: Reads used: 820053 Info: Reads filtered by duplicate: 952 Info: Reads used: 983816 Info: Reads filtered by duplicate: 1390 Info: Reads used: 1147489 Info: Reads filtered by duplicate: 1918