-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_5422835-5621255

-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 GeneMark_model.96894_t
Valid prediction for Augustus_model.g37024.t1
Valid prediction for GlimmerHMM_glimmerT_55484-T1
Valid prediction for GeneMark_model.96890_t
Valid prediction for snap_scaffold_25-snap.1182-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.96885_t
Valid prediction for GeneMark_model.96887_t
Valid prediction for GeneMark_model.96882_t
Valid prediction for Augustus_model.g37018.t1
Valid prediction for GeneMark_model.96892_t
Valid prediction for CodingQuarry_transcript_38643-T1
Valid prediction for snap_scaffold_25-snap.1175-T1
Valid prediction for GlimmerHMM_glimmerT_55493-T1
Valid prediction for GeneMark_model.96904_t
Valid prediction for snap_scaffold_25-snap.1208-T1
Valid prediction for GlimmerHMM_glimmerT_55510-T1
Valid prediction for GeneMark_model.96880_t
Valid prediction for snap_scaffold_25-snap.1201-T1
Valid prediction for GlimmerHMM_glimmerT_55487-T1
Valid prediction for snap_scaffold_25-snap.1196-T1
Valid prediction for snap_scaffold_25-snap.1200-T1
Valid prediction for GeneMark_model.96883_t
Valid prediction for snap_scaffold_25-snap.1191-T1
Valid prediction for GeneMark_model.96876_t
Valid prediction for Augustus_model.g37033.t1
Valid prediction for snap_scaffold_25-snap.1207-T1
Valid prediction for GlimmerHMM_glimmerT_55491-T1
Valid prediction for snap_scaffold_25-snap.1210-T1
Valid prediction for GlimmerHMM_glimmerT_55500-T1
Valid prediction for GlimmerHMM_glimmerT_55502-T1
Valid prediction for GeneMark_model.96871_t
Valid prediction for GlimmerHMM_glimmerT_55508-T1
Valid prediction for snap_scaffold_25-snap.1202-T1
Valid prediction for GeneMark_model.96878_t
Valid prediction for GeneMark_model.96896_t
Valid prediction for GlimmerHMM_glimmerT_55490-T1
Valid prediction for pasa_asmbl_33563.p1
Valid prediction for GeneMark_model.96905_t
Valid prediction for CodingQuarry_transcript_38644-T1
Valid prediction for HiQ_model.g37031.t1
Valid prediction for GlimmerHMM_glimmerT_55499-T1
Valid prediction for snap_scaffold_25-snap.1181-T1
Valid prediction for GlimmerHMM_glimmerT_55489-T1
Valid prediction for GlimmerHMM_glimmerT_55495-T1
Valid prediction for snap_scaffold_25-snap.1203-T1
Valid prediction for snap_scaffold_25-snap.1185-T1
Valid prediction for snap_scaffold_25-snap.1198-T1
Couldn't classify 7250, 7544
Sorry, prediction pasa_asmbl_33564.p2 fails validation.
(GCT)	 AT	7250-7544	GT	GGG
(GGG)	 AG	8108-8292	AG	GAA
-recovered pasa_asmbl_33564.p2, terminal, 8108, 8292
Valid prediction for Augustus_model.g37027.t1
Valid prediction for snap_scaffold_25-snap.1206-T1
Valid prediction for GeneMark_model.96893_t
Valid prediction for GlimmerHMM_glimmerT_55514-T1
Valid prediction for snap_scaffold_25-snap.1180-T1
Valid prediction for snap_scaffold_25-snap.1209-T1
Valid prediction for snap_scaffold_25-snap.1193-T1
Valid prediction for snap_scaffold_25-snap.1183-T1
Valid prediction for pasa_asmbl_33566.p1
Valid prediction for snap_scaffold_25-snap.1172-T1
Valid prediction for Augustus_model.g37017.t1
Valid prediction for GeneMark_model.96888_t
Valid prediction for HiQ_model.g37028.t1
Valid prediction for GlimmerHMM_glimmerT_55512-T1
Valid prediction for GlimmerHMM_glimmerT_55513-T1
Valid prediction for GlimmerHMM_glimmerT_55494-T1
Valid prediction for GeneMark_model.96889_t
Valid prediction for snap_scaffold_25-snap.1187-T1
Valid prediction for Augustus_model.g37019.t1
Valid prediction for GlimmerHMM_glimmerT_55511-T1
Valid prediction for GeneMark_model.96899_t
Valid prediction for HiQ_model.g37014.t1
Valid prediction for GeneMark_model.96902_t
Valid prediction for GlimmerHMM_glimmerT_55496-T1
Couldn't classify 147367, 147592
Sorry, prediction pasa_asmbl_33567.p1 fails validation.
(TTC)	 GT	147367-147592	GT	AGG
(AGT)	 AG	147909-148072	CA	AAC
-recovered pasa_asmbl_33567.p1, terminal, 147909, 148072
Valid prediction for GeneMark_model.96873_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_25-snap.1174-T1
Valid prediction for Augustus_model.g37020.t1
Valid prediction for GlimmerHMM_glimmerT_55486-T1
Valid prediction for GlimmerHMM_glimmerT_55509-T1
Valid prediction for GeneMark_model.96875_t
Valid prediction for GeneMark_model.96906_t
Valid prediction for Augustus_model.g37025.t1
Valid prediction for GlimmerHMM_glimmerT_55503-T1
Valid prediction for HiQ_model.g37032.t1
Valid prediction for HiQ_model.g37035.t1
Valid prediction for GeneMark_model.96870_t
Valid prediction for GlimmerHMM_glimmerT_55507-T1
Valid prediction for GeneMark_model.96886_t
Couldn't classify 2637, 2670
Couldn't classify 2916, 2992
Sorry, prediction CodingQuarry_transcript_38648-T1 fails validation.
(ATG)	 AA	2637-2670	GA	GAG
(AAA)	 GA	2916-2992	GT	CGG
(GCT)	 AG	4608-4703	AG	GAA
-recovered CodingQuarry_transcript_38648-T1, terminal, 4608, 4703
Valid prediction for GeneMark_model.96891_t
Valid prediction for snap_scaffold_25-snap.1205-T1
Valid prediction for snap_scaffold_25-snap.1178-T1
Valid prediction for snap_scaffold_25-snap.1186-T1
Valid prediction for Augustus_model.g37029.t1
Valid prediction for GeneMark_model.96903_t
Valid prediction for GlimmerHMM_glimmerT_55504-T1
Valid prediction for GeneMark_model.96879_t
Couldn't classify 46787, 46896
Sorry, prediction pasa_asmbl_34245.p1 fails validation.
(GAC)	 CG	46787-46896	GT	AGG
(TCT)	 AG	47507-47643	GT	AGG
(GTA)	 AG	48717-48901	AC	AAA
-recovered pasa_asmbl_34245.p1, terminal, 48717, 48901
-recovered pasa_asmbl_34245.p1, internal, 47507, 47643
Valid prediction for GeneMark_model.96877_t
Valid prediction for GeneMark_model.96900_t
Couldn't classify 60329, 60400
Sorry, prediction pasa_asmbl_34243.p1 fails validation.
(ATG)	 GC	53992-54451	GT	CGG
(GTG)	 AG	54631-54785	GT	AGG
(CAG)	 AG	54997-55113	GT	TGG
(GAG)	 AG	55233-55410	GT	AGG
(CAT)	 AG	55866-55954	GT	CCG
(ATG)	 AG	56192-56243	GT	TGG
(CTC)	 AG	56511-56580	GT	AGG
(CGG)	 AG	56807-56933	GT	GGG
(TTG)	 AG	57043-57162	GT	GGG
(ATC)	 AG	57260-57436	GT	TGG
(ACT)	 AG	57809-57983	GT	AGG
(ATC)	 AG	58132-58712	GT	AGG
(CCT)	 AG	58900-59050	GT	CCG
(ATG)	 AG	59225-59311	GT	CGG
(ACA)	 AG	59417-59520	GT	AGG
(TTG)	 AG	59613-59670	GT	GGG
(GAC)	 AG	59803-59906	GT	TGG
(GCT)	 AG	60329-60400	TC	CCT
-recovered pasa_asmbl_34243.p1, initial, 53992, 54451
-recovered pasa_asmbl_34243.p1, initial, 56192, 56243
-recovered pasa_asmbl_34243.p1, initial, 59225, 59311
add_exon() Sorry, pasa_asmbl_34243.p1 56511-56580-terminal-3 is invalid.
-recovered pasa_asmbl_34243.p1, terminal, 56511, 56580
-recovered pasa_asmbl_34243.p1, internal, 54631, 54785
-recovered pasa_asmbl_34243.p1, internal, 54997, 55113
-recovered pasa_asmbl_34243.p1, internal, 55233, 55410
-recovered pasa_asmbl_34243.p1, internal, 55866, 55954
-recovered pasa_asmbl_34243.p1, internal, 56192, 56243
-recovered pasa_asmbl_34243.p1, internal, 56511, 56580
-recovered pasa_asmbl_34243.p1, internal, 56807, 56933
-recovered pasa_asmbl_34243.p1, internal, 57043, 57162
-recovered pasa_asmbl_34243.p1, internal, 57260, 57436
-recovered pasa_asmbl_34243.p1, internal, 57809, 57983
-recovered pasa_asmbl_34243.p1, internal, 58132, 58712
-recovered pasa_asmbl_34243.p1, internal, 58900, 59050
-recovered pasa_asmbl_34243.p1, internal, 59225, 59311
-recovered pasa_asmbl_34243.p1, internal, 59417, 59520
-recovered pasa_asmbl_34243.p1, internal, 59613, 59670
-recovered pasa_asmbl_34243.p1, internal, 59803, 59906
Valid prediction for GeneMark_model.96901_t
Valid prediction for GeneMark_model.96874_t
Valid prediction for Augustus_model.g37016.t1
Valid prediction for GlimmerHMM_glimmerT_55515-T1
Valid prediction for GlimmerHMM_glimmerT_55498-T1
Valid prediction for Augustus_model.g37026.t1
Valid prediction for Augustus_model.g37023.t1
Valid prediction for GlimmerHMM_glimmerT_55488-T1
Valid prediction for GlimmerHMM_glimmerT_55506-T1
Valid prediction for snap_scaffold_25-snap.1204-T1
Valid prediction for CodingQuarry_transcript_38645-T1
Valid prediction for snap_scaffold_25-snap.1179-T1
Valid prediction for GlimmerHMM_glimmerT_55501-T1
Valid prediction for snap_scaffold_25-snap.1184-T1
Valid prediction for CodingQuarry_transcript_38647-T1
Valid prediction for snap_scaffold_25-snap.1212-T1
Valid prediction for HiQ_model.g37034.t1
Valid prediction for snap_scaffold_25-snap.1211-T1
Valid prediction for snap_scaffold_25-snap.1177-T1
Valid prediction for Augustus_model.g37021.t1
Valid prediction for GlimmerHMM_glimmerT_55485-T1
Valid prediction for GlimmerHMM_glimmerT_55516-T1
Valid prediction for snap_scaffold_25-snap.1197-T1
Valid prediction for snap_scaffold_25-snap.1173-T1
Valid prediction for snap_scaffold_25-snap.1189-T1
Valid prediction for CodingQuarry_transcript_38649-T1
Valid prediction for GlimmerHMM_glimmerT_55492-T1
Valid prediction for HiQ_model.g37030.t1
Valid prediction for CodingQuarry_transcript_38646-T1
Valid prediction for pasa_asmbl_34246.p1
Valid prediction for GeneMark_model.96884_t
Valid prediction for snap_scaffold_25-snap.1195-T1
Valid prediction for GeneMark_model.96872_t
Valid prediction for snap_scaffold_25-snap.1192-T1
Valid prediction for GeneMark_model.96881_t
Valid prediction for snap_scaffold_25-snap.1190-T1
Valid prediction for snap_scaffold_25-snap.1176-T1
Valid prediction for GeneMark_model.96895_t
Valid prediction for Augustus_model.g37015.t1
Valid prediction for GlimmerHMM_glimmerT_55497-T1
Couldn't classify 196243, 196297
Couldn't classify 198031, 198238
Sorry, prediction pasa_asmbl_34238.p1 fails validation.
(GAC)	 TA	196243-196297	GT	AAG
(ATC)	 AG	196638-197799	GT	AGG
(TGG)	 AG	198031-198238	AG	GTA
-recovered pasa_asmbl_34238.p1, internal, 196638, 197799
Valid prediction for GlimmerHMM_glimmerT_55505-T1
Valid prediction for GeneMark_model.96898_t
Valid prediction for HiQ_model.g37013.t1
Valid prediction for snap_scaffold_25-snap.1194-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1199-T1
Couldn't classify 61381, 61591
Sorry, prediction pasa_asmbl_34240.p1 fails validation.
(CCC)	 CA	61381-61591	GT	AGG
(ATC)	 AG	61741-61788	GT	AAG
(TGA)	 AG	62068-62150	GT	CGG
(GAC)	 AG	62427-62542	GT	AGG
(GAT)	 AG	62643-62794	GT	AGG
(TCC)	 AG	63264-63361	GT	GTG
(TCA)	 AG	63558-64098	GT	AGG
(AGT)	 AG	64695-64865	GT	AGG
(GTT)	 AG	65013-65101	AT	GAA
-recovered pasa_asmbl_34240.p1, terminal, 65013, 65101
-recovered pasa_asmbl_34240.p1, internal, 61741, 61788
-recovered pasa_asmbl_34240.p1, internal, 62068, 62150
-recovered pasa_asmbl_34240.p1, internal, 62427, 62542
-recovered pasa_asmbl_34240.p1, internal, 62643, 62794
-recovered pasa_asmbl_34240.p1, internal, 63264, 63361
-recovered pasa_asmbl_34240.p1, internal, 63558, 64098
-recovered pasa_asmbl_34240.p1, internal, 64695, 64865
Valid prediction for snap_scaffold_25-snap.1188-T1
Couldn't classify 1518, 1645
Sorry, prediction pasa_asmbl_34249.p1 fails validation.
(AAA)	 CA	1518-1645	GT	AGG
(CCA)	 AG	2074-2173	GT	AGG
(GAT)	 AG	2537-2666	GT	AGG
(CGA)	 AG	2913-2992	GT	CGG
(GCT)	 AG	4608-4703	AG	GAA
-recovered pasa_asmbl_34249.p1, terminal, 4608, 4703
-recovered pasa_asmbl_34249.p1, internal, 2074, 2173
-recovered pasa_asmbl_34249.p1, internal, 2537, 2666
-recovered pasa_asmbl_34249.p1, internal, 2913, 2992
Valid prediction for GeneMark_model.96897_t
Valid prediction for Augustus_model.g37022.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8292, rend_intergenic: 7680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56548, rend_intergenic: 50030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57595, rend_intergenic: 57369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104706, rend_intergenic: 102783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198421
-exon list size: 601


building trellis

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84.4    
84.6    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 8292, rend_intergenic: 7680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56548, rend_intergenic: 50030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57595, rend_intergenic: 57369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104706, rend_intergenic: 102783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support