long_spanning_reads v1.0.13
--------------------------------------------
Opening /projects/NBL/HS1195/30TTYAAXX_5/tophat/right_kept_reads.fq for reading
Opening /projects/NBL/HS1195/30TTYAAXX_5/tophat/tmp//segment.juncs for reading
Opening /projects/NBL/HS1195/30TTYAAXX_5/tophat/tmp//right_kept_reads_seg1.bwtout for reading
Opening /projects/NBL/HS1195/30TTYAAXX_5/tophat/tmp//right_kept_reads_seg2.bwtout for reading
Opening /projects/NBL/HS1195/30TTYAAXX_5/tophat/tmp//right_kept_reads_seg1_to_spliced.bwtout for reading
Opening /projects/NBL/HS1195/30TTYAAXX_5/tophat/tmp//right_kept_reads_seg2_to_spliced.bwtout for reading
Loading spliced hits...done
Loading junctions...done
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Warning: multiple closures found for read # 3677033
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Warning: multiple closures found for read # 3691174
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Warning: multiple closures found for read # 3708964
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Warning: multiple closures found for read # 3718902
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Warning: multiple closures found for read # 3762103
Warning: multiple closures found for read # 3762103
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Warning: multiple closures found for read # 3811928
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Warning: multiple closures found for read # 3835995
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Warning: multiple closures found for read # 3854128
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Warning: multiple closures found for read # 3891927
Warning: multiple closures found for read # 3906559
Warning: multiple closures found for read # 3909055
Warning: multiple closures found for read # 3930452
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Warning: multiple closures found for read # 3938147
Warning: multiple closures found for read # 3944099
Warning: multiple closures found for read # 3948082
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Warning: multiple closures found for read # 3952870
Warning: multiple closures found for read # 3953036
Warning: multiple closures found for read # 3957472
Warning: multiple closures found for read # 3960813
Warning: multiple closures found for read # 3961265
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Warning: multiple closures found for read # 3964566
Warning: multiple closures found for read # 3965164
Warning: multiple closures found for read # 3969110
Warning: multiple closures found for read # 3970121
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Warning: multiple closures found for read # 3987784
Warning: multiple closures found for read # 3989292
Warning: multiple closures found for read # 3993373
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Warning: multiple closures found for read # 4004467
Warning: multiple closures found for read # 4004907
Warning: multiple closures found for read # 4007109
Warning: multiple closures found for read # 4014658
Warning: multiple closures found for read # 4018604
Warning: multiple closures found for read # 4024505
Warning: multiple closures found for read # 4027902
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Warning: multiple closures found for read # 4055146
Warning: multiple closures found for read # 4060313
Warning: multiple closures found for read # 4060576
Warning: multiple closures found for read # 4067702
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Warning: multiple closures found for read # 4074970
Warning: multiple closures found for read # 4077564
Warning: multiple closures found for read # 4082956
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Warning: multiple closures found for read # 4096934
Warning: multiple closures found for read # 4101318
Warning: multiple closures found for read # 4102987
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Warning: multiple closures found for read # 4109822
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Warning: multiple closures found for read # 4109822
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Warning: multiple closures found for read # 4115934
Warning: multiple closures found for read # 4127504
Warning: multiple closures found for read # 4127967
Warning: multiple closures found for read # 4142954
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Warning: multiple closures found for read # 4158072
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Warning: multiple closures found for read # 4166514
Warning: multiple closures found for read # 4166816
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Warning: multiple closures found for read # 4179106
Warning: multiple closures found for read # 4183955
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Warning: multiple closures found for read # 4191119
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Warning: multiple closures found for read # 4891488
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Warning: multiple closures found for read # 5306522
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Warning: multiple closures found for read # 5318286
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Warning: multiple closures found for read # 5343253
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Warning: multiple closures found for read # 5411949
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Warning: multiple closures found for read # 5419374
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Warning: multiple closures found for read # 5560912
Warning: multiple closures found for read # 5561779
Warning: multiple closures found for read # 5571830
Warning: multiple closures found for read # 5572422
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Warning: multiple closures found for read # 5578086
Warning: multiple closures found for read # 5585111
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Warning: multiple closures found for read # 5609288
Warning: multiple closures found for read # 5609288
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Warning: multiple closures found for read # 5645185
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Warning: multiple closures found for read # 5653514
Warning: multiple closures found for read # 5664754
Warning: multiple closures found for read # 5670489
Warning: multiple closures found for read # 5679515
Warning: multiple closures found for read # 5680334
Warning: multiple closures found for read # 5684568
Warning: multiple closures found for read # 5689143
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Warning: multiple closures found for read # 5691729
Warning: multiple closures found for read # 5692189
Warning: multiple closures found for read # 5699257
Warning: multiple closures found for read # 5700272
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Warning: multiple closures found for read # 5703604
Warning: multiple closures found for read # 5709440
Warning: multiple closures found for read # 5712270
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Warning: multiple closures found for read # 5722492
Warning: multiple closures found for read # 5723846
Warning: multiple closures found for read # 5748862
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Warning: multiple closures found for read # 5767830
Warning: multiple closures found for read # 5769364
Warning: multiple closures found for read # 5770837
Warning: multiple closures found for read # 5775580
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Warning: multiple closures found for read # 5780237
Warning: multiple closures found for read # 5787827
Warning: multiple closures found for read # 5788812
Warning: multiple closures found for read # 5802546
Warning: multiple closures found for read # 5808002
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Warning: multiple closures found for read # 5809732
Warning: multiple closures found for read # 5810329
Warning: multiple closures found for read # 5813241
Warning: multiple closures found for read # 5813381
Warning: multiple closures found for read # 5816778
Warning: multiple closures found for read # 5820523
Warning: multiple closures found for read # 5824278
Warning: multiple closures found for read # 5830727
Warning: multiple closures found for read # 5833536
Warning: multiple closures found for read # 5835418
Warning: multiple closures found for read # 5835505
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Warning: multiple closures found for read # 5835505
Warning: multiple closures found for read # 5835505
Warning: multiple closures found for read # 5835505
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Warning: multiple closures found for read # 5835505
Warning: multiple closures found for read # 5835505
Warning: multiple closures found for read # 5835505
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Warning: multiple closures found for read # 5835505
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Warning: multiple closures found for read # 5835505
Warning: multiple closures found for read # 5835505
Warning: multiple closures found for read # 5835505
Warning: multiple closures found for read # 5835505
Warning: multiple closures found for read # 5835505
Warning: multiple closures found for read # 5835505
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Warning: multiple closures found for read # 5844385
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Warning: multiple closures found for read # 5851009
Warning: multiple closures found for read # 5858344
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Warning: multiple closures found for read # 5877917
Warning: multiple closures found for read # 5880250
Warning: multiple closures found for read # 5887265
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Warning: multiple closures found for read # 5915386
Warning: multiple closures found for read # 5919790
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Warning: multiple closures found for read # 5924793
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Warning: multiple closures found for read # 5924793
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Warning: multiple closures found for read # 5935444
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Warning: multiple closures found for read # 5942170
Warning: multiple closures found for read # 5947253
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Warning: multiple closures found for read # 5950863
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Warning: multiple closures found for read # 6018109
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Warning: multiple closures found for read # 6037673
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Warning: multiple closures found for read # 6048287
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Warning: multiple closures found for read # 6094137
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Warning: multiple closures found for read # 6107246
Warning: multiple closures found for read # 6107246
Warning: multiple closures found for read # 6107246
Warning: multiple closures found for read # 6107246
Warning: multiple closures found for read # 6107246
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Warning: multiple closures found for read # 6109622
Warning: multiple closures found for read # 6112158
Warning: multiple closures found for read # 6121976
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Warning: multiple closures found for read # 6127564
Warning: multiple closures found for read # 6129956
Warning: multiple closures found for read # 6136754
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Warning: multiple closures found for read # 6400165
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Warning: multiple closures found for read # 6951065
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Warning: multiple closures found for read # 7011322
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Warning: multiple closures found for read # 7316244
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Warning: multiple closures found for read # 7336251
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Warning: multiple closures found for read # 7347999
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Warning: multiple closures found for read # 7360888
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Warning: multiple closures found for read # 7403176
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Warning: multiple closures found for read # 7419778
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Warning: multiple closures found for read # 7424066
Warning: multiple closures found for read # 7425043
Warning: multiple closures found for read # 7425582
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Warning: multiple closures found for read # 7429524
Warning: multiple closures found for read # 7429524
Warning: multiple closures found for read # 7429524
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Warning: multiple closures found for read # 7434569
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Warning: multiple closures found for read # 7481244
Warning: multiple closures found for read # 7489254
Warning: multiple closures found for read # 7492440
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Warning: multiple closures found for read # 7494705
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Warning: multiple closures found for read # 7506582
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Warning: multiple closures found for read # 7520918
Warning: multiple closures found for read # 7526114
Warning: multiple closures found for read # 7528853
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Warning: multiple closures found for read # 7535038
Warning: multiple closures found for read # 7545942
Warning: multiple closures found for read # 7551437
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Warning: multiple closures found for read # 7560347
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Warning: multiple closures found for read # 7571839
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Warning: multiple closures found for read # 7590342
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Warning: multiple closures found for read # 7603356
Warning: multiple closures found for read # 7608891
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Warning: multiple closures found for read # 7616645
Warning: multiple closures found for read # 7616645
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Warning: multiple closures found for read # 7625092
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Warning: multiple closures found for read # 7632619
Warning: multiple closures found for read # 7635648
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Warning: multiple closures found for read # 7659059
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Warning: multiple closures found for read # 7667556
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Warning: multiple closures found for read # 7701367
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Warning: multiple closures found for read # 7713517
Warning: multiple closures found for read # 7713517
Warning: multiple closures found for read # 7713517
Warning: multiple closures found for read # 7713517
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Warning: multiple closures found for read # 7715798
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Warning: multiple closures found for read # 7723843
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Warning: multiple closures found for read # 7729499
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Warning: multiple closures found for read # 7734626
Warning: multiple closures found for read # 7740957
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Warning: multiple closures found for read # 7745805
Warning: multiple closures found for read # 7746680
Warning: multiple closures found for read # 7750887
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Warning: multiple closures found for read # 7789843
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Warning: multiple closures found for read # 7803788
Warning: multiple closures found for read # 7813189
Warning: multiple closures found for read # 7813189
Warning: multiple closures found for read # 7813189
Warning: multiple closures found for read # 7813189
Warning: multiple closures found for read # 7813189
Warning: multiple closures found for read # 7820760
Warning: multiple closures found for read # 7821808
Warning: multiple closures found for read # 7821907
Warning: multiple closures found for read # 7822726
Warning: multiple closures found for read # 7827222
Warning: multiple closures found for read # 7834516
Warning: multiple closures found for read # 7835149
Warning: multiple closures found for read # 7836178
Warning: multiple closures found for read # 7837454
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Warning: multiple closures found for read # 7839890
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Warning: multiple closures found for read # 7913550
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Warning: multiple closures found for read # 7929102
Warning: multiple closures found for read # 7931524
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Warning: multiple closures found for read # 8001099
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Warning: multiple closures found for read # 8020218
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Warning: multiple closures found for read # 8083176
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Warning: multiple closures found for read # 8106149
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Warning: multiple closures found for read # 8135160
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Warning: multiple closures found for read # 8204101
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Warning: multiple closures found for read # 8235884
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Warning: multiple closures found for read # 8280518
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Warning: multiple closures found for read # 8315967
Warning: multiple closures found for read # 8317773
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Warning: multiple closures found for read # 8321688
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Warning: multiple closures found for read # 8327954
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Warning: multiple closures found for read # 8350378
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Warning: multiple closures found for read # 8399656
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Warning: multiple closures found for read # 8424618
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Warning: multiple closures found for read # 8570846
Warning: multiple closures found for read # 8575197
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Warning: multiple closures found for read # 8630798
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Warning: multiple closures found for read # 8633643
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Warning: multiple closures found for read # 8636043
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Warning: multiple closures found for read # 8659042
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Warning: multiple closures found for read # 8681835
Warning: multiple closures found for read # 8683479
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Warning: multiple closures found for read # 8691394
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Warning: multiple closures found for read # 8816540
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Warning: multiple closures found for read # 8868295
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Warning: multiple closures found for read # 8882692
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Warning: multiple closures found for read # 8887339
Warning: multiple closures found for read # 8887754
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Warning: multiple closures found for read # 8895554
Warning: multiple closures found for read # 8901794
Warning: multiple closures found for read # 8902014
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Warning: multiple closures found for read # 8911528
Warning: multiple closures found for read # 8913054
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Warning: multiple closures found for read # 8919569
Warning: multiple closures found for read # 8919879
Warning: multiple closures found for read # 8924833
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Warning: multiple closures found for read # 8924833
Warning: multiple closures found for read # 8924833
Warning: multiple closures found for read # 8924833
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Warning: multiple closures found for read # 8930737
Warning: multiple closures found for read # 8934699
Warning: multiple closures found for read # 8940640
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Warning: multiple closures found for read # 8949634
Warning: multiple closures found for read # 8951255
Warning: multiple closures found for read # 8958679
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Warning: multiple closures found for read # 8964492
Warning: multiple closures found for read # 8964841
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Warning: multiple closures found for read # 8974068
Warning: multiple closures found for read # 8975609
Warning: multiple closures found for read # 8977209
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Warning: multiple closures found for read # 8980346
Warning: multiple closures found for read # 8981094
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Warning: multiple closures found for read # 8985664
Warning: multiple closures found for read # 8990955
Warning: multiple closures found for read # 8994881
Warning: multiple closures found for read # 8996403
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Warning: multiple closures found for read # 8997894
Warning: multiple closures found for read # 9010386
Warning: multiple closures found for read # 9010635
Warning: multiple closures found for read # 9011878
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Warning: multiple closures found for read # 9015753
Warning: multiple closures found for read # 9016151
Warning: multiple closures found for read # 9022619
Warning: multiple closures found for read # 9032682
Warning: multiple closures found for read # 9033663
Warning: multiple closures found for read # 9036940
Warning: multiple closures found for read # 9036940
Warning: multiple closures found for read # 9036940
Warning: multiple closures found for read # 9036940
Warning: multiple closures found for read # 9036940
Warning: multiple closures found for read # 9036940
Warning: multiple closures found for read # 9036940
Warning: multiple closures found for read # 9039017
Warning: multiple closures found for read # 9041496
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Warning: multiple closures found for read # 9045066
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Warning: multiple closures found for read # 9175189
Warning: multiple closures found for read # 9188442
Warning: multiple closures found for read # 9196594
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Warning: multiple closures found for read # 9198050
Warning: multiple closures found for read # 9207205
Warning: multiple closures found for read # 9207412
Warning: multiple closures found for read # 9208854
Warning: multiple closures found for read # 9212365
Warning: multiple closures found for read # 9213785
Warning: multiple closures found for read # 9225463
Warning: multiple closures found for read # 9228480
Warning: multiple closures found for read # 9228744
Warning: multiple closures found for read # 9231253
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Warning: multiple closures found for read # 9239941
Warning: multiple closures found for read # 9240642
Warning: multiple closures found for read # 9242979
Warning: multiple closures found for read # 9244064
Warning: multiple closures found for read # 9244835
Warning: multiple closures found for read # 9252802
Warning: multiple closures found for read # 9253031
Warning: multiple closures found for read # 9253889
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Warning: multiple closures found for read # 9264136
Warning: multiple closures found for read # 9266088
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Warning: multiple closures found for read # 9272650
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Warning: multiple closures found for read # 9275382
Warning: multiple closures found for read # 9276203
Warning: multiple closures found for read # 9276531
Warning: multiple closures found for read # 9283151
Warning: multiple closures found for read # 9287217
Warning: multiple closures found for read # 9287384
Warning: multiple closures found for read # 9288018
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Warning: multiple closures found for read # 9294437
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Warning: multiple closures found for read # 9304088
Warning: multiple closures found for read # 9345851
Warning: multiple closures found for read # 9371679
Warning: multiple closures found for read # 9405816
Warning: multiple closures found for read # 9431067
Warning: multiple closures found for read # 9433798
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9450770
Warning: multiple closures found for read # 9453961
Warning: multiple closures found for read # 9453961
Warning: multiple closures found for read # 9453961
Warning: multiple closures found for read # 9460018
Warning: multiple closures found for read # 9467815
Warning: multiple closures found for read # 9468030
Warning: multiple closures found for read # 9470409
Warning: multiple closures found for read # 9472016
Warning: multiple closures found for read # 9473047
Warning: multiple closures found for read # 9476241
Warning: multiple closures found for read # 9477768
Warning: multiple closures found for read # 9478239
Warning: multiple closures found for read # 9479337
Warning: multiple closures found for read # 9482273
Warning: multiple closures found for read # 9483223
Warning: multiple closures found for read # 9489490
Warning: multiple closures found for read # 9498457
Warning: multiple closures found for read # 9499311
Warning: multiple closures found for read # 9499351
Warning: multiple closures found for read # 9507812
Warning: multiple closures found for read # 9511917
Warning: multiple closures found for read # 9514989
Warning: multiple closures found for read # 9516512
Warning: multiple closures found for read # 9524581
Warning: multiple closures found for read # 9527576
Warning: multiple closures found for read # 9543194
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Warning: multiple closures found for read # 9543541
Warning: multiple closures found for read # 9543589
Warning: multiple closures found for read # 9547942
Warning: multiple closures found for read # 9553677
Warning: multiple closures found for read # 9555608
Warning: multiple closures found for read # 9559734
Warning: multiple closures found for read # 9560269
Warning: multiple closures found for read # 9561425
Warning: multiple closures found for read # 9562375
Warning: multiple closures found for read # 9562416
Warning: multiple closures found for read # 9562593
Warning: multiple closures found for read # 9567087
Warning: multiple closures found for read # 9568849
Warning: multiple closures found for read # 9577014
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Warning: multiple closures found for read # 9583137
Warning: multiple closures found for read # 9584920
Warning: multiple closures found for read # 9586833
Warning: multiple closures found for read # 9587016
Warning: multiple closures found for read # 9592409
Warning: multiple closures found for read # 9592578
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Warning: multiple closures found for read # 9602024
Warning: multiple closures found for read # 9603260
Warning: multiple closures found for read # 9607940
Warning: multiple closures found for read # 9608027
Warning: multiple closures found for read # 9608128
Warning: multiple closures found for read # 9608421
Warning: multiple closures found for read # 9608511
Warning: multiple closures found for read # 9609030
Warning: multiple closures found for read # 9612201
Warning: multiple closures found for read # 9613015
Warning: multiple closures found for read # 9616012
Warning: multiple closures found for read # 9627098
Warning: multiple closures found for read # 9643636
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Warning: multiple closures found for read # 9654365
Warning: multiple closures found for read # 9659890
Warning: multiple closures found for read # 9659970
Warning: multiple closures found for read # 9665725
Warning: multiple closures found for read # 9679519
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Warning: multiple closures found for read # 9683728
Warning: multiple closures found for read # 9687125
Warning: multiple closures found for read # 9688755
Warning: multiple closures found for read # 9692970
Warning: multiple closures found for read # 9694334
Warning: multiple closures found for read # 9694872
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Warning: multiple closures found for read # 9708630
Warning: multiple closures found for read # 9710905
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Warning: multiple closures found for read # 9714654
Warning: multiple closures found for read # 9717888
Warning: multiple closures found for read # 9718209
Warning: multiple closures found for read # 9720346
Warning: multiple closures found for read # 9729410
Warning: multiple closures found for read # 9729447
Warning: multiple closures found for read # 9730736
Warning: multiple closures found for read # 9732750
Warning: multiple closures found for read # 9734717
Warning: multiple closures found for read # 9738392
Warning: multiple closures found for read # 9738845
Warning: multiple closures found for read # 9741951
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Warning: multiple closures found for read # 9765954
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Warning: multiple closures found for read # 9784912
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Warning: multiple closures found for read # 9786650
Warning: multiple closures found for read # 9786650
Warning: multiple closures found for read # 9787333
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Warning: multiple closures found for read # 9789607
Warning: multiple closures found for read # 9798779
Warning: multiple closures found for read # 9815305
Warning: multiple closures found for read # 9815528
Warning: multiple closures found for read # 9822839
Warning: multiple closures found for read # 9827700
Warning: multiple closures found for read # 9842943
Warning: multiple closures found for read # 9842994
Warning: multiple closures found for read # 9843309
Warning: multiple closures found for read # 9844019
Warning: multiple closures found for read # 9844019
Warning: multiple closures found for read # 9858372
Warning: multiple closures found for read # 9860265
Warning: multiple closures found for read # 9861723
Warning: multiple closures found for read # 9866067
Warning: multiple closures found for read # 9873059
Warning: multiple closures found for read # 9877631
Warning: multiple closures found for read # 9894410
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