segment_juncs v1.2.0 (1752) --------------------------- Loading reference sequences... Loading CUFF.1271_From_rsch_4_4034850_0...done Loading CUFF.1337_From_sf_2_2662232_0...done Loading CUFF.1285_From_rsch_4_4085063_0...done Loading CUFF.1565_From_zu_0_3075813_0...done Loading CUFF.1275_From_po_0_3332479_0...done Loading CUFF.1649_From_zu_0_3082201_0...done Loading CUFF.1293_From_rsch_4_4107621_0...done Loading CUFF.1163_From_no_0_2951521_0...done Loading CUFF.1465_From_ws_0_3190963_0...done Loading CUFF.1055_From_ler_0_4004770_0...done Loading CUFF.1335_From_sf_2_2524453_0...done Loading CUFF.907_From_can_0_3122480_0...done Loading CUFF.1481_From_ws_0_3349444_1...done Loading CUFF.1165_From_no_0_2959683_0...done Loading CUFF.1459_From_ws_0_3182508_0...done Loading CUFF.869_From_bur_0_1873494_0...done Loading CUFF.1463_From_ws_0_3190679_0...done Loading CUFF.921_From_can_0_3233581_0...done Loading CUFF.1367_From_tsu_0_3135135_0...done Loading CUFF.1133_From_mt_0_4399784_0...done Loading CUFF.1617_From_zu_0_3278243_0...done Loading CUFF.1497_From_ws_0_3380934_0...done Loading CUFF.1315_From_rsch_4_4277566_0...done Loading CUFF.1613_From_zu_0_3259399_1...done Loading CUFF.1401_From_wil_2_3050523_0...done Loading CUFF.989_From_edi_0_2932438_0...done Loading CUFF.1173_From_no_0_3113578_1...done Loading CUFF.1495_From_ws_0_3371988_0...done Loading CUFF.1611_From_zu_0_3255503_0...done Loading CUFF.1187_From_oy_0_3098144_0...done Loading CUFF.1011_From_edi_0_2918156_0...done Loading CUFF.1603_From_zu_0_3242889_0...done Loading CUFF.1531_From_ws_0_3340488_0...done Loading CUFF.1373_From_tsu_0_3208747_0...done Loading CUFF.865_From_bur_0_1967596_0...done Loading CUFF.1361_From_tsu_0_3175121_0...done Loading CUFF.1065_From_ler_0_4153595_0...done Loading CUFF.1439_From_wil_2_3089541_0...done Loading CUFF.1119_From_hi_0_2939638_0...done Loading CUFF.1117_From_hi_0_2939638_0...done Loading CUFF.1409_From_wil_2_3066229_0...done Loading CUFF.1595_From_zu_0_3238769_0...done Loading CUFF.1077_From_ler_0_4225073_0...done Loading CUFF.913_From_can_0_3217045_0...done Loading CUFF.985_From_edi_0_2921730_0...done Loading CUFF.1281_From_oy_0_3121110_0...done Loading CUFF.973_From_edi_0_2871668_0...done Loading CUFF.943_From_ct_1_3247037_0...done Loading CUFF.1069_From_hi_0_2916184_0...done Loading CUFF.1035_From_kn_0_3751597_0...done Loading CUFF.1543_From_ws_0_3373604_0...done Loading CUFF.983_From_ct_1_3241157_0...done Loading CUFF.1311_From_rsch_4_4275442_0...done Loading CUFF.909_From_can_0_3223655_0...done Loading CUFF.1479_From_ws_0_3339092_0...done Loading CUFF.1443_From_wil_2_3052273_0...done Loading CUFF.881_From_bur_0_1969548_0...done Loading CUFF.1637_From_zu_0_3277661_0...done Loading CUFF.1313_From_po_0_3573778_0...done Loading CUFF.1385_From_sf_2_2653966_0...done Loading CUFF.1169_From_no_0_3101262_0...done Loading CUFF.1419_From_sf_2_2701328_0...done Loading CUFF.1111_From_ler_0_4165287_0...done Loading CUFF.1029_From_kn_0_3802200_0...done Loading CUFF.1625_From_zu_0_3243571_0...done Loading CUFF.1407_From_wil_2_3063473_0...done Loading CUFF.919_From_can_0_3258779_0...done Loading CUFF.1383_From_tsu_0_3242833_1...done Loading CUFF.1375_From_tsu_0_3211741_0...done Loading CUFF.1347_From_sf_2_2682779_0...done Loading CUFF.1493_From_wil_2_3087183_0...done Loading CUFF.1557_From_wu_0_2824308_0...done Loading CUFF.879_From_bur_0_2021834_0...done Loading CUFF.1377_From_tsu_0_3215671_0...done Loading CUFF.1421_From_tsu_0_3215821_0...done Loading CUFF.915_From_can_0_3231205_0...done Loading CUFF.875_From_bur_0_1999718_0...done Loading CUFF.949_From_can_0_3218459_0...done Loading CUFF.1521_From_ws_0_3344070_0...done Loading CUFF.1405_From_wil_2_3052951_0...done Loading CUFF.1089_From_ler_0_4224097_0...done Loading CUFF.1159_From_no_0_3088052_0...done Loading CUFF.1363_From_sf_2_2671632_0...done Loading CUFF.1471_From_tsu_0_3212935_0...done Loading CUFF.1007_From_edi_0_2888586_0...done Loading CUFF.1455_From_wil_2_3068737_0...done Loading CUFF.937_From_can_0_3239881_0...done Loading CUFF.1607_From_zu_0_3255169_0...done Loading CUFF.971_From_edi_0_2891226_0...done Loading CUFF.1623_From_zu_0_3289907_1...done Loading CUFF.1411_From_rsch_4_4266550_0...done Loading CUFF.1177_From_no_0_3116640_0...done Loading CUFF.1451_From_wil_2_3077447_0...done Loading CUFF.1647_From_zu_0_3289907_1...done Loading CUFF.1487_From_ws_0_3347582_0...done Loading CUFF.1175_From_hi_0_2953648_0...done Loading CUFF.1437_From_wil_2_3088151_0...done Loading CUFF.1033_From_kn_0_3799876_0...done Loading CUFF.889_From_bur_0_2032354_0...done Loading CUFF.935_From_bur_0_2020452_0...done Loading CUFF.1215_From_oy_0_3162092_0...done Loading CUFF.1633_From_zu_0_3280213_0...done Loading CUFF.1289_From_po_0_3606391_0...done Loading CUFF.1501_From_ws_0_3365892_0...done Loading CUFF.1585_From_wu_0_2837848_0...done Loading CUFF.1053_From_kn_0_3819922_1...done Loading CUFF.1267_From_no_0_3128142_0...done Loading CUFF.1413_From_sf_2_2687786_0...done Loading CUFF.1181_From_no_0_3120392_0...done Loading CUFF.941_From_bur_0_2025286_0...done Loading CUFF.1369_From_sf_2_2700286_0...done Loading CUFF.997_From_edi_0_2934714_0...done Loading CUFF.1537_From_ws_0_3382500_0...done Loading CUFF.1211_From_po_0_3269389_0...done Loading CUFF.1519_From_wu_0_2597064_0...done Loading CUFF.1507_From_wu_0_2587993_0...done Loading CUFF.1209_From_po_0_3295404_0...done Loading CUFF.1523_From_wu_0_2638225_0...done Loading CUFF.981_From_hi_0_2690171_0...done Loading CUFF.1027_From_kn_0_3558357_0...done Loading CUFF.1093_From_mt_0_4130072_0...done Loading CUFF.1219_From_po_0_3319326_0...done Loading CUFF.1547_From_wu_0_2685428_0...done Loading CUFF.1353_From_tsu_0_3002533_0...done Loading CUFF.1569_From_zu_0_3035650_0...done Loading CUFF.1141_From_mt_0_4449890_0...done Loading CUFF.1529_From_wu_0_2655159_0...done Loading CUFF.1575_From_wu_0_2831218_0...done Loading CUFF.1013_From_kn_0_3532396_0...done Loading CUFF.1095_From_mt_0_4131964_0...done Loading CUFF.1081_From_mt_0_4099484_0...done Loading CUFF.1515_From_wu_0_2648785_0...done Loading CUFF.1153_From_no_0_2923846_0...done Loading CUFF.1307_From_rsch_4_4277566_0...done Loading CUFF.1213_From_po_0_3316390_0...done Loading CUFF.1003_From_hi_0_2790034_0...done Loading CUFF.1631_From_zu_0_3277661_1...done Loading CUFF.1207_From_po_0_3308932_0...done Loading CUFF.1397_From_tsu_0_3228017_0...done Loading CUFF.1008_From_kn_0_3525938_0...done Loading CUFF.1017_From_kn_0_3566907_0...done Loading CUFF.1573_From_zu_0_3065917_0...done Loading CUFF.1099_From_mt_0_4177596_0...done Loading CUFF.1253_From_po_0_3387411_0...done Loading CUFF.1453_From_ws_0_3185408_0...done Loading CUFF.1599_From_zu_0_3200689_0...done Loading CUFF.1229_From_po_0_3339041_0...done Loading CUFF.1061_From_ler_0_4016532_0...done Loading CUFF.901_From_can_0_3094988_0...done Loading CUFF.1629_From_zu_0_3287917_0...done Loading CUFF.1139_From_ler_0_4211779_1...done Loading CUFF.1287_From_rsch_4_4099439_0...done Loading CUFF.1101_From_mt_0_4188374_0...done Loading CUFF.953_From_edi_0_2759591_0...done Loading CUFF.1597_From_zu_0_3181459_0...done Loading CUFF.1233_From_po_0_3365309_0...done Loading CUFF.991_From_edi_0_2891968_0...done Loading CUFF.993_From_hi_0_2787534_0...done Loading CUFF.1049_From_ler_0_4002120_0...done Loading CUFF.1539_From_wu_0_2702886_0...done Loading CUFF.1113_From_mt_0_4206392_0...done Loading CUFF.1431_From_ws_0_3170660_0...done Loading CUFF.1527_From_wu_0_2675967_0...done Loading CUFF.1259_From_po_0_3402348_0...done Loading CUFF.1379_From_sf_2_2656790_0...done Loading CUFF.955_From_edi_0_2766531_0...done Loading CUFF.1491_From_ws_0_3373966_0...done Loading CUFF.1121_From_mt_0_4226690_0...done Loading CUFF.1489_From_ws_0_3372620_0...done Loading CUFF.1087_From_ler_0_4211779_0...done Loading CUFF.1559_From_wu_0_2824162_0...done Loading CUFF.967_From_edi_0_2887084_2...done Loading CUFF.1645_From_wu_0_2816600_0...done Loading CUFF.1473_From_ws_0_3293243_0...done Loading CUFF.1399_From_wil_2_2978735_0...done Loading CUFF.969_From_edi_0_2888616_0...done Loading CUFF.1305_From_rsch_4_4263688_0...done Loading CUFF.911_From_can_0_3230893_0...done Loading CUFF.1639_From_zu_0_3291057_0...done Loading CUFF.1167_From_no_0_3096552_0...done Loading CUFF.1475_From_ws_0_3313321_0...done Loading CUFF.1197_From_oy_0_3103794_0...done Loading CUFF.1359_From_tsu_0_3148935_0...done Loading CUFF.1223_From_po_0_3340213_0...done Loading CUFF.1329_From_sf_2_2642906_0...done Loading CUFF.1641_From_zu_0_3291057_0...done Loading CUFF.1423_From_wil_2_3072219_0...done Loading CUFF.1325_From_sf_2_2626132_0...done Loading CUFF.1417_From_wil_2_3078633_1...done Loading CUFF.1583_From_wu_0_2829124_0...done Loading CUFF.1309_From_rsch_4_4307314_0...done Loading CUFF.1605_From_zu_0_3257369_0...done Loading CUFF.1345_From_sf_2_2689374_0...done Loading CUFF.1619_From_zu_0_3280025_0...done Loading CUFF.975_From_edi_0_2902016_0...done Loading CUFF.1545_From_wu_0_2770362_0...done Loading CUFF.1643_From_wu_0_2816600_0...done Loading CUFF.1609_From_zu_0_3260873_0...done Loading CUFF.1189_From_oy_0_3115434_0...done Loading CUFF.1467_From_ws_0_3309675_0...done Loading CUFF.1553_From_wu_0_2806776_0...done Loading CUFF.1265_From_po_0_3577252_0...done Loading CUFF.1073_From_ler_0_4209589_1...done Loading CUFF.1635_From_zu_0_3263539_0...done Loading CUFF.1579_From_wu_0_2802868_0...done Loading CUFF.1513_From_ws_0_3381290_0...done Loading CUFF.1415_From_wil_2_3082811_1...done Loading CUFF.1393_From_tsu_0_3228555_0...done Loading CUFF.1333_From_sf_2_2666154_1...done Loading CUFF.1015_From_hi_0_2966608_0...done Loading CUFF.951_From_ct_1_3280175_0...done Loading CUFF.871_From_bur_0_2012810_0...done Loading CUFF.1371_From_tsu_0_3211333_0...done Loading CUFF.1279_From_po_0_3599571_0...done Loading CUFF.1577_From_wu_0_2832848_0...done Loading CUFF.1561_From_wu_0_2827904_0...done Loading CUFF.1041_From_kn_0_3824150_0...done Loading CUFF.1627_From_zu_0_3262887_0...done Loading CUFF.1381_From_tsu_0_3240885_0...done Loading CUFF.1277_From_po_0_3599571_0...done Loading CUFF.1447_From_wil_2_3091415_1...done Loading left segment hits... Microaligned 448 segments done. Found 36 potential split-segment junctions Found 7 potential small deletions Found 3 potential small insertions Indexing extensions in ./Oy_0_R2.TOnovel/tmp/left_kept_reads_seg1_missing.fq Indexing extensions in ./Oy_0_R2.TOnovel/tmp/left_kept_reads_seg2_missing.fq Indexing extensions in ./Oy_0_R2.TOnovel/tmp/left_kept_reads_seg3_missing.fq Total extensions: 17932627 Total extensions: 17932627 Total extensions: 17932627 Looking for junctions by island end pairings Adding hits from segment file 0 to coverage map Adding hits from segment file 1 to coverage map Adding hits from segment file 2 to coverage map Map covers 10531 bases Map covers 10387 bases in sufficiently long segments Map contains 142 good islands 4200 are left looking bases 3004 are right looking bases Collecting potential splice sites in islands reporting synthetic splice junctions... Examining donor-acceptor pairings in CUFF.913_From_can_0_3217045_0 Examining donor-acceptor pairings in CUFF.1623_From_zu_0_3289907_1 Examining donor-acceptor pairings in CUFF.1467_From_ws_0_3309675_0 Examining donor-acceptor pairings in CUFF.1459_From_ws_0_3182508_0 Examining donor-acceptor pairings in CUFF.1597_From_zu_0_3181459_0 Examining donor-acceptor pairings in CUFF.1487_From_ws_0_3347582_0 Examining donor-acceptor pairings in CUFF.1531_From_ws_0_3340488_0 Examining donor-acceptor pairings in CUFF.1015_From_hi_0_2966608_0 Examining donor-acceptor pairings in CUFF.1611_From_zu_0_3255503_0 Examining donor-acceptor pairings in CUFF.989_From_edi_0_2932438_0 Examining donor-acceptor pairings in CUFF.1631_From_zu_0_3277661_1 Examining donor-acceptor pairings in CUFF.949_From_can_0_3218459_0 Examining donor-acceptor pairings in CUFF.1265_From_po_0_3577252_0 Examining donor-acceptor pairings in CUFF.1637_From_zu_0_3277661_0 Examining donor-acceptor pairings in CUFF.1117_From_hi_0_2939638_0 Examining donor-acceptor pairings in CUFF.1215_From_oy_0_3162092_0 Examining donor-acceptor pairings in CUFF.1189_From_oy_0_3115434_0 Examining donor-acceptor pairings in CUFF.1101_From_mt_0_4188374_0 Examining donor-acceptor pairings in CUFF.1573_From_zu_0_3065917_0 Examining donor-acceptor pairings in CUFF.1229_From_po_0_3339041_0 Examining donor-acceptor pairings in CUFF.1008_From_kn_0_3525938_0 Examining donor-acceptor pairings in CUFF.955_From_edi_0_2766531_0 Examining donor-acceptor pairings in CUFF.1017_From_kn_0_3566907_0 Examining donor-acceptor pairings in CUFF.1359_From_tsu_0_3148935_0 Examining donor-acceptor pairings in CUFF.1345_From_sf_2_2689374_0 Examining donor-acceptor pairings in CUFF.983_From_ct_1_3241157_0 Examining donor-acceptor pairings in CUFF.1233_From_po_0_3365309_0 Examining donor-acceptor pairings in CUFF.993_From_hi_0_2787534_0 Examining donor-acceptor pairings in CUFF.1647_From_zu_0_3289907_1 Examining donor-acceptor pairings in CUFF.1187_From_oy_0_3098144_0 Examining donor-acceptor pairings in CUFF.1003_From_hi_0_2790034_0 Examining donor-acceptor pairings in CUFF.1579_From_wu_0_2802868_0 Examining donor-acceptor pairings in CUFF.1335_From_sf_2_2524453_0 Examining donor-acceptor pairings in CUFF.1547_From_wu_0_2685428_0 Examining donor-acceptor pairings in CUFF.1165_From_no_0_2959683_0 Examining donor-acceptor pairings in CUFF.1453_From_ws_0_3185408_0 Examining donor-acceptor pairings in CUFF.1163_From_no_0_2951521_0 Examining donor-acceptor pairings in CUFF.1309_From_rsch_4_4307314_0 Examining donor-acceptor pairings in CUFF.1557_From_wu_0_2824308_0 Examining donor-acceptor pairings in CUFF.1635_From_zu_0_3263539_0 Examining donor-acceptor pairings in CUFF.973_From_edi_0_2871668_0 Examining donor-acceptor pairings in CUFF.889_From_bur_0_2032354_0 Examining donor-acceptor pairings in CUFF.1049_From_ler_0_4002120_0 Examining donor-acceptor pairings in CUFF.1523_From_wu_0_2638225_0 Examining donor-acceptor pairings in CUFF.969_From_edi_0_2888616_0 Examining donor-acceptor pairings in CUFF.1121_From_mt_0_4226690_0 Examining donor-acceptor pairings in CUFF.967_From_edi_0_2887084_2 Examining donor-acceptor pairings in CUFF.1465_From_ws_0_3190963_0 Examining donor-acceptor pairings in CUFF.1011_From_edi_0_2918156_0 Examining donor-acceptor pairings in CUFF.1473_From_ws_0_3293243_0 Examining donor-acceptor pairings in CUFF.1119_From_hi_0_2939638_0 Examining donor-acceptor pairings in CUFF.1649_From_zu_0_3082201_0 Examining donor-acceptor pairings in CUFF.1053_From_kn_0_3819922_1 Examining donor-acceptor pairings in CUFF.1431_From_ws_0_3170660_0 Examining donor-acceptor pairings in CUFF.1401_From_wil_2_3050523_0 Examining donor-acceptor pairings in CUFF.1347_From_sf_2_2682779_0 Examining donor-acceptor pairings in CUFF.1139_From_ler_0_4211779_1 Examining donor-acceptor pairings in CUFF.1607_From_zu_0_3255169_0 Found 0 potential island-end pairing junctions done Aligning 448 microexon segments in 95 windows Checked 896 segments against 95 windows for microexon junctions Found 1 potential microexon junctions -- microexon -- CUFF.1579_From_wu_0_2802868_0 190 596 + -- done -- -- seg -- CUFF.949_From_can_0_3218459_0 659 780 - CUFF.949_From_can_0_3218459_0 659 791 + CUFF.949_From_can_0_3218459_0 665 780 - CUFF.949_From_can_0_3218459_0 665 791 + CUFF.949_From_can_0_3218459_0 674 780 - CUFF.949_From_can_0_3218459_0 674 791 + CUFF.949_From_can_0_3218459_0 677 780 - CUFF.949_From_can_0_3218459_0 677 791 + CUFF.949_From_can_0_3218459_0 679 791 + CUFF.949_From_can_0_3218459_0 680 797 - CUFF.949_From_can_0_3218459_0 682 780 - CUFF.949_From_can_0_3218459_0 682 791 + CUFF.955_From_edi_0_2766531_0 32 88 - CUFF.955_From_edi_0_2766531_0 32 96 + CUFF.955_From_edi_0_2766531_0 36 105 - CUFF.955_From_edi_0_2766531_0 44 103 - CUFF.949_From_can_0_3218459_0 659 802 + CUFF.949_From_can_0_3218459_0 659 806 - CUFF.949_From_can_0_3218459_0 665 802 + CUFF.949_From_can_0_3218459_0 665 806 - CUFF.949_From_can_0_3218459_0 674 802 + CUFF.949_From_can_0_3218459_0 674 806 - CUFF.949_From_can_0_3218459_0 677 802 + CUFF.949_From_can_0_3218459_0 677 806 - CUFF.949_From_can_0_3218459_0 679 802 + CUFF.949_From_can_0_3218459_0 680 804 - CUFF.949_From_can_0_3218459_0 682 802 + CUFF.949_From_can_0_3218459_0 682 806 - CUFF.955_From_edi_0_2766531_0 32 103 - CUFF.955_From_edi_0_2766531_0 44 107 - CUFF.949_From_can_0_3218459_0 659 808 - CUFF.949_From_can_0_3218459_0 665 808 - CUFF.949_From_can_0_3218459_0 674 808 - CUFF.949_From_can_0_3218459_0 677 808 - CUFF.949_From_can_0_3218459_0 682 808 - CUFF.955_From_edi_0_2766531_0 32 107 - -- done -- -- cov -- -- done -- -- buf -- -- done -- Reporting potential splice junctions...done Reported 37 total possible splices Reporting potential deletions... Reporting potential insertions...