-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_11674241-12024554

-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 GlimmerHMM_glimmerT_48053-T1
Valid prediction for GlimmerHMM_glimmerT_48074-T1
Valid prediction for GeneMark_model.83673_t
Valid prediction for snap_scaffold_20-snap.2467-T1
Valid prediction for Augustus_model.g32130.t1
Valid prediction for snap_scaffold_20-snap.2486-T1
Valid prediction for CodingQuarry_transcript_30625-T1
Valid prediction for Augustus_model.g32109.t1
Valid prediction for GlimmerHMM_glimmerT_48073-T1
Valid prediction for snap_scaffold_20-snap.2481-T1
Valid prediction for snap_scaffold_20-snap.2515-T1
Couldn't classify 251900, 252069
Sorry, prediction pasa_asmbl_26255.p1 fails validation.
(ATG)	 AC	250928-251086	GT	AGG
(GTC)	 AG	251592-251703	GT	TGG
(ATC)	 AG	251900-252069	AG	AAA
-recovered pasa_asmbl_26255.p1, initial, 250928, 251086
-recovered pasa_asmbl_26255.p1, internal, 251592, 251703
Valid prediction for snap_scaffold_20-snap.2497-T1
Valid prediction for GlimmerHMM_glimmerT_48046-T1
Valid prediction for Augustus_model.g32124.t1
Valid prediction for snap_scaffold_20-snap.2485-T1
Valid prediction for snap_scaffold_20-snap.2514-T1
Couldn't classify 207868, 208271
Sorry, prediction pasa_asmbl_26286.p1 fails validation.
(GCG)	 AT	207868-208271	GT	AGG
(GTT)	 AG	208706-208843	GC	AGG
(ATG)	 AG	209085-209841	GT	AGG
(GAG)	 AG	210055-210257	GT	AGG
(GCA)	 AG	210419-210509	GT	AGG
(CTG)	 AG	210730-210876	GT	AGG
(GAT)	 AG	211172-211435	GT	AGG
(ATG)	 AG	211904-212128	GT	TTG
(CTA)	 AG	212253-212342	GT	AAG
(ACC)	 AG	212537-212815	GT	AGG
(GAT)	 AG	213136-213266	GT	AGG
(TGA)	 AG	213719-213923	GT	CTG
(ATG)	 AG	214290-214664	GT	AGG
(GTA)	 AG	214962-215206	GT	AGG
(GGA)	 AG	215605-215743	GT	AGG
(ATA)	 AG	215831-215915	GT	GAG
(TTT)	 AG	216581-216777	GT	CGG
(TTG)	 AG	217017-217117	GC	AGG
(GGA)	 AG	217313-217364	GT	GAG
(GAT)	 AG	217935-218146	GT	AGG
(GTC)	 AG	219173-219346	GT	AGG
(AGT)	 AG	219449-219491	GT	AAG
(GAG)	 AG	220056-220280	AG	AAA
add_exon() Sorry, pasa_asmbl_26286.p1 209085-209841-initial-1 is invalid.
-recovered pasa_asmbl_26286.p1, initial, 209085, 209841
-recovered pasa_asmbl_26286.p1, initial, 211904, 212128
-recovered pasa_asmbl_26286.p1, initial, 214290, 214664
add_exon() Sorry, pasa_asmbl_26286.p1 208706-208843-terminal-1 is invalid.
-recovered pasa_asmbl_26286.p1, terminal, 208706, 208843
add_exon() Sorry, pasa_asmbl_26286.p1 215831-215915-terminal-3 is invalid.
-recovered pasa_asmbl_26286.p1, terminal, 215831, 215915
-recovered pasa_asmbl_26286.p1, terminal, 220056, 220280
-recovered pasa_asmbl_26286.p1, internal, 208706, 208843
-recovered pasa_asmbl_26286.p1, internal, 209085, 209841
-recovered pasa_asmbl_26286.p1, internal, 210055, 210257
-recovered pasa_asmbl_26286.p1, internal, 210419, 210509
-recovered pasa_asmbl_26286.p1, internal, 210730, 210876
-recovered pasa_asmbl_26286.p1, internal, 211172, 211435
-recovered pasa_asmbl_26286.p1, internal, 211904, 212128
-recovered pasa_asmbl_26286.p1, internal, 212253, 212342
-recovered pasa_asmbl_26286.p1, internal, 212537, 212815
-recovered pasa_asmbl_26286.p1, internal, 213136, 213266
-recovered pasa_asmbl_26286.p1, internal, 213719, 213923
-recovered pasa_asmbl_26286.p1, internal, 214290, 214664
-recovered pasa_asmbl_26286.p1, internal, 214962, 215206
-recovered pasa_asmbl_26286.p1, internal, 215605, 215743
-recovered pasa_asmbl_26286.p1, internal, 215831, 215915
-recovered pasa_asmbl_26286.p1, internal, 216581, 216777
-recovered pasa_asmbl_26286.p1, internal, 217017, 217117
-recovered pasa_asmbl_26286.p1, internal, 217313, 217364
-recovered pasa_asmbl_26286.p1, internal, 217935, 218146
-recovered pasa_asmbl_26286.p1, internal, 219173, 219346
-recovered pasa_asmbl_26286.p1, internal, 219449, 219491
Valid prediction for snap_scaffold_20-snap.2493-T1
Valid prediction for GeneMark_model.83667_t
Valid prediction for CodingQuarry_transcript_30629-T1
Valid prediction for GlimmerHMM_glimmerT_48058-T1
Valid prediction for GeneMark_model.83652_t
Valid prediction for Augustus_model.g32116.t1
Valid prediction for CodingQuarry_transcript_30628-T1
Valid prediction for GlimmerHMM_glimmerT_48060-T1
Valid prediction for snap_scaffold_20-snap.2512-T1
Valid prediction for Augustus_model.g32119.t1
Valid prediction for Augustus_model.g32132.t1
Couldn't classify 204573, 204624
Couldn't classify 207401, 207606
Sorry, prediction pasa_asmbl_26253.p1 fails validation.
(TTC)	 CT	204573-204624	GT	GGG
(ATA)	 AG	204739-204851	GT	AGG
(GTG)	 AG	205132-205319	GT	AAG
(GTT)	 AG	205444-205561	GT	AGG
(GCC)	 AG	205816-205974	GT	AGG
(GAC)	 AG	206373-206675	GT	AGG
(ATG)	 AG	207006-207159	GT	TAG
(CCT)	 AG	207401-207606	GA	AGG
-recovered pasa_asmbl_26253.p1, initial, 207006, 207159
add_exon() Sorry, pasa_asmbl_26253.p1 205132-205319-terminal-2 is invalid.
-recovered pasa_asmbl_26253.p1, terminal, 205132, 205319
-recovered pasa_asmbl_26253.p1, internal, 204739, 204851
-recovered pasa_asmbl_26253.p1, internal, 205132, 205319
-recovered pasa_asmbl_26253.p1, internal, 205444, 205561
-recovered pasa_asmbl_26253.p1, internal, 205816, 205974
-recovered pasa_asmbl_26253.p1, internal, 206373, 206675
-recovered pasa_asmbl_26253.p1, internal, 207006, 207159
Valid prediction for Augustus_model.g32134.t1
Valid prediction for Augustus_model.g32108.t1
Valid prediction for Augustus_model.g32136.t1
Valid prediction for HiQ_model.g32121.t1
Valid prediction for GlimmerHMM_glimmerT_48066-T1
Valid prediction for snap_scaffold_20-snap.2510-T1
Couldn't classify 56247, 56274
Sorry, prediction pasa_asmbl_26245.p1 fails validation.
(TTG)	 GG	56247-56274	GT	AGG
(GTT)	 AG	57053-57189	GT	AGG
(ATT)	 AG	57312-57389	GT	AGG
(CAG)	 AG	58771-58953	CA	AAC
-recovered pasa_asmbl_26245.p1, terminal, 58771, 58953
-recovered pasa_asmbl_26245.p1, internal, 57053, 57189
-recovered pasa_asmbl_26245.p1, internal, 57312, 57389
Valid prediction for GeneMark_model.83661_t
Valid prediction for snap_scaffold_20-snap.2494-T1
Valid prediction for snap_scaffold_20-snap.2487-T1
Valid prediction for GlimmerHMM_glimmerT_48067-T1
Couldn't classify 199481, 199633
Couldn't classify 203627, 203716
Sorry, prediction pasa_asmbl_26252.p1 fails validation.
(GAT)	 CA	199481-199633	GT	TGG
(CCC)	 AG	202235-202408	GT	AGG
(ATT)	 AG	203627-203716	GG	CTG
-recovered pasa_asmbl_26252.p1, internal, 202235, 202408
Couldn't classify 253096, 253246
Sorry, prediction pasa_asmbl_26258.p1 fails validation.
(ACC)	 CC	253096-253246	GT	AGG
(TGC)	 AG	253514-253653	GT	AGG
(GGA)	 AG	254430-254554	GT	GGG
(GCC)	 AG	255139-255343	GT	AGG
(CAA)	 AG	255901-256153	GT	AGG
(GTG)	 AG	256648-256788	GT	AGG
(GGA)	 AG	257038-257202	GT	TGG
(GAG)	 AG	257886-258026	GT	GGG
(GTT)	 AG	258186-258355	GA	GAG
-recovered pasa_asmbl_26258.p1, terminal, 258186, 258355
-recovered pasa_asmbl_26258.p1, internal, 253514, 253653
-recovered pasa_asmbl_26258.p1, internal, 254430, 254554
-recovered pasa_asmbl_26258.p1, internal, 255139, 255343
-recovered pasa_asmbl_26258.p1, internal, 255901, 256153
-recovered pasa_asmbl_26258.p1, internal, 256648, 256788
-recovered pasa_asmbl_26258.p1, internal, 257038, 257202
-recovered pasa_asmbl_26258.p1, internal, 257886, 258026
Valid prediction for GeneMark_model.83665_t
Valid prediction for GeneMark_model.83655_t
Valid prediction for snap_scaffold_20-snap.2488-T1
Valid prediction for GeneMark_model.83668_t
Valid prediction for GeneMark_model.83658_t
Couldn't classify 54130, 54188
Couldn't classify 56107, 56171
Sorry, prediction pasa_asmbl_26244.p1 fails validation.
(GTG)	 AT	54130-54188	GT	GAG
(GTG)	 AG	54321-54483	GT	GGG
(CAT)	 AG	54900-55005	GT	TGG
(GAC)	 AG	56107-56171	TC	CCT
-recovered pasa_asmbl_26244.p1, internal, 54321, 54483
-recovered pasa_asmbl_26244.p1, internal, 54900, 55005
Valid prediction for snap_scaffold_20-snap.2495-T1
Valid prediction for snap_scaffold_20-snap.2508-T1
Valid prediction for GlimmerHMM_glimmerT_48064-T1
Valid prediction for CodingQuarry_transcript_30624-T1
Valid prediction for snap_scaffold_20-snap.2492-T1
Valid prediction for snap_scaffold_20-snap.2466-T1
Valid prediction for snap_scaffold_20-snap.2516-T1
Valid prediction for Augustus_model.g32123.t1
Valid prediction for GeneMark_model.83653_t
Valid prediction for snap_scaffold_20-snap.2465-T1
Valid prediction for GeneMark_model.83677_t
Valid prediction for snap_scaffold_20-snap.2484-T1
Valid prediction for GlimmerHMM_glimmerT_48048-T1
Valid prediction for GlimmerHMM_glimmerT_48065-T1
Valid prediction for snap_scaffold_20-snap.2518-T1
Couldn't classify 44321, 44361
Couldn't classify 48316, 48388
Sorry, prediction pasa_asmbl_26271.p1 fails validation.
(AGA)	 TA	44321-44361	GT	TAG
(TGT)	 AG	45622-45712	GT	ACG
(GGC)	 AG	46648-46685	GT	AAG
(GGA)	 AG	47018-47160	GT	GGG
(AAA)	 AG	48126-48177	GT	GGG
(GAC)	 AG	48316-48388	CA	GAC
-recovered pasa_asmbl_26271.p1, terminal, 46648, 46685
-recovered pasa_asmbl_26271.p1, internal, 45622, 45712
-recovered pasa_asmbl_26271.p1, internal, 46648, 46685
-recovered pasa_asmbl_26271.p1, internal, 47018, 47160
-recovered pasa_asmbl_26271.p1, internal, 48126, 48177
Valid prediction for GlimmerHMM_glimmerT_48068-T1
Valid prediction for GeneMark_model.83654_t
Valid prediction for snap_scaffold_20-snap.2509-T1
Valid prediction for GlimmerHMM_glimmerT_48057-T1
Valid prediction for Augustus_model.g32135.t1
Valid prediction for GeneMark_model.83660_t
Valid prediction for Augustus_model.g32118.t1
Valid prediction for snap_scaffold_20-snap.2490-T1
Valid prediction for snap_scaffold_20-snap.2496-T1
Valid prediction for snap_scaffold_20-snap.2489-T1
Valid prediction for GeneMark_model.83666_t
Valid prediction for snap_scaffold_20-snap.2468-T1
Valid prediction for Augustus_model.g32112.t1
Valid prediction for Augustus_model.g32129.t1
Valid prediction for Augustus_model.g32122.t1
Valid prediction for HiQ_model.g32125.t1
Valid prediction for GlimmerHMM_glimmerT_48071-T1
Valid prediction for GeneMark_model.83659_t
Valid prediction for GeneMark_model.83664_t
Valid prediction for snap_scaffold_20-snap.2517-T1
Valid prediction for GeneMark_model.83675_t
Valid prediction for GeneMark_model.83672_t

-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: -)Valid prediction for snap_scaffold_20-snap.2476-T1
Valid prediction for GlimmerHMM_glimmerT_48061-T1
Valid prediction for CodingQuarry_transcript_30621-T1
Valid prediction for snap_scaffold_20-snap.2500-T1
Valid prediction for snap_scaffold_20-snap.2464-T1
Valid prediction for GlimmerHMM_glimmerT_48051-T1
Valid prediction for GeneMark_model.83671_t
Couldn't classify 74139, 74315
Couldn't classify 74800, 74804
Sorry, prediction CodingQuarry_transcript_30631-T1 fails validation.
(ATG)	 GA	67515-67760	GT	CAG
(GAG)	 AG	68914-68983	GT	AGG
(GCG)	 AG	71441-71559	GT	AGG
(TTC)	 AG	71667-71800	GT	AAG
(GCT)	 AG	72078-72246	GT	ATG
(ATT)	 AG	73051-73134	GT	AGG
(GTG)	 AG	73233-73318	GT	AAG
(TTC)	 AG	73530-73604	GT	TGG
(GAT)	 AG	73691-73851	GT	GAG
(ACA)	 AG	74139-74315	GG	GGG
(ACT)	 AT	74800-74804	TT	AGT
-recovered CodingQuarry_transcript_30631-T1, initial, 67515, 67760
-recovered CodingQuarry_transcript_30631-T1, terminal, 68914, 68983
add_exon() Sorry, CodingQuarry_transcript_30631-T1 73233-73318-terminal-2 is invalid.
-recovered CodingQuarry_transcript_30631-T1, terminal, 73233, 73318
-recovered CodingQuarry_transcript_30631-T1, internal, 68914, 68983
-recovered CodingQuarry_transcript_30631-T1, internal, 71441, 71559
-recovered CodingQuarry_transcript_30631-T1, internal, 71667, 71800
-recovered CodingQuarry_transcript_30631-T1, internal, 72078, 72246
-recovered CodingQuarry_transcript_30631-T1, internal, 73051, 73134
-recovered CodingQuarry_transcript_30631-T1, internal, 73233, 73318
-recovered CodingQuarry_transcript_30631-T1, internal, 73530, 73604
-recovered CodingQuarry_transcript_30631-T1, internal, 73691, 73851
Couldn't classify 79220, 79333
Sorry, prediction pasa_asmbl_27128.p1 fails validation.
(CAG)	 CG	79220-79333	GT	GGG
(GGT)	 AG	79742-79859	GT	AGG
(GTT)	 AG	80309-80420	GT	GAG
(GAT)	 AG	81701-81870	GC	AGG
(GAA)	 AG	82135-82240	GT	TGG
(GAC)	 AG	82364-82733	GT	TTG
(CAG)	 AG	82991-83206	TC	GAT
-recovered pasa_asmbl_27128.p1, terminal, 82991, 83206
-recovered pasa_asmbl_27128.p1, internal, 79742, 79859
-recovered pasa_asmbl_27128.p1, internal, 80309, 80420
-recovered pasa_asmbl_27128.p1, internal, 81701, 81870
-recovered pasa_asmbl_27128.p1, internal, 82135, 82240
-recovered pasa_asmbl_27128.p1, internal, 82364, 82733
Valid prediction for GeneMark_model.83670_t
Valid prediction for GlimmerHMM_glimmerT_48076-T1
Valid prediction for snap_scaffold_20-snap.2461-T1
Valid prediction for GlimmerHMM_glimmerT_48070-T1
Valid prediction for snap_scaffold_20-snap.2519-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for pasa_asmbl_27136.p1
Valid prediction for GeneMark_model.83656_t
Valid prediction for GlimmerHMM_glimmerT_48069-T1
Valid prediction for Augustus_model.g32113.t1
Valid prediction for snap_scaffold_20-snap.2520-T1
Valid prediction for snap_scaffold_20-snap.2471-T1
Valid prediction for snap_scaffold_20-snap.2504-T1
Valid prediction for pasa_asmbl_27159.p1
Valid prediction for GlimmerHMM_glimmerT_48062-T1
Valid prediction for GeneMark_model.83679_t
Valid prediction for snap_scaffold_20-snap.2475-T1
Valid prediction for snap_scaffold_20-snap.2505-T1
Valid prediction for snap_scaffold_20-snap.2478-T1
Valid prediction for snap_scaffold_20-snap.2463-T1
Couldn't classify 60650, 60822
Couldn't classify 61253, 61473
Sorry, prediction CodingQuarry_transcript_30634-T1 fails validation.
(ATG)	 AA	55662-55898	GT	AAG
(GAG)	 AG	56557-56626	GT	AGG
(GCG)	 AG	58051-58169	GT	AGG
(TTC)	 AG	58408-58541	GT	AAG
(GGT)	 AG	58748-58916	GT	ACG
(ATT)	 AG	59097-59180	GT	AGG
(GTG)	 AG	59514-59599	GT	GGG
(TTC)	 AG	59710-59778	GT	TGG
(GAT)	 AG	59987-60147	GT	TTG
(ATA)	 AG	60650-60822	AG	TGA
(CCC)	 AC	61253-61473	GT	GTG
(ACC)	 AG	61730-61766	GT	ACG
(GAT)	 AG	61948-62013	GT	AAG
(GAC)	 AG	62471-62528	GT	ACG
(GAA)	 AG	62622-62686	GT	ATG
(GAC)	 AG	62814-62882	GT	TGG
(GGT)	 AG	63503-63581	GT	AGG
(GTT)	 AG	63882-63998	GT	CAG
(GAG)	 AG	64395-64453	GT	AGG
(TGG)	 AG	64574-64597	AA	AGA
-recovered CodingQuarry_transcript_30634-T1, initial, 55662, 55898
-recovered CodingQuarry_transcript_30634-T1, terminal, 56557, 56626
-recovered CodingQuarry_transcript_30634-T1, terminal, 64574, 64597
-recovered CodingQuarry_transcript_30634-T1, internal, 56557, 56626
-recovered CodingQuarry_transcript_30634-T1, internal, 58051, 58169
-recovered CodingQuarry_transcript_30634-T1, internal, 58408, 58541
-recovered CodingQuarry_transcript_30634-T1, internal, 58748, 58916
-recovered CodingQuarry_transcript_30634-T1, internal, 59097, 59180
-recovered CodingQuarry_transcript_30634-T1, internal, 59514, 59599
-recovered CodingQuarry_transcript_30634-T1, internal, 59710, 59778
-recovered CodingQuarry_transcript_30634-T1, internal, 59987, 60147
-recovered CodingQuarry_transcript_30634-T1, internal, 61730, 61766
-recovered CodingQuarry_transcript_30634-T1, internal, 61948, 62013
-recovered CodingQuarry_transcript_30634-T1, internal, 62471, 62528
-recovered CodingQuarry_transcript_30634-T1, internal, 62622, 62686
-recovered CodingQuarry_transcript_30634-T1, internal, 62814, 62882
-recovered CodingQuarry_transcript_30634-T1, internal, 63503, 63581
-recovered CodingQuarry_transcript_30634-T1, internal, 63882, 63998
-recovered CodingQuarry_transcript_30634-T1, internal, 64395, 64453
Valid prediction for CodingQuarry_transcript_30633-T1
Valid prediction for GeneMark_model.83649_t
Valid prediction for snap_scaffold_20-snap.2507-T1
Valid prediction for snap_scaffold_20-snap.2473-T1
Valid prediction for GlimmerHMM_glimmerT_48050-T1
Valid prediction for snap_scaffold_20-snap.2470-T1
Valid prediction for Augustus_model.g32131.t1
Valid prediction for snap_scaffold_20-snap.2480-T1
Valid prediction for GlimmerHMM_glimmerT_48042-T1
Valid prediction for GlimmerHMM_glimmerT_48059-T1
Valid prediction for snap_scaffold_20-snap.2501-T1
Valid prediction for snap_scaffold_20-snap.2491-T1
Valid prediction for GlimmerHMM_glimmerT_48044-T1
Valid prediction for snap_scaffold_20-snap.2482-T1
Valid prediction for pasa_asmbl_27109.p1
Valid prediction for CodingQuarry_transcript_30627-T1
Couldn't classify 252936, 253664
Sorry, prediction pasa_asmbl_26247.p1 fails validation.
(ACT)	 GG	252936-253664	GG	GGG
Valid prediction for GeneMark_model.83676_t
Valid prediction for HiQ_model.g32128.t1
Valid prediction for pasa_asmbl_27132.p1
Valid prediction for HiQ_model.g32110.t1
Valid prediction for GlimmerHMM_glimmerT_48055-T1
Valid prediction for snap_scaffold_20-snap.2499-T1
Valid prediction for Augustus_model.g32111.t1
Valid prediction for HiQ_model.g32105.t1
Valid prediction for GeneMark_model.83674_t
Valid prediction for snap_scaffold_20-snap.2474-T1
Valid prediction for Augustus_model.g32117.t1
Valid prediction for snap_scaffold_20-snap.2479-T1
Valid prediction for snap_scaffold_20-snap.2502-T1
Valid prediction for pasa_asmbl_27122.p1
Valid prediction for GlimmerHMM_glimmerT_48049-T1
Valid prediction for CodingQuarry_transcript_30623-T1
Valid prediction for GlimmerHMM_glimmerT_48056-T1
Valid prediction for GlimmerHMM_glimmerT_48072-T1
Valid prediction for GeneMark_model.83650_t
Valid prediction for Augustus_model.g32126.t1
Valid prediction for snap_scaffold_20-snap.2460-T1
Valid prediction for Augustus_model.g32120.t1
Valid prediction for GeneMark_model.83662_t
Valid prediction for HiQ_model.g32127.t1
Valid prediction for snap_scaffold_20-snap.2498-T1
Couldn't classify 3520, 3903
Sorry, prediction pasa_asmbl_27263.p1 fails validation.
(AGG)	 TC	3520-3903	AA	CCA
Valid prediction for GlimmerHMM_glimmerT_48063-T1
Valid prediction for CodingQuarry_transcript_30632-T1
Valid prediction for GeneMark_model.83669_t
Valid prediction for GeneMark_model.83663_t
Valid prediction for GeneMark_model.83678_t
Valid prediction for GlimmerHMM_glimmerT_48075-T1
Valid prediction for pasa_asmbl_27113.p1
Valid prediction for snap_scaffold_20-snap.2469-T1
Valid prediction for snap_scaffold_20-snap.2462-T1
Valid prediction for GlimmerHMM_glimmerT_48052-T1
Valid prediction for Augustus_model.g32133.t1
Valid prediction for Augustus_model.g32115.t1
Valid prediction for HiQ_model.g32107.t1
Valid prediction for pasa_asmbl_27107.p1
Couldn't classify 278473, 278525
Sorry, prediction pasa_asmbl_27119.p1 fails validation.
(GTT)	 AG	278473-278525	GT	AAG
(GTA)	 AG	278636-278717	GT	TGG
(TAT)	 AG	278850-279028	GT	TTG
(GAT)	 AG	279205-279344	GT	CTG
(CGT)	 AG	279446-279580	GT	AAG
(GTG)	 AG	279678-279775	GT	TGG
(GAG)	 AG	279891-279966	GT	GGG
(AGA)	 AG	280155-280228	GT	AGG
(ATC)	 AG	280498-280606	GT	GGG
(AGA)	 AG	280789-280874	GT	GGG
(CCT)	 AG	281214-281419	GT	AAG
(GAA)	 AG	281623-281734	TA	GAT
add_exon() Sorry, pasa_asmbl_27119.p1 278473-278525-terminal-2 is invalid.
-recovered pasa_asmbl_27119.p1, terminal, 278473, 278525
-recovered pasa_asmbl_27119.p1, terminal, 281623, 281734
-recovered pasa_asmbl_27119.p1, internal, 278473, 278525
-recovered pasa_asmbl_27119.p1, internal, 278636, 278717
-recovered pasa_asmbl_27119.p1, internal, 278850, 279028
-recovered pasa_asmbl_27119.p1, internal, 279205, 279344
-recovered pasa_asmbl_27119.p1, internal, 279446, 279580
-recovered pasa_asmbl_27119.p1, internal, 279678, 279775
-recovered pasa_asmbl_27119.p1, internal, 279891, 279966
-recovered pasa_asmbl_27119.p1, internal, 280155, 280228
-recovered pasa_asmbl_27119.p1, internal, 280498, 280606
-recovered pasa_asmbl_27119.p1, internal, 280789, 280874
-recovered pasa_asmbl_27119.p1, internal, 281214, 281419
Valid prediction for GlimmerHMM_glimmerT_48043-T1
Valid prediction for HiQ_model.g32114.t1
Valid prediction for Augustus_model.g32106.t1
Valid prediction for GlimmerHMM_glimmerT_48054-T1
Valid prediction for GeneMark_model.83657_t
Couldn't classify 60650, 60822
Couldn't classify 61253, 61473
Sorry, prediction CodingQuarry_transcript_30635-T1 fails validation.
(ATG)	 AA	55662-55898	GT	AAG
(GAG)	 AG	56557-56626	GT	AGG
(GCG)	 AG	58051-58169	GT	AGG
(TTC)	 AG	58408-58541	GT	AAG
(GGT)	 AG	58748-58916	GT	ACG
(ATT)	 AG	59097-59180	GT	AGG
(GTG)	 AG	59514-59599	GT	GGG
(TTC)	 AG	59710-59778	GT	TGG
(GAT)	 AG	59987-60147	GT	TTG
(ATA)	 AG	60650-60822	AG	TGA
(CCC)	 AC	61253-61473	GT	GTG
(ACC)	 AG	61730-61766	GT	ACG
(GAT)	 AG	61948-62013	GT	AAG
(GAC)	 AG	62471-62528	GT	ACG
(GAA)	 AG	62622-62686	GT	ATG
(AAG)	 AG	62811-62882	GT	TGG
(GGT)	 AG	63503-63581	GT	AGG
(GTT)	 AG	63882-63998	GT	CAG
(GAG)	 AG	64395-64453	GT	AGG
(TGG)	 AG	64574-64597	AA	AGA
-recovered CodingQuarry_transcript_30635-T1, initial, 55662, 55898
-recovered CodingQuarry_transcript_30635-T1, terminal, 56557, 56626
-recovered CodingQuarry_transcript_30635-T1, terminal, 64574, 64597
-recovered CodingQuarry_transcript_30635-T1, internal, 56557, 56626
-recovered CodingQuarry_transcript_30635-T1, internal, 58051, 58169
-recovered CodingQuarry_transcript_30635-T1, internal, 58408, 58541
-recovered CodingQuarry_transcript_30635-T1, internal, 58748, 58916
-recovered CodingQuarry_transcript_30635-T1, internal, 59097, 59180
-recovered CodingQuarry_transcript_30635-T1, internal, 59514, 59599
-recovered CodingQuarry_transcript_30635-T1, internal, 59710, 59778
-recovered CodingQuarry_transcript_30635-T1, internal, 59987, 60147
-recovered CodingQuarry_transcript_30635-T1, internal, 61730, 61766
-recovered CodingQuarry_transcript_30635-T1, internal, 61948, 62013
-recovered CodingQuarry_transcript_30635-T1, internal, 62471, 62528
-recovered CodingQuarry_transcript_30635-T1, internal, 62622, 62686
-recovered CodingQuarry_transcript_30635-T1, internal, 62811, 62882
-recovered CodingQuarry_transcript_30635-T1, internal, 63503, 63581
-recovered CodingQuarry_transcript_30635-T1, internal, 63882, 63998
-recovered CodingQuarry_transcript_30635-T1, internal, 64395, 64453
Valid prediction for GlimmerHMM_glimmerT_48047-T1
Valid prediction for snap_scaffold_20-snap.2506-T1
Valid prediction for CodingQuarry_transcript_30622-T1
Valid prediction for snap_scaffold_20-snap.2472-T1
Valid prediction for snap_scaffold_20-snap.2483-T1
Valid prediction for snap_scaffold_20-snap.2477-T1
Valid prediction for snap_scaffold_20-snap.2513-T1
Valid prediction for GeneMark_model.83651_t
Valid prediction for snap_scaffold_20-snap.2511-T1
Valid prediction for snap_scaffold_20-snap.2503-T1
Valid prediction for GlimmerHMM_glimmerT_48045-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 350314
-exon list size: 700


building trellis

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81.2    
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99.1    
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99.4    
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99.7    
99.9    
-found 46 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 45 predictions persist after filtering for low support