segment_juncs v1.2.0 (1752) --------------------------- Loading reference sequences... Loading CUFF.1649_From_zu_0_3082201_0...done Loading CUFF.1231_From_oy_0_2965192_0...done Loading CUFF.1337_From_sf_2_2662232_0...done Loading CUFF.1509_From_wu_0_2616263_0...done Loading CUFF.1149_From_mt_0_4217716_0...done Loading CUFF.1275_From_po_0_3332479_0...done Loading CUFF.1615_From_zu_0_3118546_0...done Loading CUFF.1211_From_po_0_3269389_0...done Loading CUFF.1519_From_wu_0_2597064_0...done Loading CUFF.1335_From_sf_2_2524453_0...done Loading CUFF.1507_From_wu_0_2587993_0...done Loading CUFF.1155_From_no_0_2905273_0...done Loading CUFF.1271_From_rsch_4_4034850_0...done Loading CUFF.1209_From_po_0_3295404_0...done Loading CUFF.1523_From_wu_0_2638225_0...done Loading CUFF.867_From_bur_0_1863298_0...done Loading CUFF.1349_From_mt_0_4528444_1...done Loading CUFF.995_From_hi_0_2751582_0...done Loading CUFF.981_From_hi_0_2690171_0...done Loading CUFF.1027_From_kn_0_3558357_0...done Loading CUFF.963_From_edi_0_2744702_0...done Loading CUFF.1503_From_wu_0_2588697_0...done Loading CUFF.1093_From_mt_0_4130072_0...done Loading CUFF.1219_From_po_0_3319326_0...done Loading CUFF.1119_From_hi_0_2939638_0...done Loading CUFF.1019_From_edi_0_2859720_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.1045_From_kn_0_3605300_0...done Loading CUFF.1531_From_ws_0_3340488_0...done Loading CUFF.1497_From_ws_0_3380934_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.1079_From_mt_0_4085357_0...done Loading CUFF.921_From_can_0_3233581_0...done Loading CUFF.869_From_bur_0_1873494_0...done Loading CUFF.1081_From_mt_0_4099484_0...done Loading CUFF.1505_From_wu_0_2607348_0...done Loading CUFF.1427_From_ws_0_3077529_0...done Loading CUFF.1515_From_wu_0_2648785_0...done Loading CUFF.1285_From_rsch_4_4085063_0...done Loading CUFF.1153_From_no_0_2923846_0...done Loading CUFF.1307_From_rsch_4_4277566_0...done Loading CUFF.1281_From_oy_0_3121110_0...done Loading CUFF.1301_From_rsch_4_4111713_0...done Loading CUFF.907_From_can_0_3122480_0...done Loading CUFF.1213_From_po_0_3316390_0...done Loading CUFF.1535_From_wu_0_2676799_0...done Loading CUFF.1003_From_hi_0_2790034_0...done Loading CUFF.1395_From_wil_2_2904915_0...done Loading CUFF.1631_From_zu_0_3277661_1...done Loading CUFF.1109_From_mt_0_4194856_0...done Loading CUFF.1207_From_po_0_3308932_0...done Loading CUFF.1397_From_tsu_0_3228017_0...done Loading CUFF.1459_From_ws_0_3182508_0...done Loading CUFF.1613_From_zu_0_3259399_1...done Loading CUFF.1008_From_kn_0_3525938_0...done Loading CUFF.1495_From_ws_0_3371988_0...done Loading CUFF.1017_From_kn_0_3566907_0...done Loading CUFF.1165_From_no_0_2959683_0...done Loading CUFF.1493_From_wil_2_3087183_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.1293_From_rsch_4_4107621_0...done Loading CUFF.1591_From_zu_0_3092045_0...done Loading CUFF.1313_From_po_0_3573778_0...done Loading CUFF.1117_From_hi_0_2939638_0...done Loading CUFF.895_From_can_0_3069992_0...done Loading CUFF.1069_From_hi_0_2916184_0...done Loading CUFF.1637_From_zu_0_3277661_0...done Loading CUFF.1163_From_no_0_2951521_0...done Loading CUFF.1611_From_zu_0_3255503_0...done Loading CUFF.1367_From_tsu_0_3135135_0...done Loading CUFF.1453_From_ws_0_3185408_0...done Loading CUFF.1599_From_zu_0_3200689_0...done Loading CUFF.1315_From_rsch_4_4277566_0...done Loading CUFF.1229_From_po_0_3339041_0...done Loading CUFF.1385_From_sf_2_2653966_0...done Loading CUFF.1617_From_zu_0_3278243_0...done Loading CUFF.1521_From_ws_0_3344070_0...done Loading CUFF.1061_From_ler_0_4016532_0...done Loading CUFF.927_From_ct_1_3108889_0...done Loading CUFF.901_From_can_0_3094988_0...done Loading CUFF.1625_From_zu_0_3243571_0...done Loading CUFF.1481_From_ws_0_3349444_1...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.973_From_edi_0_2871668_0...done Loading CUFF.1597_From_zu_0_3181459_0...done Loading CUFF.1465_From_ws_0_3190963_0...done Loading CUFF.1233_From_po_0_3365309_0...done Loading CUFF.991_From_edi_0_2891968_0...done Loading CUFF.1603_From_zu_0_3242889_0...done Loading CUFF.937_From_can_0_3239881_0...done Loading CUFF.993_From_hi_0_2787534_0...done Loading CUFF.1049_From_ler_0_4002120_0...done Loading CUFF.929_From_can_0_3263637_0...done Loading CUFF.1157_From_no_0_2939843_0...done Loading CUFF.1055_From_ler_0_4004770_0...done Loading CUFF.1539_From_wu_0_2702886_0...done Loading CUFF.989_From_edi_0_2932438_0...done Loading CUFF.1011_From_edi_0_2918156_0...done Loading CUFF.1593_From_zu_0_3112556_0...done Loading CUFF.1113_From_mt_0_4206392_0...done Loading CUFF.1431_From_ws_0_3170660_0...done Loading CUFF.1443_From_wil_2_3052273_0...done Loading CUFF.1533_From_wu_0_2683442_0...done Loading CUFF.881_From_bur_0_1969548_0...done Loading CUFF.1401_From_wil_2_3050523_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.1295_From_rsch_4_4118037_0...done Loading CUFF.1007_From_edi_0_2888586_0...done Loading CUFF.935_From_bur_0_2020452_0...done Loading CUFF.1491_From_ws_0_3373966_0...done Loading CUFF.1563_From_ws_0_3381390_0...done Loading CUFF.1133_From_mt_0_4399784_0...done Loading CUFF.1251_From_po_0_3400198_0...done Loading CUFF.1121_From_mt_0_4226690_0...done Loading CUFF.1411_From_rsch_4_4266550_0...done Loading CUFF.1489_From_ws_0_3372620_0...done Loading CUFF.1463_From_ws_0_3190679_0...done Loading CUFF.1087_From_ler_0_4211779_0...done Loading CUFF.1559_From_wu_0_2824162_0...done Loading CUFF.983_From_ct_1_3241157_0...done Loading CUFF.1175_From_hi_0_2953648_0...done Loading CUFF.967_From_edi_0_2887084_2...done Loading CUFF.1455_From_wil_2_3068737_0...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.1373_From_tsu_0_3208747_0...done Loading CUFF.985_From_edi_0_2921730_0...done Loading CUFF.913_From_can_0_3217045_0...done Loading CUFF.1433_From_wil_2_3079625_0...done Loading CUFF.961_From_ct_1_3302721_0...done Loading CUFF.1601_From_zu_0_3250197_1...done Loading CUFF.1173_From_no_0_3113578_1...done Loading CUFF.1187_From_oy_0_3098144_0...done Loading CUFF.1351_From_tsu_0_3175121_0...done Loading CUFF.1543_From_ws_0_3373604_0...done Loading CUFF.1409_From_wil_2_3066229_0...done Loading CUFF.911_From_can_0_3230893_0...done Loading CUFF.1639_From_zu_0_3291057_0...done Loading CUFF.1075_From_edi_0_2906444_0...done Loading CUFF.1471_From_tsu_0_3212935_0...done Loading CUFF.1413_From_sf_2_2687786_0...done Loading CUFF.1167_From_no_0_3096552_0...done Loading CUFF.875_From_bur_0_1999718_0...done Loading CUFF.1475_From_ws_0_3313321_0...done Loading CUFF.1483_From_ws_0_3364198_0...done Loading CUFF.1565_From_zu_0_3075813_0...done Loading CUFF.1363_From_sf_2_2671632_0...done Loading CUFF.1197_From_oy_0_3103794_0...done Loading CUFF.1311_From_rsch_4_4275442_0...done Loading CUFF.1343_From_sf_2_2689374_0...done Loading CUFF.1339_From_sf_2_2689374_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.1407_From_wil_2_3063473_0...done Loading CUFF.1641_From_zu_0_3291057_0...done Loading CUFF.1035_From_kn_0_3751597_0...done Loading CUFF.1169_From_no_0_3101262_0...done Loading CUFF.1423_From_wil_2_3072219_0...done Loading CUFF.1361_From_tsu_0_3175121_0...done Loading CUFF.1325_From_sf_2_2626132_0...done Loading CUFF.1261_From_po_0_3599571_0...done Loading CUFF.1375_From_tsu_0_3211741_0...done Loading CUFF.1417_From_wil_2_3078633_1...done Loading CUFF.1583_From_wu_0_2829124_0...done Loading CUFF.1267_From_no_0_3128142_0...done Loading CUFF.1309_From_rsch_4_4307314_0...done Loading CUFF.1499_From_ws_0_3382714_0...done Loading CUFF.1177_From_no_0_3116640_0...done Loading CUFF.1605_From_zu_0_3257369_0...done Loading CUFF.865_From_bur_0_1967596_0...done Loading CUFF.949_From_can_0_3218459_0...done Loading CUFF.1419_From_sf_2_2701328_0...done Loading CUFF.1345_From_sf_2_2689374_0...done Loading CUFF.1619_From_zu_0_3280025_0...done Loading CUFF.1065_From_ler_0_4153595_0...done Loading CUFF.1595_From_zu_0_3238769_0...done Loading CUFF.1111_From_ler_0_4165287_0...done Loading CUFF.1215_From_oy_0_3162092_0...done Loading CUFF.975_From_edi_0_2902016_0...done Loading CUFF.1545_From_wu_0_2770362_0...done Loading CUFF.1089_From_ler_0_4224097_0...done Loading CUFF.943_From_ct_1_3247037_0...done Loading CUFF.1077_From_ler_0_4225073_0...done Loading CUFF.1607_From_zu_0_3255169_0...done Loading CUFF.1487_From_ws_0_3347582_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.1439_From_wil_2_3089541_0...done Loading CUFF.879_From_bur_0_2021834_0...done Loading CUFF.1265_From_po_0_3577252_0...done Loading CUFF.1073_From_ler_0_4209589_1...done Loading CUFF.1479_From_ws_0_3339092_0...done Loading CUFF.1451_From_wil_2_3077447_0...done Loading CUFF.1347_From_sf_2_2682779_0...done Loading CUFF.1635_From_zu_0_3263539_0...done Loading CUFF.1579_From_wu_0_2802868_0...done Loading CUFF.1365_From_tsu_0_3179519_0...done Loading CUFF.1513_From_ws_0_3381290_0...done Loading CUFF.915_From_can_0_3231205_0...done Loading CUFF.1383_From_tsu_0_3242833_1...done Loading CUFF.1415_From_wil_2_3082811_1...done Loading CUFF.1421_From_tsu_0_3215821_0...done Loading CUFF.919_From_can_0_3258779_0...done Loading CUFF.909_From_can_0_3223655_0...done Loading CUFF.1029_From_kn_0_3802200_0...done Loading CUFF.1393_From_tsu_0_3228555_0...done Loading CUFF.1437_From_wil_2_3088151_0...done Loading CUFF.1377_From_tsu_0_3215671_0...done Loading CUFF.1633_From_zu_0_3280213_0...done Loading CUFF.1333_From_sf_2_2666154_1...done Loading CUFF.1405_From_wil_2_3052951_0...done Loading CUFF.971_From_edi_0_2891226_0...done Loading CUFF.1623_From_zu_0_3289907_1...done Loading CUFF.1557_From_wu_0_2824308_0...done Loading CUFF.1015_From_hi_0_2966608_0...done Loading CUFF.951_From_ct_1_3280175_0...done Loading CUFF.1159_From_no_0_3088052_0...done Loading CUFF.1621_From_zu_0_3275363_0...done Loading CUFF.871_From_bur_0_2012810_0...done Loading CUFF.889_From_bur_0_2032354_0...done Loading CUFF.1647_From_zu_0_3289907_1...done Loading CUFF.1289_From_po_0_3606391_0...done Loading CUFF.1053_From_kn_0_3819922_1...done Loading CUFF.877_From_bur_0_2022518_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.1033_From_kn_0_3799876_0...done Loading CUFF.1561_From_wu_0_2827904_0...done Loading CUFF.1041_From_kn_0_3824150_0...done Loading CUFF.1369_From_sf_2_2700286_0...done Loading CUFF.1627_From_zu_0_3262887_0...done Loading CUFF.899_From_bur_0_2022518_0...done Loading CUFF.941_From_bur_0_2025286_0...done Loading CUFF.1585_From_wu_0_2837848_0...done Loading CUFF.1269_From_po_0_3606391_1...done Loading CUFF.1381_From_tsu_0_3240885_0...done Loading CUFF.1181_From_no_0_3120392_0...done Loading CUFF.1501_From_ws_0_3365892_0...done Loading CUFF.1425_From_wil_2_3091415_1...done Loading CUFF.1537_From_ws_0_3382500_0...done Loading CUFF.873_From_bur_0_2020452_0...done Loading CUFF.1277_From_po_0_3599571_0...done Loading CUFF.1447_From_wil_2_3091415_1...done Loading CUFF.897_From_bur_0_2022518_0...done Loading CUFF.997_From_edi_0_2934714_0...done Loading CUFF.977_From_edi_0_2934714_0...done Loading CUFF.979_From_edi_0_2934714_0...done Loading CUFF.1485_From_ws_0_3371988_0...done Loading left segment hits... Microaligned 95 segments done. Found 2 potential split-segment junctions Found 4 potential small deletions Found 0 potential small insertions Indexing extensions in ./col_0.TOnovel/tmp/left_kept_reads_seg1_missing.fq Indexing extensions in ./col_0.TOnovel/tmp/left_kept_reads_seg2_missing.fq Indexing extensions in ./col_0.TOnovel/tmp/left_kept_reads_seg3_missing.fq Total extensions: 34639295 Total extensions: 34639295 Total extensions: 34639295 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 3879 bases Map covers 3827 bases in sufficiently long segments Map contains 53 good islands 1181 are left looking bases 485 are right looking bases Collecting potential splice sites in islands reporting synthetic splice junctions... Examining donor-acceptor pairings in CUFF.927_From_ct_1_3108889_0 Examining donor-acceptor pairings in CUFF.961_From_ct_1_3302721_0 Examining donor-acceptor pairings in CUFF.1219_From_po_0_3319326_0 Examining donor-acceptor pairings in CUFF.1275_From_po_0_3332479_0 Examining donor-acceptor pairings in CUFF.1621_From_zu_0_3275363_0 Examining donor-acceptor pairings in CUFF.1271_From_rsch_4_4034850_0 Examining donor-acceptor pairings in CUFF.1259_From_po_0_3402348_0 Examining donor-acceptor pairings in CUFF.995_From_hi_0_2751582_0 Examining donor-acceptor pairings in CUFF.1019_From_edi_0_2859720_0 Examining donor-acceptor pairings in CUFF.1361_From_tsu_0_3175121_0 Examining donor-acceptor pairings in CUFF.1349_From_mt_0_4528444_1 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.1163_From_no_0_2951521_0 Examining donor-acceptor pairings in CUFF.941_From_bur_0_2025286_0 Examining donor-acceptor pairings in CUFF.1301_From_rsch_4_4111713_0 Examining donor-acceptor pairings in CUFF.1649_From_zu_0_3082201_0 Examining donor-acceptor pairings in CUFF.963_From_edi_0_2744702_0 Examining donor-acceptor pairings in CUFF.1563_From_ws_0_3381390_0 Examining donor-acceptor pairings in CUFF.1267_From_no_0_3128142_0 Found 0 potential island-end pairing junctions done Aligning 95 microexon segments in 39 windows Checked 190 segments against 39 windows for microexon junctions Found 1 potential microexon junctions -- microexon -- CUFF.961_From_ct_1_3302721_0 165 334 + -- done -- -- seg -- CUFF.961_From_ct_1_3302721_0 240 298 - CUFF.961_From_ct_1_3302721_0 244 298 - -- done -- -- cov -- -- done -- -- buf -- -- done -- Reporting potential splice junctions...done Reported 3 total possible splices Reporting potential deletions... Reporting potential insertions...