long_spanning_reads v1.0.13
--------------------------------------------
Opening /projects/NBL/HS1195/30TTYAAXX_6/tophat_wj/right_kept_reads.fq for reading
Opening /projects/NBL/HS1195/30TTYAAXX_6/tophat_wj/all.juncs for reading
Opening /projects/NBL/HS1195/30TTYAAXX_6/tophat_wj/tmp//segment.juncs for reading
Opening /projects/NBL/HS1195/30TTYAAXX_6/tophat_wj/tmp//right_kept_reads_seg1.bwtout for reading
Opening /projects/NBL/HS1195/30TTYAAXX_6/tophat_wj/tmp//right_kept_reads_seg2.bwtout for reading
Opening /projects/NBL/HS1195/30TTYAAXX_6/tophat_wj/tmp//right_kept_reads_seg1_to_spliced.bwtout for reading
Opening /projects/NBL/HS1195/30TTYAAXX_6/tophat_wj/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 # 6267637
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Warning: multiple closures found for read # 6384886
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Warning: multiple closures found for read # 6406730
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Warning: multiple closures found for read # 6501451
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Warning: multiple closures found for read # 6749821
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Warning: multiple closures found for read # 6754361
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Warning: multiple closures found for read # 6767394
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Warning: multiple closures found for read # 6775522
Warning: multiple closures found for read # 6775796
Warning: multiple closures found for read # 6781432
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Warning: multiple closures found for read # 6802280
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Warning: multiple closures found for read # 6804890
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Warning: multiple closures found for read # 6814995
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Warning: multiple closures found for read # 6818289
Warning: multiple closures found for read # 6820483
Warning: multiple closures found for read # 6821793
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Warning: multiple closures found for read # 6877905
Warning: multiple closures found for read # 6879703
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Warning: multiple closures found for read # 6920510
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Warning: multiple closures found for read # 6924453
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Warning: multiple closures found for read # 6927632
Warning: multiple closures found for read # 6930949
Warning: multiple closures found for read # 6930985
Warning: multiple closures found for read # 6938488
Warning: multiple closures found for read # 6962362
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Warning: multiple closures found for read # 6990366
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Warning: multiple closures found for read # 6997873
Warning: multiple closures found for read # 7003116
Warning: multiple closures found for read # 7007529
Warning: multiple closures found for read # 7013368
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Warning: multiple closures found for read # 7020700
Warning: multiple closures found for read # 7021792
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Warning: multiple closures found for read # 7027781
Warning: multiple closures found for read # 7033757
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Warning: multiple closures found for read # 7041127
Warning: multiple closures found for read # 7050025
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Warning: multiple closures found for read # 7065038
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Warning: multiple closures found for read # 7199645
Warning: multiple closures found for read # 7205991
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Warning: multiple closures found for read # 7214202
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Warning: multiple closures found for read # 7269444
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Warning: multiple closures found for read # 7307836
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Warning: multiple closures found for read # 7315927
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Warning: multiple closures found for read # 7330594
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Warning: multiple closures found for read # 7363022
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Warning: multiple closures found for read # 7372336
Warning: multiple closures found for read # 7372475
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Warning: multiple closures found for read # 7374206
Warning: multiple closures found for read # 7380230
Warning: multiple closures found for read # 7382678
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Warning: multiple closures found for read # 7410681
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Warning: multiple closures found for read # 7462781
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Warning: multiple closures found for read # 7470377
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Warning: multiple closures found for read # 7508188
Warning: multiple closures found for read # 7509236
Warning: multiple closures found for read # 7511696
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Warning: multiple closures found for read # 7526948
Warning: multiple closures found for read # 7538511
Warning: multiple closures found for read # 7542053
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Warning: multiple closures found for read # 7588386
Warning: multiple closures found for read # 7596894
Warning: multiple closures found for read # 7611435
Warning: multiple closures found for read # 7611931
Warning: multiple closures found for read # 7612175
Warning: multiple closures found for read # 7614711
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Warning: multiple closures found for read # 7619814
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Warning: multiple closures found for read # 7632395
Warning: multiple closures found for read # 7633807
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Warning: multiple closures found for read # 7637686
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Warning: multiple closures found for read # 7651482
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Warning: multiple closures found for read # 7673079
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Warning: multiple closures found for read # 7684077
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Warning: multiple closures found for read # 7689682
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Warning: multiple closures found for read # 7710359
Warning: multiple closures found for read # 7712242
Warning: multiple closures found for read # 7717755
Warning: multiple closures found for read # 7718398
Warning: multiple closures found for read # 7726721
Warning: multiple closures found for read # 7734723
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Warning: multiple closures found for read # 7745104
Warning: multiple closures found for read # 7759093
Warning: multiple closures found for read # 7771159
Warning: multiple closures found for read # 7782435
Warning: multiple closures found for read # 7789109
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Warning: multiple closures found for read # 7793748
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Warning: multiple closures found for read # 7797603
Warning: multiple closures found for read # 7803122
Warning: multiple closures found for read # 7811499
Warning: multiple closures found for read # 7814191
Warning: multiple closures found for read # 7814245
Warning: multiple closures found for read # 7814397
Warning: multiple closures found for read # 7815433
Warning: multiple closures found for read # 7826358
Warning: multiple closures found for read # 7833117
Warning: multiple closures found for read # 7850936
Warning: multiple closures found for read # 7855820
Warning: multiple closures found for read # 7856852
Warning: multiple closures found for read # 7861980
Warning: multiple closures found for read # 7862575
Warning: multiple closures found for read # 7862575
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Warning: multiple closures found for read # 7862575
Warning: multiple closures found for read # 7862575
Warning: multiple closures found for read # 7862575
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Warning: multiple closures found for read # 7868134
Warning: multiple closures found for read # 7870966
Warning: multiple closures found for read # 7872379
Warning: multiple closures found for read # 7872697
Warning: multiple closures found for read # 7874590
Warning: multiple closures found for read # 7875785
Warning: multiple closures found for read # 7876707
Warning: multiple closures found for read # 7877248
Warning: multiple closures found for read # 7879364
Warning: multiple closures found for read # 7879513
Warning: multiple closures found for read # 7885235
Warning: multiple closures found for read # 7893746
Warning: multiple closures found for read # 7894152
Warning: multiple closures found for read # 7895077
Warning: multiple closures found for read # 7899233
Warning: multiple closures found for read # 7904071
Warning: multiple closures found for read # 7910894
Warning: multiple closures found for read # 7911510
Warning: multiple closures found for read # 7915730
Warning: multiple closures found for read # 7916702
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Warning: multiple closures found for read # 7922716
Warning: multiple closures found for read # 7924178
Warning: multiple closures found for read # 7934736
Warning: multiple closures found for read # 7936247
Warning: multiple closures found for read # 7936247
Warning: multiple closures found for read # 7938863
Warning: multiple closures found for read # 7939856
Warning: multiple closures found for read # 7940184
Warning: multiple closures found for read # 7941195
Warning: multiple closures found for read # 7945080
Warning: multiple closures found for read # 7947480
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Warning: multiple closures found for read # 7947754
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Warning: multiple closures found for read # 7950058
Warning: multiple closures found for read # 7956054
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Warning: multiple closures found for read # 7968191
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Warning: multiple closures found for read # 7971791
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Warning: multiple closures found for read # 7978247
Warning: multiple closures found for read # 7978969
Warning: multiple closures found for read # 7985088
Warning: multiple closures found for read # 7987751
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Warning: multiple closures found for read # 7999141
Warning: multiple closures found for read # 8005251
Warning: multiple closures found for read # 8008849
Warning: multiple closures found for read # 8015530
Warning: multiple closures found for read # 8019415
Warning: multiple closures found for read # 8020989
Warning: multiple closures found for read # 8023493
Warning: multiple closures found for read # 8029420
Warning: multiple closures found for read # 8032385
Warning: multiple closures found for read # 8045126
Warning: multiple closures found for read # 8046193
Warning: multiple closures found for read # 8049959
Warning: multiple closures found for read # 8053956
Warning: multiple closures found for read # 8054662
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Warning: multiple closures found for read # 8063195
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Warning: multiple closures found for read # 8065526
Warning: multiple closures found for read # 8065526
Warning: multiple closures found for read # 8065526
Warning: multiple closures found for read # 8065526
Warning: multiple closures found for read # 8065526
Warning: multiple closures found for read # 8065526
Warning: multiple closures found for read # 8065526
Warning: multiple closures found for read # 8065526
Warning: multiple closures found for read # 8065526
Warning: multiple closures found for read # 8067050
Warning: multiple closures found for read # 8068097
Warning: multiple closures found for read # 8068965
Warning: multiple closures found for read # 8070851
Warning: multiple closures found for read # 8070851
Warning: multiple closures found for read # 8070851
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Warning: multiple closures found for read # 8104235
Warning: multiple closures found for read # 8106158
Warning: multiple closures found for read # 8116745
Warning: multiple closures found for read # 8119021
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Warning: multiple closures found for read # 8126038
Warning: multiple closures found for read # 8127058
Warning: multiple closures found for read # 8135339
Warning: multiple closures found for read # 8135494
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Warning: multiple closures found for read # 8151853
Warning: multiple closures found for read # 8154282
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Warning: multiple closures found for read # 8187193
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Warning: multiple closures found for read # 8196978
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Warning: multiple closures found for read # 8204185
Warning: multiple closures found for read # 8204800
Warning: multiple closures found for read # 8210527
Warning: multiple closures found for read # 8225328
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Warning: multiple closures found for read # 8228791
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Warning: multiple closures found for read # 8230986
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Warning: multiple closures found for read # 8254432
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Warning: multiple closures found for read # 8256989
Warning: multiple closures found for read # 8261515
Warning: multiple closures found for read # 8268855
Warning: multiple closures found for read # 8269573
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Warning: multiple closures found for read # 8275370
Warning: multiple closures found for read # 8277409
Warning: multiple closures found for read # 8282698
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Warning: multiple closures found for read # 8296727
Warning: multiple closures found for read # 8299941
Warning: multiple closures found for read # 8304389
Warning: multiple closures found for read # 8314351
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Warning: multiple closures found for read # 8316447
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Warning: multiple closures found for read # 8412517
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Warning: multiple closures found for read # 8678370
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Warning: multiple closures found for read # 8713613
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Warning: multiple closures found for read # 8794351
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Warning: multiple closures found for read # 8802500
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Warning: multiple closures found for read # 8826123
Warning: multiple closures found for read # 8828916
Warning: multiple closures found for read # 8838638
Warning: multiple closures found for read # 8853238
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Warning: multiple closures found for read # 8866243
Warning: multiple closures found for read # 8869075
Warning: multiple closures found for read # 8870059
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Warning: multiple closures found for read # 8881750
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Warning: multiple closures found for read # 8897381
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Warning: multiple closures found for read # 8905318
Warning: multiple closures found for read # 8910982
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Warning: multiple closures found for read # 8950755
Warning: multiple closures found for read # 8955350
Warning: multiple closures found for read # 8967374
Warning: multiple closures found for read # 8983016
Warning: multiple closures found for read # 8985097
Warning: multiple closures found for read # 8987941
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Warning: multiple closures found for read # 8996352
Warning: multiple closures found for read # 8998120
Warning: multiple closures found for read # 8998354
Warning: multiple closures found for read # 8999393
Warning: multiple closures found for read # 9001783
Warning: multiple closures found for read # 9005208
Warning: multiple closures found for read # 9009263
Warning: multiple closures found for read # 9009986
Warning: multiple closures found for read # 9021050
Warning: multiple closures found for read # 9025818
Warning: multiple closures found for read # 9031119
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Warning: multiple closures found for read # 9037027
Warning: multiple closures found for read # 9048707
Warning: multiple closures found for read # 9054283
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Warning: multiple closures found for read # 9068717
Warning: multiple closures found for read # 9070341
Warning: multiple closures found for read # 9076628
Warning: multiple closures found for read # 9077665
Warning: multiple closures found for read # 9086671
Warning: multiple closures found for read # 9089940
Warning: multiple closures found for read # 9092109
Warning: multiple closures found for read # 9099384
Warning: multiple closures found for read # 9103477
Warning: multiple closures found for read # 9111461
Warning: multiple closures found for read # 9111690
Warning: multiple closures found for read # 9116211
Warning: multiple closures found for read # 9117619
Warning: multiple closures found for read # 9120108
Warning: multiple closures found for read # 9125292
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Warning: multiple closures found for read # 9129325
Warning: multiple closures found for read # 9130356
Warning: multiple closures found for read # 9131029
Warning: multiple closures found for read # 9131107
Warning: multiple closures found for read # 9135364
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Warning: multiple closures found for read # 9135697
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Warning: multiple closures found for read # 9139395
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Warning: multiple closures found for read # 9227495
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Warning: multiple closures found for read # 9232608
Warning: multiple closures found for read # 9235000
Warning: multiple closures found for read # 9241025
Warning: multiple closures found for read # 9247463
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Warning: multiple closures found for read # 9295656
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Warning: multiple closures found for read # 9313664
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Warning: multiple closures found for read # 9333235
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Warning: multiple closures found for read # 9380269
Warning: multiple closures found for read # 9386104
Warning: multiple closures found for read # 9389734
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Warning: multiple closures found for read # 9394659
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Warning: multiple closures found for read # 9407357
Warning: multiple closures found for read # 9414718
Warning: multiple closures found for read # 9417598
Warning: multiple closures found for read # 9421588
Warning: multiple closures found for read # 9425204
Warning: multiple closures found for read # 9429382
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Warning: multiple closures found for read # 9447467
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Warning: multiple closures found for read # 9450939
Warning: multiple closures found for read # 9453167
Warning: multiple closures found for read # 9463079
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Warning: multiple closures found for read # 9510579
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Warning: multiple closures found for read # 9521284
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Warning: multiple closures found for read # 9535752
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Warning: multiple closures found for read # 9558835
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Warning: multiple closures found for read # 9591586
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Warning: multiple closures found for read # 9615547
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Warning: multiple closures found for read # 9628658
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Warning: multiple closures found for read # 9630615
Warning: multiple closures found for read # 9636397
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Warning: multiple closures found for read # 9658297
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Warning: multiple closures found for read # 9660759
Warning: multiple closures found for read # 9661998
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Warning: multiple closures found for read # 9674574
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Warning: multiple closures found for read # 9686448
Warning: multiple closures found for read # 9688283
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Warning: multiple closures found for read # 9714257
Warning: multiple closures found for read # 9718929
Warning: multiple closures found for read # 9724652
Warning: multiple closures found for read # 9727221
Warning: multiple closures found for read # 9728659
Warning: multiple closures found for read # 9730922
Warning: multiple closures found for read # 9744881
Warning: multiple closures found for read # 9754392
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Warning: multiple closures found for read # 9759632
Warning: multiple closures found for read # 9764810
Warning: multiple closures found for read # 9774396
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Warning: multiple closures found for read # 9779942
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Warning: multiple closures found for read # 9789916
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Warning: multiple closures found for read # 9804796
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Warning: multiple closures found for read # 9809744
Warning: multiple closures found for read # 9820686
Warning: multiple closures found for read # 9822777
Warning: multiple closures found for read # 9823286
Warning: multiple closures found for read # 9824024
Warning: multiple closures found for read # 9831027
Warning: multiple closures found for read # 9832819
Warning: multiple closures found for read # 9836017
Warning: multiple closures found for read # 9838575
Warning: multiple closures found for read # 9838713
Warning: multiple closures found for read # 9840969
Warning: multiple closures found for read # 9840969
Warning: multiple closures found for read # 9842614
Warning: multiple closures found for read # 9846202
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Warning: multiple closures found for read # 9848326
Warning: multiple closures found for read # 9857279
Warning: multiple closures found for read # 9858191
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Warning: multiple closures found for read # 9864910
Warning: multiple closures found for read # 9869364
Warning: multiple closures found for read # 9881783
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Warning: multiple closures found for read # 9887115
Warning: multiple closures found for read # 9891549
Warning: multiple closures found for read # 9893071
Warning: multiple closures found for read # 9895667
Warning: multiple closures found for read # 9897512
Warning: multiple closures found for read # 9897573
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Warning: multiple closures found for read # 9901626
Warning: multiple closures found for read # 9902129
Warning: multiple closures found for read # 9906115
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9913525
Warning: multiple closures found for read # 9920790
Warning: multiple closures found for read # 9925443
Warning: multiple closures found for read # 9926450
Warning: multiple closures found for read # 9929338
Warning: multiple closures found for read # 9943339
Warning: multiple closures found for read # 9945276
Warning: multiple closures found for read # 9947836
Warning: multiple closures found for read # 9947836
Warning: multiple closures found for read # 9971014
Warning: multiple closures found for read # 9973698
Warning: multiple closures found for read # 9976768
Warning: multiple closures found for read # 9977926
Warning: multiple closures found for read # 9978193
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Warning: multiple closures found for read # 9981041
Warning: multiple closures found for read # 9981969
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Warning: multiple closures found for read # 9996760
Warning: multiple closures found for read # 10024376
Warning: multiple closures found for read # 10025027
Warning: multiple closures found for read # 10026488
Warning: multiple closures found for read # 10029968
Warning: multiple closures found for read # 10030093
Warning: multiple closures found for read # 10036090
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10040927
Warning: multiple closures found for read # 10056514
Warning: multiple closures found for read # 10057369
Warning: multiple closures found for read # 10061308
Warning: multiple closures found for read # 10063739
Warning: multiple closures found for read # 10064477
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Warning: multiple closures found for read # 10071053
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Warning: multiple closures found for read # 10072825
Warning: multiple closures found for read # 10084637
Warning: multiple closures found for read # 10087158
Warning: multiple closures found for read # 10089064
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Warning: multiple closures found for read # 10099863
Warning: multiple closures found for read # 10101116
Warning: multiple closures found for read # 10103196
Warning: multiple closures found for read # 10108893
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Warning: multiple closures found for read # 10113029
Warning: multiple closures found for read # 10114268
Warning: multiple closures found for read # 10116997
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Warning: multiple closures found for read # 10123681
Warning: multiple closures found for read # 10131021
Warning: multiple closures found for read # 10133843
Warning: multiple closures found for read # 10140146
Warning: multiple closures found for read # 10140146
Warning: multiple closures found for read # 10140146
Warning: multiple closures found for read # 10140146
Warning: multiple closures found for read # 10140146
Warning: multiple closures found for read # 10140146
Warning: multiple closures found for read # 10140146
Warning: multiple closures found for read # 10140483
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Warning: multiple closures found for read # 10141204
Warning: multiple closures found for read # 10146207
Warning: multiple closures found for read # 10150862
Warning: multiple closures found for read # 10156189
Warning: multiple closures found for read # 10160245
Warning: multiple closures found for read # 10174582
Warning: multiple closures found for read # 10178020
Warning: multiple closures found for read # 10181492
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Warning: multiple closures found for read # 11352903
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Warning: multiple closures found for read # 11870739
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