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 1104 segments done. Found 24 potential split-segment junctions Found 5 potential small deletions Found 5 potential small insertions Indexing extensions in ./Tsu_0_R2.TOnovel/tmp/left_kept_reads_seg1_missing.fq Indexing extensions in ./Tsu_0_R2.TOnovel/tmp/left_kept_reads_seg2_missing.fq Indexing extensions in ./Tsu_0_R2.TOnovel/tmp/left_kept_reads_seg3_missing.fq Total extensions: 16570234 Total extensions: 16570234 Total extensions: 16570234 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 12192 bases Map covers 12007 bases in sufficiently long segments Map contains 185 good islands 6181 are left looking bases 4260 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.1471_From_tsu_0_3212935_0 Examining donor-acceptor pairings in CUFF.1561_From_wu_0_2827904_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.1329_From_sf_2_2642906_0 Examining donor-acceptor pairings in CUFF.1027_From_kn_0_3558357_0 Examining donor-acceptor pairings in CUFF.1467_From_ws_0_3309675_0 Examining donor-acceptor pairings in CUFF.1253_From_po_0_3387411_0 Examining donor-acceptor pairings in CUFF.1459_From_ws_0_3182508_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.1531_From_ws_0_3340488_0 Examining donor-acceptor pairings in CUFF.1015_From_hi_0_2966608_0 Examining donor-acceptor pairings in CUFF.1609_From_zu_0_3260873_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.1513_From_ws_0_3381290_0 Examining donor-acceptor pairings in CUFF.1073_From_ler_0_4209589_1 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.911_From_can_0_3230893_0 Examining donor-acceptor pairings in CUFF.1007_From_edi_0_2888586_0 Examining donor-acceptor pairings in CUFF.1437_From_wil_2_3088151_0 Examining donor-acceptor pairings in CUFF.1101_From_mt_0_4188374_0 Examining donor-acceptor pairings in CUFF.1223_From_po_0_3340213_0 Examining donor-acceptor pairings in CUFF.1367_From_tsu_0_3135135_0 Examining donor-acceptor pairings in CUFF.921_From_can_0_3233581_0 Examining donor-acceptor pairings in CUFF.1289_From_po_0_3606391_0 Examining donor-acceptor pairings in CUFF.1229_From_po_0_3339041_0 Examining donor-acceptor pairings in CUFF.955_From_edi_0_2766531_0 Examining donor-acceptor pairings in CUFF.1259_From_po_0_3402348_0 Examining donor-acceptor pairings in CUFF.1017_From_kn_0_3566907_0 Examining donor-acceptor pairings in CUFF.1413_From_sf_2_2687786_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.971_From_edi_0_2891226_0 Examining donor-acceptor pairings in CUFF.1361_From_tsu_0_3175121_0 Examining donor-acceptor pairings in CUFF.993_From_hi_0_2787534_0 Examining donor-acceptor pairings in CUFF.1381_From_tsu_0_3240885_0 Examining donor-acceptor pairings in CUFF.1373_From_tsu_0_3208747_0 Examining donor-acceptor pairings in CUFF.1169_From_no_0_3101262_0 Examining donor-acceptor pairings in CUFF.1325_From_sf_2_2626132_0 Examining donor-acceptor pairings in CUFF.1003_From_hi_0_2790034_0 Examining donor-acceptor pairings in CUFF.1383_From_tsu_0_3242833_1 Examining donor-acceptor pairings in CUFF.1547_From_wu_0_2685428_0 Examining donor-acceptor pairings in CUFF.1559_From_wu_0_2824162_0 Examining donor-acceptor pairings in CUFF.1311_From_rsch_4_4275442_0 Examining donor-acceptor pairings in CUFF.1453_From_ws_0_3185408_0 Examining donor-acceptor pairings in CUFF.1553_From_wu_0_2806776_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.1415_From_wil_2_3082811_1 Examining donor-acceptor pairings in CUFF.1633_From_zu_0_3280213_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.967_From_edi_0_2887084_2 Examining donor-acceptor pairings in CUFF.1543_From_ws_0_3373604_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.1417_From_wil_2_3078633_1 Examining donor-acceptor pairings in CUFF.1053_From_kn_0_3819922_1 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.1095_From_mt_0_4131964_0 Examining donor-acceptor pairings in CUFF.1627_From_zu_0_3262887_0 Examining donor-acceptor pairings in CUFF.1421_From_tsu_0_3215821_0 Examining donor-acceptor pairings in CUFF.1401_From_wil_2_3050523_0 Examining donor-acceptor pairings in CUFF.1267_From_no_0_3128142_0 Examining donor-acceptor pairings in CUFF.1139_From_ler_0_4211779_1 Examining donor-acceptor pairings in CUFF.1141_From_mt_0_4449890_0 Examining donor-acceptor pairings in CUFF.1607_From_zu_0_3255169_0 Found 3 potential island-end pairing junctions done Aligning 1104 microexon segments in 100 windows window 100 Checked 2208 segments against 100 windows for microexon junctions Found 1 potential microexon junctions -- microexon -- CUFF.1513_From_ws_0_3381290_0 293 612 - -- done -- -- seg -- CUFF.1543_From_ws_0_3373604_0 303 389 - CUFF.1543_From_ws_0_3373604_0 306 389 + CUFF.1543_From_ws_0_3373604_0 309 389 + CUFF.1543_From_ws_0_3373604_0 313 389 - CUFF.1543_From_ws_0_3373604_0 317 389 + CUFF.1543_From_ws_0_3373604_0 325 392 + CUFF.1543_From_ws_0_3373604_0 328 389 + CUFF.1543_From_ws_0_3373604_0 330 389 + CUFF.1543_From_ws_0_3373604_0 303 397 - CUFF.1543_From_ws_0_3373604_0 306 397 + CUFF.1543_From_ws_0_3373604_0 309 397 + CUFF.1543_From_ws_0_3373604_0 313 397 - CUFF.1543_From_ws_0_3373604_0 317 397 + CUFF.1543_From_ws_0_3373604_0 325 395 + CUFF.1543_From_ws_0_3373604_0 328 397 + CUFF.1543_From_ws_0_3373604_0 330 397 + CUFF.1543_From_ws_0_3373604_0 303 400 - CUFF.1543_From_ws_0_3373604_0 306 400 + CUFF.1543_From_ws_0_3373604_0 309 400 + CUFF.1543_From_ws_0_3373604_0 313 400 - CUFF.1543_From_ws_0_3373604_0 317 400 + CUFF.1543_From_ws_0_3373604_0 325 403 + CUFF.1543_From_ws_0_3373604_0 328 400 + CUFF.1543_From_ws_0_3373604_0 330 400 + -- done -- -- cov -- CUFF.1401_From_wil_2_3050523_0 94 173 + CUFF.1471_From_tsu_0_3212935_0 102 386 - CUFF.1421_From_tsu_0_3215821_0 511 620 - -- done -- -- buf -- -- done -- Reporting potential splice junctions...done Reported 28 total possible splices Reporting potential deletions... Reporting potential insertions...