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 591 segments done. Found 45 potential split-segment junctions Found 6 potential small deletions Found 3 potential small insertions Indexing extensions in ./Tsu_0_R1.TOnovel/tmp/left_kept_reads_seg1_missing.fq Indexing extensions in ./Tsu_0_R1.TOnovel/tmp/left_kept_reads_seg2_missing.fq Indexing extensions in ./Tsu_0_R1.TOnovel/tmp/left_kept_reads_seg3_missing.fq Total extensions: 14481581 Total extensions: 14481581 Total extensions: 14481581 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 11998 bases Map covers 11815 bases in sufficiently long segments Map contains 184 good islands 5818 are left looking bases 4185 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.1329_From_sf_2_2642906_0 Examining donor-acceptor pairings in CUFF.1027_From_kn_0_3558357_0 Examining donor-acceptor pairings in CUFF.1419_From_sf_2_2701328_0 Examining donor-acceptor pairings in CUFF.1253_From_po_0_3387411_0 Examining donor-acceptor pairings in CUFF.1597_From_zu_0_3181459_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.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.1215_From_oy_0_3162092_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.869_From_bur_0_1873494_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.1259_From_po_0_3402348_0 Examining donor-acceptor pairings in CUFF.1017_From_kn_0_3566907_0 Examining donor-acceptor pairings in CUFF.1569_From_zu_0_3035650_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.1515_From_wu_0_2648785_0 Examining donor-acceptor pairings in CUFF.983_From_ct_1_3241157_0 Examining donor-acceptor pairings in CUFF.1093_From_mt_0_4130072_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.1153_From_no_0_2923846_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.1335_From_sf_2_2524453_0 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.1163_From_no_0_2951521_0 Examining donor-acceptor pairings in CUFF.1553_From_wu_0_2806776_0 Examining donor-acceptor pairings in CUFF.1527_From_wu_0_2675967_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.1049_From_ler_0_4002120_0 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.943_From_ct_1_3247037_0 Examining donor-acceptor pairings in CUFF.1121_From_mt_0_4226690_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.1377_From_tsu_0_3215671_0 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.1423_From_wil_2_3072219_0 Examining donor-acceptor pairings in CUFF.1431_From_ws_0_3170660_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.1087_From_ler_0_4211779_0 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 7 potential island-end pairing junctions done Aligning 591 microexon segments in 101 windows window 100 Checked 1182 segments against 101 windows for microexon junctions Found 2 potential microexon junctions -- microexon -- CUFF.1421_From_tsu_0_3215821_0 511 620 - CUFF.1627_From_zu_0_3262887_0 550 639 + -- done -- -- seg -- 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_0 333 389 + CUFF.1543_From_ws_0_3373604_0 337 397 + CUFF.1543_From_ws_0_3373604_0 342 397 + CUFF.1421_From_tsu_0_3215821_0 493 616 + CUFF.1421_From_tsu_0_3215821_0 496 616 - CUFF.1421_From_tsu_0_3215821_0 501 616 + CUFF.1421_From_tsu_0_3215821_0 504 610 + CUFF.1421_From_tsu_0_3215821_0 505 616 - CUFF.1421_From_tsu_0_3215821_0 507 610 + CUFF.1421_From_tsu_0_3215821_0 511 616 - CUFF.1421_From_tsu_0_3215821_0 513 606 - CUFF.1421_From_tsu_0_3215821_0 513 610 + CUFF.1421_From_tsu_0_3215821_0 515 606 - CUFF.1421_From_tsu_0_3215821_0 515 610 + CUFF.1421_From_tsu_0_3215821_0 521 616 - 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_0 333 397 + CUFF.1543_From_ws_0_3373604_0 337 400 + CUFF.1421_From_tsu_0_3215821_0 493 620 + CUFF.1421_From_tsu_0_3215821_0 496 620 - CUFF.1421_From_tsu_0_3215821_0 501 620 + CUFF.1421_From_tsu_0_3215821_0 505 620 - CUFF.1421_From_tsu_0_3215821_0 511 620 - CUFF.1421_From_tsu_0_3215821_0 521 620 - 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 + CUFF.1543_From_ws_0_3373604_0 333 400 + CUFF.1543_From_ws_0_3373604_0 337 407 + CUFF.1543_From_ws_0_3373604_0 313 407 - CUFF.1543_From_ws_0_3373604_0 317 407 + CUFF.1543_From_ws_0_3373604_0 328 407 + CUFF.1543_From_ws_0_3373604_0 330 407 + CUFF.1543_From_ws_0_3373604_0 333 407 + -- done -- -- cov -- CUFF.1163_From_no_0_2951521_0 31 88 + CUFF.1163_From_no_0_2951521_0 31 92 + CUFF.1421_From_tsu_0_3215821_0 511 620 - CUFF.1289_From_po_0_3606391_0 682 1510 + CUFF.1163_From_no_0_2951521_0 31 105 + CUFF.1633_From_zu_0_3280213_0 754 1582 + CUFF.1163_From_no_0_2951521_0 31 109 + -- done -- -- buf -- -- done -- Reporting potential splice junctions...done Reported 52 total possible splices Reporting potential deletions... Reporting potential insertions...