-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_4713818-4847011

-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 Augustus_model.g37899.t1
Valid prediction for snap_scaffold_26-snap.1066-T1
Valid prediction for GlimmerHMM_glimmerT_56903-T1
Valid prediction for Augustus_model.g37893.t1
Valid prediction for GlimmerHMM_glimmerT_56881-T1
Valid prediction for GeneMark_model.99373_t
Valid prediction for snap_scaffold_26-snap.1036-T1
Valid prediction for snap_scaffold_26-snap.1053-T1
Valid prediction for snap_scaffold_26-snap.1048-T1
Valid prediction for Augustus_model.g37895.t1
Valid prediction for snap_scaffold_26-snap.1065-T1
Valid prediction for snap_scaffold_26-snap.1047-T1
Valid prediction for GeneMark_model.99357_t
Valid prediction for GeneMark_model.99343_t
Valid prediction for GlimmerHMM_glimmerT_56886-T1
Valid prediction for snap_scaffold_26-snap.1069-T1
Valid prediction for Augustus_model.g37886.t1
Valid prediction for GeneMark_model.99363_t
Valid prediction for snap_scaffold_26-snap.1034-T1
Valid prediction for GeneMark_model.99355_t
Valid prediction for snap_scaffold_26-snap.1062-T1
Valid prediction for Augustus_model.g37900.t1
Valid prediction for snap_scaffold_26-snap.1039-T1
Couldn't classify 114211, 114313
Sorry, prediction pasa_asmbl_35458.p1 fails validation.
(GGC)	 TA	114211-114313	GT	AGG
(AGT)	 AG	114406-114455	GT	AGG
(ATT)	 AG	117404-117447	GT	AGG
(GTC)	 AG	118056-118176	GT	AGG
(GCC)	 AG	118750-118848	GT	AGG
(GAG)	 AG	120729-120875	GT	GAG
-recovered pasa_asmbl_35458.p1, terminal, 120729, 120875
-recovered pasa_asmbl_35458.p1, internal, 114406, 114455
-recovered pasa_asmbl_35458.p1, internal, 117404, 117447
-recovered pasa_asmbl_35458.p1, internal, 118056, 118176
-recovered pasa_asmbl_35458.p1, internal, 118750, 118848
-recovered pasa_asmbl_35458.p1, internal, 120729, 120875
Valid prediction for GlimmerHMM_glimmerT_56897-T1
Valid prediction for GlimmerHMM_glimmerT_56894-T1
Valid prediction for GlimmerHMM_glimmerT_56892-T1
Valid prediction for GlimmerHMM_glimmerT_56902-T1
Valid prediction for GeneMark_model.99348_t
Valid prediction for snap_scaffold_26-snap.1054-T1
Valid prediction for Augustus_model.g37891.t1
Valid prediction for snap_scaffold_26-snap.1045-T1
Valid prediction for snap_scaffold_26-snap.1050-T1
Valid prediction for GeneMark_model.99376_t
Valid prediction for Augustus_model.g37887.t1
Valid prediction for GlimmerHMM_glimmerT_56888-T1
Couldn't classify 108792, 108847
Sorry, prediction pasa_asmbl_35456.p1 fails validation.
(ATG)	 AT	105675-105742	GT	AGG
(GGC)	 AG	105903-106054	GT	AGG
(ACG)	 AG	106225-106330	GT	AGG
(GTT)	 AG	107278-107326	GT	GGG
(CTT)	 AG	108126-108162	GT	AGG
(GAA)	 AG	108792-108847	GG	CAG
-recovered pasa_asmbl_35456.p1, initial, 105675, 105742
-recovered pasa_asmbl_35456.p1, terminal, 105903, 106054
-recovered pasa_asmbl_35456.p1, internal, 105903, 106054
-recovered pasa_asmbl_35456.p1, internal, 106225, 106330
-recovered pasa_asmbl_35456.p1, internal, 107278, 107326
-recovered pasa_asmbl_35456.p1, internal, 108126, 108162
Valid prediction for snap_scaffold_26-snap.1057-T1
Couldn't classify 70730, 70753
Couldn't classify 73704, 74021
Sorry, prediction pasa_asmbl_35451.p2 fails validation.
(GAC)	 TG	70730-70753	GT	AGG
(GTT)	 AG	71912-72103	GT	AGG
(GAG)	 AG	73704-74021	AA	AGA
-recovered pasa_asmbl_35451.p2, internal, 71912, 72103
Valid prediction for GeneMark_model.99347_t
Valid prediction for GeneMark_model.99367_t
Valid prediction for GeneMark_model.99341_t
Valid prediction for GlimmerHMM_glimmerT_56900-T1
Valid prediction for GlimmerHMM_glimmerT_56891-T1
Valid prediction for snap_scaffold_26-snap.1044-T1
Valid prediction for GeneMark_model.99352_t
Couldn't classify 74172, 74882
Sorry, prediction pasa_asmbl_35452.p1 fails validation.
(GGG)	 AC	74172-74882	TA	AAT
Valid prediction for snap_scaffold_26-snap.1056-T1
Valid prediction for Augustus_model.g37885.t1
Valid prediction for GeneMark_model.99354_t
Valid prediction for Augustus_model.g37892.t1
Valid prediction for GlimmerHMM_glimmerT_56895-T1
Valid prediction for snap_scaffold_26-snap.1035-T1
Valid prediction for GeneMark_model.99360_t
Valid prediction for GeneMark_model.99372_t
Valid prediction for GeneMark_model.99369_t
Valid prediction for snap_scaffold_26-snap.1051-T1
Valid prediction for snap_scaffold_26-snap.1041-T1
Valid prediction for Augustus_model.g37894.t1
Valid prediction for GeneMark_model.99358_t
Valid prediction for GeneMark_model.99345_t
Valid prediction for Augustus_model.g37889.t1
Valid prediction for snap_scaffold_26-snap.1038-T1
Valid prediction for GeneMark_model.99365_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_26-snap.1055-T1
Valid prediction for CodingQuarry_transcript_40240-T1
Valid prediction for snap_scaffold_26-snap.1049-T1
Valid prediction for snap_scaffold_26-snap.1040-T1
Valid prediction for GlimmerHMM_glimmerT_56880-T1
Valid prediction for GeneMark_model.99361_t
Couldn't classify 33817, 33996
Sorry, prediction pasa_asmbl_34870.p1 fails validation.
(ATG)	 GG	28604-29173	GT	AGG
(GTA)	 AG	30401-30696	GT	ATG
(GCC)	 AG	31263-31404	GT	AGG
(ATG)	 AG	32377-32460	GT	AGG
(ATA)	 AG	33817-33996	GG	CCG
-recovered pasa_asmbl_34870.p1, initial, 28604, 29173
-recovered pasa_asmbl_34870.p1, initial, 32377, 32460
-recovered pasa_asmbl_34870.p1, internal, 30401, 30696
-recovered pasa_asmbl_34870.p1, internal, 31263, 31404
-recovered pasa_asmbl_34870.p1, internal, 32377, 32460
Valid prediction for GeneMark_model.99370_t
Valid prediction for snap_scaffold_26-snap.1061-T1
Valid prediction for GeneMark_model.99340_t
Valid prediction for GeneMark_model.99351_t
Valid prediction for GlimmerHMM_glimmerT_56879-T1
Valid prediction for GeneMark_model.99359_t
Valid prediction for Augustus_model.g37890.t1
Valid prediction for snap_scaffold_26-snap.1064-T1
Valid prediction for GlimmerHMM_glimmerT_56882-T1
Valid prediction for snap_scaffold_26-snap.1060-T1
Valid prediction for snap_scaffold_26-snap.1058-T1
Valid prediction for snap_scaffold_26-snap.1042-T1
Valid prediction for snap_scaffold_26-snap.1068-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_56887-T1
Valid prediction for GeneMark_model.99375_t
Valid prediction for GeneMark_model.99349_t
Valid prediction for snap_scaffold_26-snap.1067-T1
Valid prediction for GeneMark_model.99353_t
Valid prediction for GeneMark_model.99362_t
Valid prediction for GeneMark_model.99364_t
Valid prediction for GeneMark_model.99356_t
Valid prediction for GlimmerHMM_glimmerT_56885-T1
Valid prediction for snap_scaffold_26-snap.1063-T1
Valid prediction for GlimmerHMM_glimmerT_56898-T1
Valid prediction for GeneMark_model.99371_t
Valid prediction for GeneMark_model.99368_t
Valid prediction for snap_scaffold_26-snap.1046-T1
Valid prediction for GlimmerHMM_glimmerT_56899-T1
Valid prediction for Augustus_model.g37896.t1
Valid prediction for GlimmerHMM_glimmerT_56890-T1
Valid prediction for GeneMark_model.99346_t
Valid prediction for CodingQuarry_transcript_40239-T1
Valid prediction for GlimmerHMM_glimmerT_56901-T1
Valid prediction for snap_scaffold_26-snap.1059-T1
Valid prediction for GlimmerHMM_glimmerT_56884-T1
Valid prediction for Augustus_model.g37898.t1
Valid prediction for snap_scaffold_26-snap.1043-T1
Valid prediction for GeneMark_model.99374_t
Valid prediction for Augustus_model.g37888.t1
Valid prediction for GeneMark_model.99377_t
Valid prediction for GlimmerHMM_glimmerT_56889-T1
Valid prediction for GeneMark_model.99350_t
Valid prediction for GeneMark_model.99342_t
Valid prediction for GlimmerHMM_glimmerT_56896-T1
Valid prediction for snap_scaffold_26-snap.1052-T1
Valid prediction for GeneMark_model.99366_t
Valid prediction for GlimmerHMM_glimmerT_56893-T1
Valid prediction for Augustus_model.g37897.t1
Valid prediction for GlimmerHMM_glimmerT_56883-T1
Valid prediction for snap_scaffold_26-snap.1037-T1
Valid prediction for GeneMark_model.99344_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21078, rend_intergenic: 18052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23358, rend_intergenic: 22177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25600, rend_intergenic: 23486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37727, rend_intergenic: 34572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67747, rend_intergenic: 64457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74785, rend_intergenic: 68849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130763, rend_intergenic: 128035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 133194
-exon list size: 521


building trellis

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80.3    
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81.3    
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86.4    
86.6    
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88.3    
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88.9    
89.1    
89.3    
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89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
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91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
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94.6    
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95.2    
95.4    
95.6    
95.8    
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96.2    
96.4    
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96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 21078, rend_intergenic: 18052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23358, rend_intergenic: 22177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25600, rend_intergenic: 23486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37727, rend_intergenic: 34572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67747, rend_intergenic: 64457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74785, rend_intergenic: 68849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130763, rend_intergenic: 128035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support