long_spanning_reads v1.0.13
--------------------------------------------
Opening /projects/NBL/HS1195/30TTYAAXX_7/tophat_wj/right_kept_reads.fq for reading
Opening /projects/NBL/HS1195/30TTYAAXX_7/tophat_wj/all.juncs for reading
Opening /projects/NBL/HS1195/30TTYAAXX_7/tophat_wj/tmp//segment.juncs for reading
Opening /projects/NBL/HS1195/30TTYAAXX_7/tophat_wj/tmp//right_kept_reads_seg1.bwtout for reading
Opening /projects/NBL/HS1195/30TTYAAXX_7/tophat_wj/tmp//right_kept_reads_seg2.bwtout for reading
Opening /projects/NBL/HS1195/30TTYAAXX_7/tophat_wj/tmp//right_kept_reads_seg1_to_spliced.bwtout for reading
Opening /projects/NBL/HS1195/30TTYAAXX_7/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 # 4617691
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Warning: multiple closures found for read # 5019448
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Warning: multiple closures found for read # 5149796
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Warning: multiple closures found for read # 5269291
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Warning: multiple closures found for read # 5411741
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Warning: multiple closures found for read # 5412888
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Warning: multiple closures found for read # 5420277
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Warning: multiple closures found for read # 5471924
Warning: multiple closures found for read # 5491623
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Warning: multiple closures found for read # 5498539
Warning: multiple closures found for read # 5498539
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Warning: multiple closures found for read # 5507768
Warning: multiple closures found for read # 5508344
Warning: multiple closures found for read # 5511256
Warning: multiple closures found for read # 5520728
Warning: multiple closures found for read # 5527466
Warning: multiple closures found for read # 5528056
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Warning: multiple closures found for read # 5544823
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Warning: multiple closures found for read # 5560024
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Warning: multiple closures found for read # 5571951
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Warning: multiple closures found for read # 5581746
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Warning: multiple closures found for read # 5586837
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Warning: multiple closures found for read # 5597184
Warning: multiple closures found for read # 5599426
Warning: multiple closures found for read # 5602335
Warning: multiple closures found for read # 5604166
Warning: multiple closures found for read # 5604934
Warning: multiple closures found for read # 5605636
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Warning: multiple closures found for read # 5705028
Warning: multiple closures found for read # 5710000
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Warning: multiple closures found for read # 5716795
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Warning: multiple closures found for read # 5808018
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Warning: multiple closures found for read # 5818563
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Warning: multiple closures found for read # 5826000
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Warning: multiple closures found for read # 5853414
Warning: multiple closures found for read # 5863015
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Warning: multiple closures found for read # 6020176
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Warning: multiple closures found for read # 6080542
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Warning: multiple closures found for read # 6402011
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Warning: multiple closures found for read # 6787336
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Warning: multiple closures found for read # 6800234
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Warning: multiple closures found for read # 6803029
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Warning: multiple closures found for read # 6816217
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Warning: multiple closures found for read # 6846495
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Warning: multiple closures found for read # 6869652
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Warning: multiple closures found for read # 6888652
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Warning: multiple closures found for read # 6915866
Warning: multiple closures found for read # 6916987
Warning: multiple closures found for read # 6923371
Warning: multiple closures found for read # 6939407
Warning: multiple closures found for read # 6942510
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Warning: multiple closures found for read # 6945474
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Warning: multiple closures found for read # 6950562
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Warning: multiple closures found for read # 7000508
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Warning: multiple closures found for read # 7014052
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Warning: multiple closures found for read # 7062207
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Warning: multiple closures found for read # 7193264
Warning: multiple closures found for read # 7207889
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Warning: multiple closures found for read # 7298115
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Warning: multiple closures found for read # 7302072
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Warning: multiple closures found for read # 7316531
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Warning: multiple closures found for read # 7316637
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Warning: multiple closures found for read # 7351088
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Warning: multiple closures found for read # 7411380
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Warning: multiple closures found for read # 7447470
Warning: multiple closures found for read # 7450927
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Warning: multiple closures found for read # 7459514
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Warning: multiple closures found for read # 7480757
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Warning: multiple closures found for read # 7505427
Warning: multiple closures found for read # 7508998
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Warning: multiple closures found for read # 7522510
Warning: multiple closures found for read # 7530947
Warning: multiple closures found for read # 7531478
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Warning: multiple closures found for read # 7569417
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Warning: multiple closures found for read # 7583910
Warning: multiple closures found for read # 7585435
Warning: multiple closures found for read # 7587998
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Warning: multiple closures found for read # 7590243
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Warning: multiple closures found for read # 7599374
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Warning: multiple closures found for read # 7602958
Warning: multiple closures found for read # 7628973
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Warning: multiple closures found for read # 7633325
Warning: multiple closures found for read # 7639871
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Warning: multiple closures found for read # 7656936
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Warning: multiple closures found for read # 7661898
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Warning: multiple closures found for read # 7669712
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Warning: multiple closures found for read # 7675876
Warning: multiple closures found for read # 7681228
Warning: multiple closures found for read # 7682964
Warning: multiple closures found for read # 7686425
Warning: multiple closures found for read # 7686942
Warning: multiple closures found for read # 7690107
Warning: multiple closures found for read # 7700286
Warning: multiple closures found for read # 7709247
Warning: multiple closures found for read # 7710336
Warning: multiple closures found for read # 7713189
Warning: multiple closures found for read # 7715561
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Warning: multiple closures found for read # 7718297
Warning: multiple closures found for read # 7719232
Warning: multiple closures found for read # 7722267
Warning: multiple closures found for read # 7725391
Warning: multiple closures found for read # 7733062
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Warning: multiple closures found for read # 7741894
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Warning: multiple closures found for read # 7759207
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Warning: multiple closures found for read # 7762769
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Warning: multiple closures found for read # 7766855
Warning: multiple closures found for read # 7770025
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Warning: multiple closures found for read # 7774452
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Warning: multiple closures found for read # 7777317
Warning: multiple closures found for read # 7777317
Warning: multiple closures found for read # 7778778
Warning: multiple closures found for read # 7782520
Warning: multiple closures found for read # 7785602
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Warning: multiple closures found for read # 7789100
Warning: multiple closures found for read # 7789140
Warning: multiple closures found for read # 7796489
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Warning: multiple closures found for read # 7796489
Warning: multiple closures found for read # 7804063
Warning: multiple closures found for read # 7808977
Warning: multiple closures found for read # 7809263
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Warning: multiple closures found for read # 7815659
Warning: multiple closures found for read # 7816461
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Warning: multiple closures found for read # 7829243
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Warning: multiple closures found for read # 7846532
Warning: multiple closures found for read # 7847105
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Warning: multiple closures found for read # 7854089
Warning: multiple closures found for read # 7855184
Warning: multiple closures found for read # 7856855
Warning: multiple closures found for read # 7867681
Warning: multiple closures found for read # 7869922
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Warning: multiple closures found for read # 7891689
Warning: multiple closures found for read # 7893430
Warning: multiple closures found for read # 7899623
Warning: multiple closures found for read # 7906302
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Warning: multiple closures found for read # 7910921
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Warning: multiple closures found for read # 7912699
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Warning: multiple closures found for read # 7922601
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Warning: multiple closures found for read # 7933924
Warning: multiple closures found for read # 7935334
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Warning: multiple closures found for read # 7985001
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Warning: multiple closures found for read # 8002316
Warning: multiple closures found for read # 8005922
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Warning: multiple closures found for read # 8016333
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Warning: multiple closures found for read # 8022898
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Warning: multiple closures found for read # 8041986
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Warning: multiple closures found for read # 8080998
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Warning: multiple closures found for read # 8086003
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Warning: multiple closures found for read # 8095101
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Warning: multiple closures found for read # 8119424
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Warning: multiple closures found for read # 8132137
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Warning: multiple closures found for read # 9815057
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Warning: multiple closures found for read # 9839108
Warning: multiple closures found for read # 9842579
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Warning: multiple closures found for read # 9867340
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Warning: multiple closures found for read # 9926826
Warning: multiple closures found for read # 9929675
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Warning: multiple closures found for read # 9961847
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Warning: multiple closures found for read # 9977077
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Warning: multiple closures found for read # 9986312
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Warning: multiple closures found for read # 9996802
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Warning: multiple closures found for read # 10003079
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Warning: multiple closures found for read # 10013189
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Warning: multiple closures found for read # 10072254
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Warning: multiple closures found for read # 10090272
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Warning: multiple closures found for read # 10099754
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Warning: multiple closures found for read # 10103375
Warning: multiple closures found for read # 10104990
Warning: multiple closures found for read # 10105215
Warning: multiple closures found for read # 10109305
Warning: multiple closures found for read # 10111189
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Warning: multiple closures found for read # 10123837
Warning: multiple closures found for read # 10131322
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Warning: multiple closures found for read # 10131892
Warning: multiple closures found for read # 10137551
Warning: multiple closures found for read # 10139053
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Warning: multiple closures found for read # 10148035
Warning: multiple closures found for read # 10154377
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Warning: multiple closures found for read # 10180250
Warning: multiple closures found for read # 10180250
Warning: multiple closures found for read # 10180250
Warning: multiple closures found for read # 10180250
Warning: multiple closures found for read # 10180250
Warning: multiple closures found for read # 10180250
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Warning: multiple closures found for read # 10183176
Warning: multiple closures found for read # 10184171
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Warning: multiple closures found for read # 10190268
Warning: multiple closures found for read # 10191849
Warning: multiple closures found for read # 10199499
Warning: multiple closures found for read # 10205887
Warning: multiple closures found for read # 10213469
Warning: multiple closures found for read # 10216173
Warning: multiple closures found for read # 10220443
Warning: multiple closures found for read # 10221404
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Warning: multiple closures found for read # 10224064
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Warning: multiple closures found for read # 10245814
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Warning: multiple closures found for read # 10260383
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Warning: multiple closures found for read # 10299156
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Warning: multiple closures found for read # 10317255
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Warning: multiple closures found for read # 10327496
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Warning: multiple closures found for read # 10380956
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Warning: multiple closures found for read # 10524199
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Warning: multiple closures found for read # 10604865
Warning: multiple closures found for read # 10604865
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Warning: multiple closures found for read # 10612838
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Warning: multiple closures found for read # 10628167
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Warning: multiple closures found for read # 10633330
Warning: multiple closures found for read # 10636845
Warning: multiple closures found for read # 10645592
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Warning: multiple closures found for read # 10670216
Warning: multiple closures found for read # 10673142
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Warning: multiple closures found for read # 10702635
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Warning: multiple closures found for read # 10730995