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 334 segments done. Found 54 potential split-segment junctions Found 4 potential small deletions Found 6 potential small insertions Indexing extensions in ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg1_missing.fq Indexing extensions in ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg2_missing.fq Indexing extensions in ./Mt_0_R1.TOnovel/tmp/left_kept_reads_seg3_missing.fq Total extensions: 19019213 Total extensions: 19019213 Total extensions: 19019213 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 9683 bases Map covers 9534 bases in sufficiently long segments Map contains 147 good islands 4590 are left looking bases 3251 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.1371_From_tsu_0_3211333_0 Examining donor-acceptor pairings in CUFF.1279_From_po_0_3599571_0 Examining donor-acceptor pairings in CUFF.1133_From_mt_0_4399784_0 Examining donor-acceptor pairings in CUFF.1253_From_po_0_3387411_0 Examining donor-acceptor pairings in CUFF.1035_From_kn_0_3751597_0 Examining donor-acceptor pairings in CUFF.1399_From_wil_2_2978735_0 Examining donor-acceptor pairings in CUFF.1531_From_ws_0_3340488_0 Examining donor-acceptor pairings in CUFF.1577_From_wu_0_2832848_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.1305_From_rsch_4_4263688_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.911_From_can_0_3230893_0 Examining donor-acceptor pairings in CUFF.1177_From_no_0_3116640_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.1101_From_mt_0_4188374_0 Examining donor-acceptor pairings in CUFF.1099_From_mt_0_4177596_0 Examining donor-acceptor pairings in CUFF.1617_From_zu_0_3278243_0 Examining donor-acceptor pairings in CUFF.1573_From_zu_0_3065917_0 Examining donor-acceptor pairings in CUFF.1197_From_oy_0_3103794_0 Examining donor-acceptor pairings in CUFF.1008_From_kn_0_3525938_0 Examining donor-acceptor pairings in CUFF.1277_From_po_0_3599571_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.1639_From_zu_0_3291057_0 Examining donor-acceptor pairings in CUFF.919_From_can_0_3258779_0 Examining donor-acceptor pairings in CUFF.1641_From_zu_0_3291057_0 Examining donor-acceptor pairings in CUFF.1169_From_no_0_3101262_0 Examining donor-acceptor pairings in CUFF.1579_From_wu_0_2802868_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.997_From_edi_0_2934714_0 Examining donor-acceptor pairings in CUFF.871_From_bur_0_2012810_0 Examining donor-acceptor pairings in CUFF.935_From_bur_0_2020452_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.1635_From_zu_0_3263539_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.1491_From_ws_0_3373966_0 Examining donor-acceptor pairings in CUFF.969_From_edi_0_2888616_0 Examining donor-acceptor pairings in CUFF.1377_From_tsu_0_3215671_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.1423_From_wil_2_3072219_0 Examining donor-acceptor pairings in CUFF.1481_From_ws_0_3349444_1 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.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 Found 1 potential island-end pairing junctions done Aligning 334 microexon segments in 92 windows Checked 668 segments against 92 windows for microexon junctions Found 0 potential microexon junctions -- microexon -- -- done -- -- seg -- CUFF.1277_From_po_0_3599571_0 183 308 - CUFF.1277_From_po_0_3599571_0 183 316 - CUFF.1277_From_po_0_3599571_0 188 301 + CUFF.1277_From_po_0_3599571_0 193 308 - CUFF.1277_From_po_0_3599571_0 193 316 - CUFF.1277_From_po_0_3599571_0 195 308 - CUFF.1277_From_po_0_3599571_0 195 316 - CUFF.1277_From_po_0_3599571_0 201 308 - CUFF.1277_From_po_0_3599571_0 201 316 - CUFF.1277_From_po_0_3599571_0 203 301 + CUFF.1277_From_po_0_3599571_0 204 308 - CUFF.1277_From_po_0_3599571_0 204 316 - CUFF.1579_From_wu_0_2802868_0 190 572 - CUFF.1579_From_wu_0_2802868_0 190 593 + CUFF.1579_From_wu_0_2802868_0 197 602 - CUFF.1579_From_wu_0_2802868_0 204 572 - CUFF.1579_From_wu_0_2802868_0 204 593 + CUFF.1579_From_wu_0_2802868_0 206 602 + CUFF.1579_From_wu_0_2802868_0 213 572 - CUFF.1579_From_wu_0_2802868_0 213 593 + CUFF.935_From_bur_0_2020452_0 321 433 + CUFF.935_From_bur_0_2020452_0 321 457 - CUFF.935_From_bur_0_2020452_0 323 437 + CUFF.935_From_bur_0_2020452_0 326 437 + CUFF.935_From_bur_0_2020452_0 330 433 + CUFF.935_From_bur_0_2020452_0 331 437 - CUFF.935_From_bur_0_2020452_0 331 447 - CUFF.935_From_bur_0_2020452_0 340 437 + CUFF.935_From_bur_0_2020452_0 343 437 + CUFF.935_From_bur_0_2020452_0 346 433 + CUFF.935_From_bur_0_2020452_0 346 457 - CUFF.1277_From_po_0_3599571_0 188 310 + CUFF.1277_From_po_0_3599571_0 203 310 + CUFF.1579_From_wu_0_2802868_0 190 578 - CUFF.1579_From_wu_0_2802868_0 190 596 + CUFF.1579_From_wu_0_2802868_0 204 578 - CUFF.1579_From_wu_0_2802868_0 204 596 + CUFF.1579_From_wu_0_2802868_0 213 578 - CUFF.1579_From_wu_0_2802868_0 213 596 + CUFF.935_From_bur_0_2020452_0 321 454 + CUFF.935_From_bur_0_2020452_0 321 460 - CUFF.935_From_bur_0_2020452_0 323 441 + CUFF.935_From_bur_0_2020452_0 326 441 + CUFF.935_From_bur_0_2020452_0 330 454 + CUFF.935_From_bur_0_2020452_0 331 441 - CUFF.935_From_bur_0_2020452_0 340 441 + CUFF.935_From_bur_0_2020452_0 343 441 + CUFF.935_From_bur_0_2020452_0 346 454 + CUFF.935_From_bur_0_2020452_0 346 460 - CUFF.1277_From_po_0_3599571_0 188 327 + CUFF.1277_From_po_0_3599571_0 203 327 + CUFF.1579_From_wu_0_2802868_0 190 581 - CUFF.1579_From_wu_0_2802868_0 204 581 - CUFF.1579_From_wu_0_2802868_0 213 581 - -- done -- -- cov -- CUFF.1197_From_oy_0_3103794_0 73 289 + -- done -- -- buf -- -- done -- Reporting potential splice junctions...done Reported 55 total possible splices Reporting potential deletions... Reporting potential insertions...