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 594 segments done. Found 36 potential split-segment junctions Found 2 potential small deletions Found 4 potential small insertions Indexing extensions in ./No_0_R1.TOnovel/tmp/left_kept_reads_seg1_missing.fq Indexing extensions in ./No_0_R1.TOnovel/tmp/left_kept_reads_seg2_missing.fq Indexing extensions in ./No_0_R1.TOnovel/tmp/left_kept_reads_seg3_missing.fq Total extensions: 15057765 Total extensions: 15057765 Total extensions: 15057765 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 8577 bases Map covers 8451 bases in sufficiently long segments Map contains 125 good islands 3583 are left looking bases 2776 are right looking bases Collecting potential splice sites in islands reporting synthetic splice junctions... Examining donor-acceptor pairings in CUFF.951_From_ct_1_3280175_0 Examining donor-acceptor pairings in CUFF.1605_From_zu_0_3257369_0 Examining donor-acceptor pairings in CUFF.1463_From_ws_0_3190679_0 Examining donor-acceptor pairings in CUFF.1371_From_tsu_0_3211333_0 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.1399_From_wil_2_2978735_0 Examining donor-acceptor pairings in CUFF.1015_From_hi_0_2966608_0 Examining donor-acceptor pairings in CUFF.949_From_can_0_3218459_0 Examining donor-acceptor pairings in CUFF.1305_From_rsch_4_4263688_0 Examining donor-acceptor pairings in CUFF.911_From_can_0_3230893_0 Examining donor-acceptor pairings in CUFF.1271_From_rsch_4_4034850_0 Examining donor-acceptor pairings in CUFF.1177_From_no_0_3116640_0 Examining donor-acceptor pairings in CUFF.1101_From_mt_0_4188374_0 Examining donor-acceptor pairings in CUFF.1099_From_mt_0_4177596_0 Examining donor-acceptor pairings in CUFF.921_From_can_0_3233581_0 Examining donor-acceptor pairings in CUFF.1259_From_po_0_3402348_0 Examining donor-acceptor pairings in CUFF.1359_From_tsu_0_3148935_0 Examining donor-acceptor pairings in CUFF.1515_From_wu_0_2648785_0 Examining donor-acceptor pairings in CUFF.1361_From_tsu_0_3175121_0 Examining donor-acceptor pairings in CUFF.1167_From_no_0_3096552_0 Examining donor-acceptor pairings in CUFF.1153_From_no_0_2923846_0 Examining donor-acceptor pairings in CUFF.1055_From_ler_0_4004770_0 Examining donor-acceptor pairings in CUFF.1639_From_zu_0_3291057_0 Examining donor-acceptor pairings in CUFF.1003_From_hi_0_2790034_0 Examining donor-acceptor pairings in CUFF.1547_From_wu_0_2685428_0 Examining donor-acceptor pairings in CUFF.1281_From_oy_0_3121110_0 Examining donor-acceptor pairings in CUFF.1313_From_po_0_3573778_0 Examining donor-acceptor pairings in CUFF.1453_From_ws_0_3185408_0 Examining donor-acceptor pairings in CUFF.1309_From_rsch_4_4307314_0 Examining donor-acceptor pairings in CUFF.941_From_bur_0_2025286_0 Examining donor-acceptor pairings in CUFF.973_From_edi_0_2871668_0 Examining donor-acceptor pairings in CUFF.1049_From_ler_0_4002120_0 Examining donor-acceptor pairings in CUFF.1529_From_wu_0_2655159_0 Examining donor-acceptor pairings in CUFF.1013_From_kn_0_3532396_0 Examining donor-acceptor pairings in CUFF.943_From_ct_1_3247037_0 Examining donor-acceptor pairings in CUFF.969_From_edi_0_2888616_0 Examining donor-acceptor pairings in CUFF.1619_From_zu_0_3280025_0 Examining donor-acceptor pairings in CUFF.1397_From_tsu_0_3228017_0 Examining donor-acceptor pairings in CUFF.1423_From_wil_2_3072219_0 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.1411_From_rsch_4_4266550_0 Examining donor-acceptor pairings in CUFF.1475_From_ws_0_3313321_0 Examining donor-acceptor pairings in CUFF.1267_From_no_0_3128142_0 Examining donor-acceptor pairings in CUFF.1603_From_zu_0_3242889_0 Examining donor-acceptor pairings in CUFF.1493_From_wil_2_3087183_0 Examining donor-acceptor pairings in CUFF.915_From_can_0_3231205_0 Examining donor-acceptor pairings in CUFF.1613_From_zu_0_3259399_1 Examining donor-acceptor pairings in CUFF.1607_From_zu_0_3255169_0 Found 2 potential island-end pairing junctions done Aligning 594 microexon segments in 79 windows Checked 1188 segments against 79 windows for microexon junctions Found 0 potential microexon junctions -- microexon -- -- done -- -- seg -- CUFF.949_From_can_0_3218459_0 79 158 - CUFF.949_From_can_0_3218459_0 79 169 + CUFF.949_From_can_0_3218459_0 81 171 - CUFF.949_From_can_0_3218459_0 86 171 + CUFF.949_From_can_0_3218459_0 88 158 - CUFF.949_From_can_0_3218459_0 88 169 + CUFF.949_From_can_0_3218459_0 93 158 - CUFF.949_From_can_0_3218459_0 93 169 + CUFF.949_From_can_0_3218459_0 97 169 + CUFF.949_From_can_0_3218459_0 101 171 + CUFF.949_From_can_0_3218459_0 106 171 + CUFF.949_From_can_0_3218459_0 588 791 + CUFF.949_From_can_0_3218459_0 596 773 - CUFF.949_From_can_0_3218459_0 605 773 - CUFF.949_From_can_0_3218459_0 79 162 - CUFF.949_From_can_0_3218459_0 81 174 - CUFF.949_From_can_0_3218459_0 86 174 + CUFF.949_From_can_0_3218459_0 88 162 - CUFF.949_From_can_0_3218459_0 93 162 - CUFF.949_From_can_0_3218459_0 101 174 + CUFF.949_From_can_0_3218459_0 106 174 + CUFF.949_From_can_0_3218459_0 596 797 - CUFF.949_From_can_0_3218459_0 605 797 - CUFF.949_From_can_0_3218459_0 79 177 - CUFF.949_From_can_0_3218459_0 81 189 - CUFF.949_From_can_0_3218459_0 86 189 + CUFF.949_From_can_0_3218459_0 88 177 - CUFF.949_From_can_0_3218459_0 93 177 - CUFF.949_From_can_0_3218459_0 101 189 + CUFF.949_From_can_0_3218459_0 106 189 + CUFF.949_From_can_0_3218459_0 79 180 - CUFF.949_From_can_0_3218459_0 88 180 - CUFF.949_From_can_0_3218459_0 93 180 - CUFF.949_From_can_0_3218459_0 79 186 - CUFF.949_From_can_0_3218459_0 88 186 - CUFF.949_From_can_0_3218459_0 93 186 - -- done -- -- cov -- CUFF.949_From_can_0_3218459_0 93 169 + CUFF.949_From_can_0_3218459_0 121 408 + -- done -- -- buf -- -- done -- Reporting potential splice junctions...done Reported 37 total possible splices Reporting potential deletions... Reporting potential insertions...