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 378 segments done. Found 13 potential split-segment junctions Found 6 potential small deletions Found 3 potential small insertions Indexing extensions in ./Rsch_4_R2.TOnovel/tmp/left_kept_reads_seg1_missing.fq Indexing extensions in ./Rsch_4_R2.TOnovel/tmp/left_kept_reads_seg2_missing.fq Indexing extensions in ./Rsch_4_R2.TOnovel/tmp/left_kept_reads_seg3_missing.fq Total extensions: 18629086 Total extensions: 18629086 Total extensions: 18629086 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 11554 bases Map covers 11382 bases in sufficiently long segments Map contains 168 good islands 5104 are left looking bases 3875 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.1605_From_zu_0_3257369_0 Examining donor-acceptor pairings in CUFF.1253_From_po_0_3387411_0 Examining donor-acceptor pairings in CUFF.1219_From_po_0_3319326_0 Examining donor-acceptor pairings in CUFF.1629_From_zu_0_3287917_0 Examining donor-acceptor pairings in CUFF.1287_From_rsch_4_4099439_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.975_From_edi_0_2902016_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.1265_From_po_0_3577252_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.1007_From_edi_0_2888586_0 Examining donor-acceptor pairings in CUFF.869_From_bur_0_1873494_0 Examining donor-acceptor pairings in CUFF.921_From_can_0_3233581_0 Examining donor-acceptor pairings in CUFF.1539_From_wu_0_2702886_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.1175_From_hi_0_2953648_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.1361_From_tsu_0_3175121_0 Examining donor-acceptor pairings in CUFF.1167_From_no_0_3096552_0 Examining donor-acceptor pairings in CUFF.1639_From_zu_0_3291057_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.907_From_can_0_3122480_0 Examining donor-acceptor pairings in CUFF.1165_From_no_0_2959683_0 Examining donor-acceptor pairings in CUFF.1559_From_wu_0_2824162_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.1309_From_rsch_4_4307314_0 Examining donor-acceptor pairings in CUFF.941_From_bur_0_2025286_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.1495_From_ws_0_3371988_0 Examining donor-acceptor pairings in CUFF.943_From_ct_1_3247037_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.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.1011_From_edi_0_2918156_0 Examining donor-acceptor pairings in CUFF.1417_From_wil_2_3078633_1 Examining donor-acceptor pairings in CUFF.1333_From_sf_2_2666154_1 Examining donor-acceptor pairings in CUFF.1053_From_kn_0_3819922_1 Examining donor-acceptor pairings in CUFF.1095_From_mt_0_4131964_0 Examining donor-acceptor pairings in CUFF.1401_From_wil_2_3050523_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.1139_From_ler_0_4211779_1 Examining donor-acceptor pairings in CUFF.1087_From_ler_0_4211779_0 Found 0 potential island-end pairing junctions done Aligning 378 microexon segments in 112 windows window 100 Checked 756 segments against 112 windows for microexon junctions Found 0 potential microexon junctions -- microexon -- -- done -- -- seg -- CUFF.1007_From_edi_0_2888586_0 614 867 + CUFF.1007_From_edi_0_2888586_0 614 874 - CUFF.1007_From_edi_0_2888586_0 616 871 - CUFF.1007_From_edi_0_2888586_0 625 867 + CUFF.1007_From_edi_0_2888586_0 631 867 + CUFF.1007_From_edi_0_2888586_0 631 874 - CUFF.1007_From_edi_0_2888586_0 633 871 - CUFF.1007_From_edi_0_2888586_0 635 867 + CUFF.1007_From_edi_0_2888586_0 635 874 - CUFF.1007_From_edi_0_2888586_0 639 871 - CUFF.1007_From_edi_0_2888586_0 614 879 - CUFF.1007_From_edi_0_2888586_0 631 879 - CUFF.1007_From_edi_0_2888586_0 635 879 - -- done -- -- cov -- -- done -- -- buf -- -- done -- Reporting potential splice junctions...done Reported 13 total possible splices Reporting potential deletions... Reporting potential insertions...