-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_14553702-14857441 -reading genomic sequence. ** Processing features (+) -finding all potential splice sites, looking for GT/GC donors and AG acceptors. -finding all potential starts and stops. (strand: +) -loading gene prediction evidence. (strand: +)Valid prediction for snap_scaffold_3-snap.2789-T1 Valid prediction for snap_scaffold_3-snap.2817-T1 Valid prediction for snap_scaffold_3-snap.2809-T1 Valid prediction for snap_scaffold_3-snap.2782-T1 Valid prediction for snap_scaffold_3-snap.2795-T1 Valid prediction for Augustus_model.g5139.t1 Couldn't classify 267621, 267705 Sorry, prediction pasa_asmbl_40551.p1 fails validation. (GAT) GA 267621-267705 GT TGG (GTG) AG 267957-268015 GT CAG (TGT) AG 268370-268435 GT ACG (AGG) AG 268543-268619 GT AGG (GTC) AG 268973-269141 GT AGG (CTT) AG 269371-269523 GT AGG (AAC) AG 269813-269863 CA GAC -recovered pasa_asmbl_40551.p1, terminal, 269813, 269863 -recovered pasa_asmbl_40551.p1, internal, 267957, 268015 -recovered pasa_asmbl_40551.p1, internal, 268370, 268435 -recovered pasa_asmbl_40551.p1, internal, 268543, 268619 -recovered pasa_asmbl_40551.p1, internal, 268973, 269141 -recovered pasa_asmbl_40551.p1, internal, 269371, 269523 Valid prediction for snap_scaffold_3-snap.2790-T1 Valid prediction for GlimmerHMM_glimmerT_7768-T1 Valid prediction for GlimmerHMM_glimmerT_7773-T1 Valid prediction for GlimmerHMM_glimmerT_7778-T1 Couldn't classify 121141, 121159 Couldn't classify 122939, 123786 Sorry, prediction pasa_asmbl_40544.p1 fails validation. (CCG) AA 121141-121159 GT GAG (GCG) AG 122939-123786 AG CTA Valid prediction for Augustus_model.g5146.t1 Valid prediction for Augustus_model.g5147.t1 Couldn't classify 90166, 90319 Couldn't classify 91386, 91477 Sorry, prediction pasa_asmbl_40536.p1 fails validation. (AGA) GC 90166-90319 GT TTG (GTC) AG 91040-91198 GT AGG (CGT) AG 91386-91477 GG CCG -recovered pasa_asmbl_40536.p1, internal, 91040, 91198 Valid prediction for snap_scaffold_3-snap.2799-T1 Valid prediction for snap_scaffold_3-snap.2802-T1 Couldn't classify 98416, 98560 Couldn't classify 100799, 100835 Sorry, prediction pasa_asmbl_40537.p1 fails validation. (TGC) GG 98416-98560 GT AGG (GTT) AG 99076-99201 GT GAG (GTC) AG 99696-99823 GT AGG (CTG) AG 99951-100042 GT AGG (GGA) AG 100314-100448 GT AGG (TGT) AG 100799-100835 AA ACA -recovered pasa_asmbl_40537.p1, internal, 99076, 99201 -recovered pasa_asmbl_40537.p1, internal, 99696, 99823 -recovered pasa_asmbl_40537.p1, internal, 99951, 100042 -recovered pasa_asmbl_40537.p1, internal, 100314, 100448 Valid prediction for snap_scaffold_3-snap.2771-T1 Valid prediction for GlimmerHMM_glimmerT_7776-T1 Valid prediction for pasa_asmbl_40545.p1 Valid prediction for snap_scaffold_3-snap.2787-T1 Valid prediction for CodingQuarry_transcript_46374-T1 Valid prediction for snap_scaffold_3-snap.2814-T1 Valid prediction for pasa_asmbl_40546.p1 Valid prediction for CodingQuarry_transcript_46368-T1 Valid prediction for snap_scaffold_3-snap.2800-T1 Valid prediction for GlimmerHMM_glimmerT_7787-T1 Valid prediction for pasa_asmbl_40552.p1 Valid prediction for snap_scaffold_3-snap.2810-T1 Valid prediction for snap_scaffold_3-snap.2808-T1 Couldn't classify 106744, 106950 Couldn't classify 107656, 107863 Sorry, prediction pasa_asmbl_40540.p1 fails validation. (GTG) AG 106744-106950 GT ACG (GCA) AG 107098-107235 GT AGG (GAG) AG 107339-107517 GT AGG (GAG) AG 107656-107863 GA GGG add_exon() Sorry, pasa_asmbl_40540.p1 107339-107517-terminal-2 is invalid. -recovered pasa_asmbl_40540.p1, terminal, 107339, 107517 -recovered pasa_asmbl_40540.p1, internal, 106744, 106950 -recovered pasa_asmbl_40540.p1, internal, 107098, 107235 -recovered pasa_asmbl_40540.p1, internal, 107339, 107517 Couldn't classify 76694, 76903 Sorry, prediction pasa_asmbl_40535.p1 fails validation. (ATG) CG 70855-71117 GT AGG (GGG) AG 73704-73779 GT AGG (ACT) AG 76694-76903 CC TGC -recovered pasa_asmbl_40535.p1, initial, 70855, 71117 -recovered pasa_asmbl_40535.p1, internal, 73704, 73779 Valid prediction for GlimmerHMM_glimmerT_7788-T1 Valid prediction for snap_scaffold_3-snap.2784-T1 Valid prediction for pasa_asmbl_40548.p1 Valid prediction for HiQ_model.g5145.t1 Valid prediction for snap_scaffold_3-snap.2770-T1 Valid prediction for GlimmerHMM_glimmerT_7772-T1 Valid prediction for GlimmerHMM_glimmerT_7782-T1 Valid prediction for snap_scaffold_3-snap.2797-T1 Valid prediction for GlimmerHMM_glimmerT_7774-T1 Valid prediction for snap_scaffold_3-snap.2781-T1 Valid prediction for snap_scaffold_3-snap.2786-T1 Couldn't classify 170106, 170894 Sorry, prediction pasa_asmbl_40550.p1 fails validation. (CAG) GA 170106-170894 CT GAC Valid prediction for HiQ_model.g5132.t1 Valid prediction for snap_scaffold_3-snap.2779-T1 Valid prediction for snap_scaffold_3-snap.2769-T1 Valid prediction for CodingQuarry_transcript_46366-T1 Valid prediction for snap_scaffold_3-snap.2788-T1 Couldn't classify 81859, 82055 Sorry, prediction Augustus_model.g5131.t1 fails validation. (AGT) AG 81859-82055 GT AGG (GTG) AG 84143-84385 GT GGG (GGC) AG 84636-84707 GT AGG (GGC) AG 85052-85148 GT AGG (GTC) AG 85410-85483 GT ATG (GAT) AG 87560-87698 GT CAG (GCA) AG 87828-87904 GT AGG (ATC) AG 89533-89737 GT CAG (CCA) AG 90155-90319 GT TTG (GTC) AG 91040-91198 GT AGG (CGT) AG 91386-91590 GT GGG (GAT) AG 92333-92478 GT AGG (GAG) AG 93009-93095 GT AGG (ACG) AG 96422-96541 GT CGG (TGG) AG 96979-97060 GT AGG (GGG) AG 97151-97268 GT CGG (AAA) AG 97504-97708 GT CGG (GCC) AG 97930-98083 GT AGG (GTT) AG 98388-98560 GT AGG (GTT) AG 99076-99201 GT GAG (GTC) AG 99696-99823 GT AGG (CTG) AG 99951-100042 GT AGG (GGA) AG 100314-100448 GT AGG (TGT) AG 100799-100888 GT GTG (GCT) AG 101011-101107 GT TGG (GAG) AG 101343-101535 GT TGG (CCA) AG 101756-102030 GT AGG (GAC) AG 102403-102624 GT ATG (ACT) AG 102979-103170 GT AGG (GTG) AG 103458-103491 GT ACG (ATC) AG 105515-105675 GT GAG (GTG) AG 106744-106950 GT ACG (GCA) AG 107098-107235 GT AGG (GAG) AG 107339-107517 GT AGG (GAG) AG 107656-107798 GT CGG (CTG) AG 108380-108480 GT AGG (GCT) AG 108595-108813 GT GGG (GTG) AG 108942-109164 GT TGG (GCA) AG 110102-110220 GT AGG (GGT) AG 110314-110401 GT AGG (GCA) AG 110491-110713 GT AGG (GTG) AG 110863-111007 GT AGG (GTG) AG 111423-111632 GT AGG (GCC) AG 112398-112453 GT AGG (GCC) AG 112568-112683 GT AGG (ATG) AG 112890-112987 GT AGG (GTC) AG 114053-114169 GT AGG (ATC) AG 114913-115053 GT ACG (AGT) AG 116472-116549 GT AGG (GAG) AG 117574-117798 GT AGG (GTG) AG 118664-118796 GT GGG (AGC) AG 119023-119148 GT AGG (GTG) AG 120941-121159 GT GAG (GCG) AG 122939-124594 GT AGG (GAT) AG 124705-124874 GT AGG (GTG) AG 125052-125296 GT AGG (GCA) AG 125525-125692 GT AGG (TCT) AG 125926-126083 GT AGG (AAG) AG 126478-126677 GT AGG (GCG) AG 126865-127014 GT AGG (GAG) AG 127202-127362 GT AGG (GTG) AG 127975-128131 GT AGG (GAG) AG 128380-128604 GT GGG (AAC) AG 128745-128810 GT AGG (GTG) AG 129350-129589 GT AGG (GTG) AG 129885-129974 GT AGG (GCT) AG 130148-130228 GT AGG (GTG) AG 130717-130983 GT AGG (GTG) AG 131148-131431 GT AGG (CTA) AG 132548-132644 GT CTG (GGC) AG 132739-132858 GT GGG (TTG) AG 133021-133122 GT TGG (CCC) AG 133243-133371 GT AGG (GTC) AG 133447-133579 GT TGG (GTA) AG 134255-134358 GT AGG (GAG) AG 134559-134747 GT AGG (CTG) AG 134997-135104 GT AGG (AAC) AG 135476-135685 GT AGG (GCT) AG 135800-135907 GT AGG (ATG) AG 136213-136378 GT AGG (GTC) AG 136860-136975 AC AAA add_exon() Sorry, Augustus_model.g5131.t1 112890-112987-initial-1 is invalid. -recovered Augustus_model.g5131.t1, initial, 112890, 112987 -recovered Augustus_model.g5131.t1, initial, 136213, 136378 add_exon() Sorry, Augustus_model.g5131.t1 92333-92478-terminal-2 is invalid. -recovered Augustus_model.g5131.t1, terminal, 92333, 92478 add_exon() Sorry, Augustus_model.g5131.t1 98388-98560-terminal-2 is invalid. -recovered Augustus_model.g5131.t1, terminal, 98388, 98560 add_exon() Sorry, Augustus_model.g5131.t1 107339-107517-terminal-2 is invalid. -recovered Augustus_model.g5131.t1, terminal, 107339, 107517 add_exon() Sorry, Augustus_model.g5131.t1 110314-110401-terminal-3 is invalid. -recovered Augustus_model.g5131.t1, terminal, 110314, 110401 add_exon() Sorry, Augustus_model.g5131.t1 112568-112683-terminal-2 is invalid. -recovered Augustus_model.g5131.t1, terminal, 112568, 112683 -recovered Augustus_model.g5131.t1, terminal, 136860, 136975 -recovered Augustus_model.g5131.t1, internal, 81859, 82055 -recovered Augustus_model.g5131.t1, internal, 84143, 84385 -recovered Augustus_model.g5131.t1, internal, 84636, 84707 -recovered Augustus_model.g5131.t1, internal, 85052, 85148 -recovered Augustus_model.g5131.t1, internal, 85410, 85483 -recovered Augustus_model.g5131.t1, internal, 87560, 87698 -recovered Augustus_model.g5131.t1, internal, 87828, 87904 -recovered Augustus_model.g5131.t1, internal, 89533, 89737 -recovered Augustus_model.g5131.t1, internal, 90155, 90319 -recovered Augustus_model.g5131.t1, internal, 91040, 91198 -recovered Augustus_model.g5131.t1, internal, 91386, 91590 -recovered Augustus_model.g5131.t1, internal, 92333, 92478 -recovered Augustus_model.g5131.t1, internal, 93009, 93095 -recovered Augustus_model.g5131.t1, internal, 96422, 96541 -recovered Augustus_model.g5131.t1, internal, 96979, 97060 -recovered Augustus_model.g5131.t1, internal, 97151, 97268 -recovered Augustus_model.g5131.t1, internal, 97504, 97708 -recovered Augustus_model.g5131.t1, internal, 97930, 98083 -recovered Augustus_model.g5131.t1, internal, 98388, 98560 -recovered Augustus_model.g5131.t1, internal, 99076, 99201 -recovered Augustus_model.g5131.t1, internal, 99696, 99823 -recovered Augustus_model.g5131.t1, internal, 99951, 100042 -recovered Augustus_model.g5131.t1, internal, 100314, 100448 -recovered Augustus_model.g5131.t1, internal, 100799, 100888 -recovered Augustus_model.g5131.t1, internal, 101011, 101107 -recovered Augustus_model.g5131.t1, internal, 101343, 101535 -recovered Augustus_model.g5131.t1, internal, 101756, 102030 -recovered Augustus_model.g5131.t1, internal, 102403, 102624 -recovered Augustus_model.g5131.t1, internal, 102979, 103170 -recovered Augustus_model.g5131.t1, internal, 103458, 103491 -recovered Augustus_model.g5131.t1, internal, 105515, 105675 -recovered Augustus_model.g5131.t1, internal, 106744, 106950 -recovered Augustus_model.g5131.t1, internal, 107098, 107235 -recovered Augustus_model.g5131.t1, internal, 107339, 107517 -recovered Augustus_model.g5131.t1, internal, 107656, 107798 -recovered Augustus_model.g5131.t1, internal, 108380, 108480 -recovered Augustus_model.g5131.t1, internal, 108595, 108813 -recovered Augustus_model.g5131.t1, internal, 108942, 109164 -recovered Augustus_model.g5131.t1, internal, 110102, 110220 -recovered Augustus_model.g5131.t1, internal, 110314, 110401 -recovered Augustus_model.g5131.t1, internal, 110491, 110713 -recovered Augustus_model.g5131.t1, internal, 110863, 111007 -recovered Augustus_model.g5131.t1, internal, 111423, 111632 -recovered Augustus_model.g5131.t1, internal, 112398, 112453 -recovered Augustus_model.g5131.t1, internal, 112568, 112683 -recovered Augustus_model.g5131.t1, internal, 112890, 112987 -recovered Augustus_model.g5131.t1, internal, 114053, 114169 -recovered Augustus_model.g5131.t1, internal, 114913, 115053 -recovered Augustus_model.g5131.t1, internal, 116472, 116549 -recovered Augustus_model.g5131.t1, internal, 117574, 117798 -recovered Augustus_model.g5131.t1, internal, 118664, 118796 -recovered Augustus_model.g5131.t1, internal, 119023, 119148 -recovered Augustus_model.g5131.t1, internal, 120941, 121159 -recovered Augustus_model.g5131.t1, internal, 122939, 124594 -recovered Augustus_model.g5131.t1, internal, 124705, 124874 -recovered Augustus_model.g5131.t1, internal, 125052, 125296 -recovered Augustus_model.g5131.t1, internal, 125525, 125692 -recovered Augustus_model.g5131.t1, internal, 125926, 126083 -recovered Augustus_model.g5131.t1, internal, 126478, 126677 -recovered Augustus_model.g5131.t1, internal, 126865, 127014 -recovered Augustus_model.g5131.t1, internal, 127202, 127362 -recovered Augustus_model.g5131.t1, internal, 127975, 128131 -recovered Augustus_model.g5131.t1, internal, 128380, 128604 -recovered Augustus_model.g5131.t1, internal, 128745, 128810 -recovered Augustus_model.g5131.t1, internal, 129350, 129589 -recovered Augustus_model.g5131.t1, internal, 129885, 129974 -recovered Augustus_model.g5131.t1, internal, 130148, 130228 -recovered Augustus_model.g5131.t1, internal, 130717, 130983 -recovered Augustus_model.g5131.t1, internal, 131148, 131431 -recovered Augustus_model.g5131.t1, internal, 132548, 132644 -recovered Augustus_model.g5131.t1, internal, 132739, 132858 -recovered Augustus_model.g5131.t1, internal, 133021, 133122 -recovered Augustus_model.g5131.t1, internal, 133243, 133371 -recovered Augustus_model.g5131.t1, internal, 133447, 133579 -recovered Augustus_model.g5131.t1, internal, 134255, 134358 -recovered Augustus_model.g5131.t1, internal, 134559, 134747 -recovered Augustus_model.g5131.t1, internal, 134997, 135104 -recovered Augustus_model.g5131.t1, internal, 135476, 135685 -recovered Augustus_model.g5131.t1, internal, 135800, 135907 -recovered Augustus_model.g5131.t1, internal, 136213, 136378 Valid prediction for snap_scaffold_3-snap.2785-T1 Valid prediction for HiQ_model.g5136.t1 Valid prediction for GlimmerHMM_glimmerT_7781-T1 Couldn't classify 278122, 278196 Sorry, prediction pasa_asmbl_40555.p1 fails validation. (AAG) CC 278122-278196 GT AGG (GTG) AG 278579-278831 GT AGG (CTA) AG 279015-279262 GT AGG (GTG) AG 280179-280268 GT AGG (GGG) AG 280592-280696 GT TGG (GTG) AG 280868-281000 GT AGG (GCC) AG 281514-281605 GT AGG (AAG) AG 281732-281842 GT AGG (AGC) AG 282590-282709 GT GAG (GGT) AG 282990-283040 GT GAG (CAG) AG 284721-284944 GT AGG (CCC) AG 285485-285637 GT AGG (TAA) AG 288060-288217 GT AGG (ACC) AG 289083-289262 GT GGG (CGA) AG 290516-290677 GT AGG (GTA) AG 290869-291025 GT GGG (GCC) AG 291457-291556 GG GAG -recovered pasa_asmbl_40555.p1, terminal, 291457, 291556 -recovered pasa_asmbl_40555.p1, internal, 278579, 278831 -recovered pasa_asmbl_40555.p1, internal, 279015, 279262 -recovered pasa_asmbl_40555.p1, internal, 280179, 280268 -recovered pasa_asmbl_40555.p1, internal, 280592, 280696 -recovered pasa_asmbl_40555.p1, internal, 280868, 281000 -recovered pasa_asmbl_40555.p1, internal, 281514, 281605 -recovered pasa_asmbl_40555.p1, internal, 281732, 281842 -recovered pasa_asmbl_40555.p1, internal, 282590, 282709 -recovered pasa_asmbl_40555.p1, internal, 282990, 283040 -recovered pasa_asmbl_40555.p1, internal, 284721, 284944 -recovered pasa_asmbl_40555.p1, internal, 285485, 285637 -recovered pasa_asmbl_40555.p1, internal, 288060, 288217 -recovered pasa_asmbl_40555.p1, internal, 289083, 289262 -recovered pasa_asmbl_40555.p1, internal, 290516, 290677 -recovered pasa_asmbl_40555.p1, internal, 290869, 291025 Couldn't classify 101911, 102030 Couldn't classify 102979, 103224 Sorry, prediction pasa_asmbl_40538.p1 fails validation. (CTG) CC 101911-102030 GT AGG (GAC) AG 102403-102624 GT ATG (ACT) AG 102979-103224 CC TCC -recovered pasa_asmbl_40538.p1, internal, 102403, 102624 Valid prediction for snap_scaffold_3-snap.2793-T1 Sorry, intron length (7) is less than minimum required (10) Valid prediction for snap_scaffold_3-snap.2813-T1 Couldn't classify 110568, 110713 Couldn't classify 120941, 121050 Sorry, prediction pasa_asmbl_40542.p1 fails validation. (GGG) TT 110568-110713 GT AGG (GTG) AG 110863-111007 GT AGG (GTG) AG 111423-111632 GT AGG (GCC) AG 112398-112453 GT AGG (GCC) AG 112568-112683 GT AGG (ATG) AG 112890-112987 GT AGG (GTC) AG 114053-114169 GT AGG (ATC) AG 114913-115053 GT ACG (GAG) AG 117574-117798 GT AGG (GTG) AG 118664-118796 GT GGG (AGC) AG 119023-119148 GT AGG (GTG) AG 120941-121050 GC TCG add_exon() Sorry, pasa_asmbl_40542.p1 112890-112987-initial-1 is invalid. -recovered pasa_asmbl_40542.p1, initial, 112890, 112987 add_exon() Sorry, pasa_asmbl_40542.p1 112568-112683-terminal-2 is invalid. -recovered pasa_asmbl_40542.p1, terminal, 112568, 112683 -recovered pasa_asmbl_40542.p1, internal, 110863, 111007 -recovered pasa_asmbl_40542.p1, internal, 111423, 111632 -recovered pasa_asmbl_40542.p1, internal, 112398, 112453 -recovered pasa_asmbl_40542.p1, internal, 112568, 112683 -recovered pasa_asmbl_40542.p1, internal, 112890, 112987 -recovered pasa_asmbl_40542.p1, internal, 114053, 114169 -recovered pasa_asmbl_40542.p1, internal, 114913, 115053 -recovered pasa_asmbl_40542.p1, internal, 117574, 117798 -recovered pasa_asmbl_40542.p1, internal, 118664, 118796 -recovered pasa_asmbl_40542.p1, internal, 119023, 119148 -recovered pasa_asmbl_40542.p1, internal, 120941, 121050 Valid prediction for GlimmerHMM_glimmerT_7789-T1 -loading the search evidence (protein and EST search results, strand: +) -scoring exons (strand: +) ** Processing features (-) -finding all potential splice sites, looking for GT/GC donors and AG acceptors. -finding all potential starts and stops. (strand: -) -loading gene prediction evidence. (strand: -)Couldn't classify 76923, 76952 Sorry, prediction pasa_asmbl_39423.p1 fails validation. (CGT) GA 76923-76952 GT ATG (GTG) AG 77486-77599 GT AGG (GCA) AG 78732-78945 GT GGG (GTT) AG 79901-80150 GT AGG (TGA) AG 80694-81029 GT AGG (CAG) AG 81521-81835 GT AGG (CAC) AG 82366-82509 GT AGG (TCC) AG 82970-83765 AA AGA -recovered pasa_asmbl_39423.p1, terminal, 82970, 83765 -recovered pasa_asmbl_39423.p1, internal, 77486, 77599 -recovered pasa_asmbl_39423.p1, internal, 78732, 78945 -recovered pasa_asmbl_39423.p1, internal, 79901, 80150 -recovered pasa_asmbl_39423.p1, internal, 80694, 81029 -recovered pasa_asmbl_39423.p1, internal, 81521, 81835 -recovered pasa_asmbl_39423.p1, internal, 82366, 82509 Valid prediction for Augustus_model.g5128.t1 Valid prediction for CodingQuarry_transcript_46365-T1 Valid prediction for snap_scaffold_3-snap.2791-T1 Valid prediction for Augustus_model.g5126.t1 Valid prediction for Augustus_model.g5133.t1 Valid prediction for Augustus_model.g5129.t1 Valid prediction for HiQ_model.g5134.t1 Valid prediction for snap_scaffold_3-snap.2804-T1 Valid prediction for pasa_asmbl_39413.p1 Valid prediction for snap_scaffold_3-snap.2792-T1 Valid prediction for snap_scaffold_3-snap.2815-T1 Valid prediction for HiQ_model.g5127.t1 Valid prediction for pasa_asmbl_39416.p1 Valid prediction for GlimmerHMM_glimmerT_7769-T1 Valid prediction for snap_scaffold_3-snap.2783-T1 Valid prediction for snap_scaffold_3-snap.2798-T1 Valid prediction for snap_scaffold_3-snap.2775-T1 Valid prediction for GlimmerHMM_glimmerT_7790-T1 Valid prediction for GlimmerHMM_glimmerT_7783-T1 Valid prediction for snap_scaffold_3-snap.2780-T1 Valid prediction for Augustus_model.g5138.t1 Couldn't classify 292215, 292298 Sorry, prediction pasa_asmbl_39398.p1 fails validation. (ATG) AA 278893-278973 GT GTG (GTG) AG 281225-281277 GT TGG (CTT) AG 281372-281426 GT AGG (AAA) AG 282290-282346 GT TGG (AGC) AG 282446-282506 GT TGG (ACT) AG 283757-283844 GT ATG (ACT) AG 286314-286403 GT TGG (CTG) AG 286744-286782 GT ATG (ATG) AG 288127-288205 GT GGG (ATG) AG 289661-289708 GT AGG (GTG) AG 292215-292298 TA GGT -recovered pasa_asmbl_39398.p1, initial, 278893, 278973 add_exon() Sorry, pasa_asmbl_39398.p1 288127-288205-initial-1 is invalid. -recovered pasa_asmbl_39398.p1, initial, 288127, 288205 -recovered pasa_asmbl_39398.p1, initial, 289661, 289708 -recovered pasa_asmbl_39398.p1, internal, 281225, 281277 -recovered pasa_asmbl_39398.p1, internal, 281372, 281426 -recovered pasa_asmbl_39398.p1, internal, 282290, 282346 -recovered pasa_asmbl_39398.p1, internal, 282446, 282506 -recovered pasa_asmbl_39398.p1, internal, 283757, 283844 -recovered pasa_asmbl_39398.p1, internal, 286314, 286403 -recovered pasa_asmbl_39398.p1, internal, 286744, 286782 -recovered pasa_asmbl_39398.p1, internal, 288127, 288205 -recovered pasa_asmbl_39398.p1, internal, 289661, 289708 Valid prediction for pasa_asmbl_39408.p1 Couldn't classify 86648, 86740 Sorry, prediction pasa_asmbl_39418.p1 fails validation. (GCA) TA 86648-86740 GT ATG (GAC) AG 87609-87751 GT AGG (AGA) AG 88521-89145 GT CCG (ATG) AG 89903-90229 GT AGG (GAG) AG 90714-90828 GT AGG (GAA) AG 91343-91504 GT CCG (ACT) AG 92817-92998 GT TTG (GAT) AG 93165-93228 GT AGG (AGT) AG 93555-93611 GT AGG (GAG) AG 94856-94881 GT ATG (CTG) AG 95309-95416 GT AGG (GAG) AG 95924-96016 GT AGG (GCA) AG 96678-97051 GT AGG (GGT) AG 97712-97767 GT AGG (TGA) AG 98578-98776 GT AGG (AGG) AG 100158-100481 GT AGG (GTC) AG 100847-100955 GT AGG (TGT) AG 101582-101684 GT AAG (CTG) AG 101793-101815 TC GAT -recovered pasa_asmbl_39418.p1, initial, 89903, 90229 -recovered pasa_asmbl_39418.p1, terminal, 101793, 101815 -recovered pasa_asmbl_39418.p1, internal, 87609, 87751 -recovered pasa_asmbl_39418.p1, internal, 88521, 89145 -recovered pasa_asmbl_39418.p1, internal, 89903, 90229 -recovered pasa_asmbl_39418.p1, internal, 90714, 90828 -recovered pasa_asmbl_39418.p1, internal, 91343, 91504 -recovered pasa_asmbl_39418.p1, internal, 92817, 92998 -recovered pasa_asmbl_39418.p1, internal, 93165, 93228 -recovered pasa_asmbl_39418.p1, internal, 93555, 93611 -recovered pasa_asmbl_39418.p1, internal, 94856, 94881 -recovered pasa_asmbl_39418.p1, internal, 95309, 95416 -recovered pasa_asmbl_39418.p1, internal, 95924, 96016 -recovered pasa_asmbl_39418.p1, internal, 96678, 97051 -recovered pasa_asmbl_39418.p1, internal, 97712, 97767 -recovered pasa_asmbl_39418.p1, internal, 98578, 98776 -recovered pasa_asmbl_39418.p1, internal, 100158, 100481 -recovered pasa_asmbl_39418.p1, internal, 100847, 100955 -recovered pasa_asmbl_39418.p1, internal, 101582, 101684 Valid prediction for snap_scaffold_3-snap.2776-T1 Valid prediction for HiQ_model.g5125.t1 Valid prediction for GlimmerHMM_glimmerT_7770-T1 Valid prediction for GlimmerHMM_glimmerT_7771-T1 Valid prediction for snap_scaffold_3-snap.2768-T1 Valid prediction for snap_scaffold_3-snap.2806-T1 Valid prediction for CodingQuarry_transcript_46367-T1 Valid prediction for snap_scaffold_3-snap.2773-T1 Valid prediction for snap_scaffold_3-snap.2772-T1 Valid prediction for CodingQuarry_transcript_46373-T1 Valid prediction for pasa_asmbl_39430.p1 Valid prediction for GlimmerHMM_glimmerT_7780-T1 Valid prediction for GlimmerHMM_glimmerT_7785-T1 Valid prediction for Augustus_model.g5140.t1 Valid prediction for pasa_asmbl_39403.p1 Valid prediction for snap_scaffold_3-snap.2807-T1 Valid prediction for GlimmerHMM_glimmerT_7777-T1 Valid prediction for HiQ_model.g5143.t1 Valid prediction for snap_scaffold_3-snap.2805-T1 Valid prediction for Augustus_model.g5137.t1 Valid prediction for CodingQuarry_transcript_46363-T1 Valid prediction for Augustus_model.g5141.t1 Valid prediction for snap_scaffold_3-snap.2777-T1 Valid prediction for snap_scaffold_3-snap.2774-T1 Valid prediction for snap_scaffold_3-snap.2816-T1 Valid prediction for CodingQuarry_transcript_46364-T1 Valid prediction for CodingQuarry_transcript_46370-T1 Valid prediction for Augustus_model.g5144.t1 Valid prediction for GlimmerHMM_glimmerT_7786-T1 Valid prediction for GlimmerHMM_glimmerT_7775-T1 Valid prediction for pasa_asmbl_39411.p1 Valid prediction for GlimmerHMM_glimmerT_7779-T1 Valid prediction for GlimmerHMM_glimmerT_7784-T1 Valid prediction for snap_scaffold_3-snap.2794-T1 Valid prediction for snap_scaffold_3-snap.2796-T1 Valid prediction for snap_scaffold_3-snap.2801-T1 Valid prediction for snap_scaffold_3-snap.2778-T1 Valid prediction for Augustus_model.g5142.t1 Valid prediction for snap_scaffold_3-snap.2803-T1 Couldn't classify 241628, 241677 Sorry, prediction pasa_asmbl_39409.p1 fails validation. (ACC) CC 241628-241677 GT GGG (TGT) AG 241762-241815 GT AGG (CTA) AG 241956-242030 GT AGG (TTC) AG 242488-242625 GT AGG (GAC) AG 243035-243143 GT AGG (TGT) AG 243268-243370 GT AGG (AGA) AG 243484-243500 TC GAT -recovered pasa_asmbl_39409.p1, terminal, 243484, 243500 -recovered pasa_asmbl_39409.p1, internal, 241762, 241815 -recovered pasa_asmbl_39409.p1, internal, 241956, 242030 -recovered pasa_asmbl_39409.p1, internal, 242488, 242625 -recovered pasa_asmbl_39409.p1, internal, 243035, 243143 -recovered pasa_asmbl_39409.p1, internal, 243268, 243370 Valid prediction for Augustus_model.g5130.t1 Valid prediction for snap_scaffold_3-snap.2812-T1 Valid prediction for snap_scaffold_3-snap.2811-T1 Valid prediction for HiQ_model.g5135.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22609, rend_intergenic: 3532 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 55895, rend_intergenic: 53528 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 94023, rend_intergenic: 85860 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 218864, rend_intergenic: 206239 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 235970, rend_intergenic: 234136 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 286046, rend_intergenic: 276613 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 296962, rend_intergenic: 291830 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 301174, rend_intergenic: 298596 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 303740 -exon list size: 574 building trellis 0.2 0.3 0.5 0.7 0.9 1.0 1.2 1.4 1.6 1.7 1.9 2.1 2.3 2.4 2.6 2.8 3.0 3.1 3.3 3.5 3.6 3.8 4.0 4.2 4.3 4.5 4.7 4.9 5.0 5.2 5.4 5.6 5.7 5.9 6.1 6.2 6.4 6.6 6.8 6.9 7.1 7.3 7.5 7.6 7.8 8.0 8.2 8.3 8.5 8.7 8.9 9.0 9.2 9.4 9.5 9.7 9.9 10.1 10.2 10.4 10.6 10.8 10.9 11.1 11.3 11.5 11.6 11.8 12.0 12.2 12.3 12.5 12.7 12.8 13.0 13.2 13.4 13.5 13.7 13.9 14.1 14.2 14.4 14.6 14.8 14.9 15.1 15.3 15.5 15.6 15.8 16.0 16.1 16.3 16.5 16.7 16.8 17.0 17.2 17.4 17.5 17.7 17.9 18.1 18.2 18.4 18.6 18.8 18.9 19.1 19.3 19.4 19.6 19.8 20.0 20.1 20.3 20.5 20.7 20.8 21.0 21.2 21.4 21.5 21.7 21.9 22.0 22.2 22.4 22.6 22.7 22.9 23.1 23.3 23.4 23.6 23.8 24.0 24.1 24.3 24.5 24.7 24.8 25.0 25.2 25.3 25.5 25.7 25.9 26.0 26.2 26.4 26.6 26.7 26.9 27.1 27.3 27.4 27.6 27.8 28.0 28.1 28.3 28.5 28.6 28.8 29.0 29.2 29.3 29.5 29.7 29.9 30.0 30.2 30.4 30.6 30.7 30.9 31.1 31.2 31.4 31.6 31.8 31.9 32.1 32.3 32.5 32.6 32.8 33.0 33.2 33.3 33.5 33.7 33.9 34.0 34.2 34.4 34.5 34.7 34.9 35.1 35.2 35.4 35.6 35.8 35.9 36.1 36.3 36.5 36.6 36.8 37.0 37.2 37.3 37.5 37.7 37.8 38.0 38.2 38.4 38.5 38.7 38.9 39.1 39.2 39.4 39.6 39.8 39.9 40.1 40.3 40.5 40.6 40.8 41.0 41.1 41.3 41.5 41.7 41.8 42.0 42.2 42.4 42.5 42.7 42.9 43.1 43.2 43.4 43.6 43.8 43.9 44.1 44.3 44.4 44.6 44.8 45.0 45.1 45.3 45.5 45.7 45.8 46.0 46.2 46.4 46.5 46.7 46.9 47.0 47.2 47.4 47.6 47.7 47.9 48.1 48.3 48.4 48.6 48.8 49.0 49.1 49.3 49.5 49.7 49.8 50.0 50.2 50.3 50.5 50.7 50.9 51.0 51.2 51.4 51.6 51.7 51.9 52.1 52.3 52.4 52.6 52.8 53.0 53.1 53.3 53.5 53.6 53.8 54.0 54.2 54.3 54.5 54.7 54.9 55.0 55.2 55.4 55.6 55.7 55.9 56.1 56.2 56.4 56.6 56.8 56.9 57.1 57.3 57.5 57.6 57.8 58.0 58.2 58.3 58.5 58.7 58.9 59.0 59.2 59.4 59.5 59.7 59.9 60.1 60.2 60.4 60.6 60.8 60.9 61.1 61.3 61.5 61.6 61.8 62.0 62.2 62.3 62.5 62.7 62.8 63.0 63.2 63.4 63.5 63.7 63.9 64.1 64.2 64.4 64.6 64.8 64.9 65.1 65.3 65.5 65.6 65.8 66.0 66.1 66.3 66.5 66.7 66.8 67.0 67.2 67.4 67.5 67.7 67.9 68.1 68.2 68.4 68.6 68.8 68.9 69.1 69.3 69.4 69.6 69.8 70.0 70.1 70.3 70.5 70.7 70.8 71.0 71.2 71.4 71.5 71.7 71.9 72.0 72.2 72.4 72.6 72.7 72.9 73.1 73.3 73.4 73.6 73.8 74.0 74.1 74.3 74.5 74.7 74.8 75.0 75.2 75.3 75.5 75.7 75.9 76.0 76.2 76.4 76.6 76.7 76.9 77.1 77.3 77.4 77.6 77.8 78.0 78.1 78.3 78.5 78.6 78.8 79.0 79.2 79.3 79.5 79.7 79.9 80.0 80.2 80.4 80.6 80.7 80.9 81.1 81.2 81.4 81.6 81.8 81.9 82.1 82.3 82.5 82.6 82.8 83.0 83.2 83.3 83.5 83.7 83.9 84.0 84.2 84.4 84.5 84.7 84.9 85.1 85.2 85.4 85.6 85.8 85.9 86.1 86.3 86.5 86.6 86.8 87.0 87.2 87.3 87.5 87.7 87.8 88.0 88.2 88.4 88.5 88.7 88.9 89.1 89.2 89.4 89.6 89.8 89.9 90.1 90.3 90.5 90.6 90.8 91.0 91.1 91.3 91.5 91.7 91.8 92.0 92.2 92.4 92.5 92.7 92.9 93.1 93.2 93.4 93.6 93.8 93.9 94.1 94.3 94.4 94.6 94.8 95.0 95.1 95.3 95.5 95.7 95.8 96.0 96.2 96.4 96.5 96.7 96.9 97.0 97.2 97.4 97.6 97.7 97.9 98.1 98.3 98.4 98.6 98.8 99.0 99.1 99.3 99.5 99.7 99.8 -found 30 predictions from path traversal Error with prediction: snap lend_intergenic: 22609, rend_intergenic: 3532 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 55895, rend_intergenic: 53528 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 94023, rend_intergenic: 85860 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 218864, rend_intergenic: 206239 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 235970, rend_intergenic: 234136 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 286046, rend_intergenic: 276613 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 296962, rend_intergenic: 291830 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 301174, rend_intergenic: 298596 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 26 predictions persist after filtering for low support