-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_6208112-6473298

-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_31776-T1
Valid prediction for CodingQuarry_transcript_13077-T1
Valid prediction for GlimmerHMM_glimmerT_31764-T1
Valid prediction for snap_scaffold_13-snap.1173-T1
Valid prediction for snap_scaffold_13-snap.1201-T1
Valid prediction for HiQ_model.g21143.t1
Valid prediction for GlimmerHMM_glimmerT_31769-T1
Valid prediction for pasa_asmbl_10916.p1
Valid prediction for GlimmerHMM_glimmerT_31761-T1
Valid prediction for GlimmerHMM_glimmerT_31754-T1
Valid prediction for snap_scaffold_13-snap.1183-T1
Valid prediction for CodingQuarry_transcript_13073-T1
Couldn't classify 198399, 198539
Sorry, prediction pasa_asmbl_10933.p2 fails validation.
(ATG)	 CT	197801-198001	GT	AGG
(ACT)	 AG	198120-198263	GT	ACG
(ACC)	 AG	198399-198539	CA	ATC
-recovered pasa_asmbl_10933.p2, initial, 197801, 198001
-recovered pasa_asmbl_10933.p2, internal, 198120, 198263
Valid prediction for Augustus_model.g21134.t1
Valid prediction for GlimmerHMM_glimmerT_31771-T1
Valid prediction for Augustus_model.g21140.t1
Valid prediction for CodingQuarry_transcript_13074-T1
Valid prediction for snap_scaffold_13-snap.1193-T1
Valid prediction for GlimmerHMM_glimmerT_31773-T1
Valid prediction for pasa_asmbl_10934.p1
Valid prediction for pasa_asmbl_10924.p1
Valid prediction for CodingQuarry_transcript_13076-T1
Valid prediction for GlimmerHMM_glimmerT_31758-T1
Valid prediction for pasa_asmbl_11594.p1
Valid prediction for snap_scaffold_13-snap.1184-T1
Valid prediction for snap_scaffold_13-snap.1199-T1
Valid prediction for CodingQuarry_transcript_13065-T1
Valid prediction for GlimmerHMM_glimmerT_31755-T1
Valid prediction for snap_scaffold_13-snap.1186-T1
Valid prediction for snap_scaffold_13-snap.1187-T1
Valid prediction for snap_scaffold_13-snap.1192-T1
Valid prediction for Augustus_model.g21131.t1
Valid prediction for pasa_asmbl_10937.p1
Valid prediction for HiQ_model.g21142.t1
Valid prediction for snap_scaffold_13-snap.1182-T1
Couldn't classify 81640, 81846
Sorry, prediction pasa_asmbl_10922.p1 fails validation.
(ACA)	 GG	81640-81846	GT	AGG
(ATT)	 AG	82485-82555	GT	AGG
(AAC)	 AG	82687-82774	GT	AGG
(GCC)	 AG	83430-83582	GT	ATG
(ACA)	 AG	86361-86525	GT	AGG
(TCC)	 AG	87284-87345	GT	AGG
(AAA)	 AG	87807-87918	GT	AGG
(GGA)	 AG	88219-88318	GT	AGG
(GGA)	 AG	88432-88537	GT	GTG
(CCA)	 AG	88923-89076	AC	AAA
-recovered pasa_asmbl_10922.p1, terminal, 88923, 89076
-recovered pasa_asmbl_10922.p1, internal, 82485, 82555
-recovered pasa_asmbl_10922.p1, internal, 82687, 82774
-recovered pasa_asmbl_10922.p1, internal, 83430, 83582
-recovered pasa_asmbl_10922.p1, internal, 86361, 86525
-recovered pasa_asmbl_10922.p1, internal, 87284, 87345
-recovered pasa_asmbl_10922.p1, internal, 87807, 87918
-recovered pasa_asmbl_10922.p1, internal, 88219, 88318
-recovered pasa_asmbl_10922.p1, internal, 88432, 88537
Valid prediction for HiQ_model.g21136.t1
Valid prediction for snap_scaffold_13-snap.1179-T1
Valid prediction for GlimmerHMM_glimmerT_31760-T1
Valid prediction for snap_scaffold_13-snap.1177-T1
Valid prediction for CodingQuarry_transcript_13066-T1
Valid prediction for GlimmerHMM_glimmerT_31774-T1
Valid prediction for snap_scaffold_13-snap.1167-T1
Valid prediction for GlimmerHMM_glimmerT_31775-T1
Valid prediction for snap_scaffold_13-snap.1196-T1
Valid prediction for pasa_asmbl_10919.p1
Valid prediction for HiQ_model.g21133.t1
Valid prediction for snap_scaffold_13-snap.1171-T1
Valid prediction for snap_scaffold_13-snap.1176-T1
Valid prediction for snap_scaffold_13-snap.1190-T1
Valid prediction for snap_scaffold_13-snap.1172-T1
Valid prediction for snap_scaffold_13-snap.1194-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: -)Valid prediction for snap_scaffold_13-snap.1200-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g21138.t1
Valid prediction for pasa_asmbl_9784.p1
Valid prediction for snap_scaffold_13-snap.1180-T1
Valid prediction for snap_scaffold_13-snap.1188-T1
Valid prediction for GlimmerHMM_glimmerT_31778-T1
Valid prediction for snap_scaffold_13-snap.1175-T1
Valid prediction for HiQ_model.g21141.t1
Valid prediction for Augustus_model.g21135.t1
Valid prediction for Augustus_model.g21132.t1
Valid prediction for snap_scaffold_13-snap.1166-T1
Valid prediction for snap_scaffold_13-snap.1169-T1
Valid prediction for snap_scaffold_13-snap.1191-T1
Valid prediction for CodingQuarry_transcript_13069-T1
Valid prediction for GlimmerHMM_glimmerT_31753-T1
Valid prediction for CodingQuarry_transcript_13075-T1
Valid prediction for HiQ_model.g21139.t1
Valid prediction for GlimmerHMM_glimmerT_31770-T1
Valid prediction for CodingQuarry_transcript_13067-T1
Valid prediction for snap_scaffold_13-snap.1178-T1
Valid prediction for snap_scaffold_13-snap.1189-T1
Valid prediction for GlimmerHMM_glimmerT_31765-T1
Valid prediction for snap_scaffold_13-snap.1168-T1
Valid prediction for Augustus_model.g21145.t1
Couldn't classify 90681, 90708
Couldn't classify 90736, 90786
Sorry, prediction CodingQuarry_transcript_13070-T1 fails validation.
(ATG)	 AG	89852-89960	GT	GGG
(CTG)	 AG	90177-90364	GT	AGG
(GGT)	 AG	90463-90576	GT	TGG
(AAC)	 AG	90681-90708	CC	GCC
(AGA)	 AC	90736-90786	GT	AGG
(GTG)	 AG	90889-91049	GT	AGG
(GTG)	 AG	91153-91479	CC	GAC
-recovered CodingQuarry_transcript_13070-T1, initial, 89852, 89960
-recovered CodingQuarry_transcript_13070-T1, terminal, 91153, 91479
-recovered CodingQuarry_transcript_13070-T1, internal, 89852, 89960
-recovered CodingQuarry_transcript_13070-T1, internal, 90177, 90364
-recovered CodingQuarry_transcript_13070-T1, internal, 90463, 90576
-recovered CodingQuarry_transcript_13070-T1, internal, 90889, 91049
Valid prediction for snap_scaffold_13-snap.1195-T1
Valid prediction for snap_scaffold_13-snap.1181-T1
Valid prediction for pasa_asmbl_9778.p1
Valid prediction for GlimmerHMM_glimmerT_31763-T1
Valid prediction for GlimmerHMM_glimmerT_31779-T1
Valid prediction for snap_scaffold_13-snap.1185-T1
Valid prediction for pasa_asmbl_9781.p1
Valid prediction for snap_scaffold_13-snap.1170-T1
Valid prediction for pasa_asmbl_9779.p1
Valid prediction for Augustus_model.g21144.t1
Valid prediction for GlimmerHMM_glimmerT_31757-T1
Valid prediction for GlimmerHMM_glimmerT_31766-T1
Couldn't classify 90177, 90219
Couldn't classify 90716, 90786
Sorry, prediction CodingQuarry_transcript_13072-T1 fails validation.
(ATG)	 AG	78901-78975	GT	AGG
(ATT)	 AG	79844-80076	GT	AGG
(ATC)	 AG	80188-80285	GT	AGG
(GAA)	 AG	80511-80620	GT	AGG
(ACC)	 AG	80788-80898	GT	TGG
(ATG)	 AG	81038-81123	GT	AGG
(GAT)	 AG	81222-81309	GT	GGG
(AAT)	 AG	81415-81583	GT	GGG
(GCT)	 AG	81700-81767	GT	AGG
(TTT)	 AG	82035-82178	GT	GGG
(GAG)	 AG	82285-82454	GT	GAG
(TGA)	 AG	82636-82725	GT	TGG
(GTA)	 AG	82806-82962	GT	GGG
(CAC)	 AG	83141-83260	GT	AGG
(AGG)	 AG	83337-83506	GT	AGG
(GCA)	 AG	83692-83809	GT	AGG
(TTC)	 AG	83945-84040	GT	CGG
(GTG)	 AG	84198-84301	GT	AAG
(GTT)	 AG	84389-84520	GT	CAG
(CTT)	 AG	84645-84807	GT	AGG
(GAT)	 AG	84922-85035	GT	AGG
(GTG)	 AG	85151-85249	GT	ATG
(AAA)	 AG	85358-85473	GT	AAG
(CCC)	 AG	85572-85718	GT	AGG
(GTT)	 AG	85871-85960	GT	GGG
(GGC)	 AG	86050-86185	GT	AGG
(GTA)	 AG	86294-86350	GT	GGG
(CCT)	 AG	86802-86934	GT	AGG
(CGG)	 AG	87113-87182	GT	AGG
(GTG)	 AG	87285-87474	GT	AGG
(CAA)	 AG	87887-87976	GT	AGG
(GGT)	 AG	88085-88171	GT	AAG
(GAA)	 AG	88297-88356	GT	CTG
(GGT)	 AG	88894-88965	GT	AGG
(CCC)	 AG	89166-89300	GT	TGG
(AAG)	 AG	89828-89960	GT	GGG
(CTG)	 AG	90177-90219	AG	CCA
(CTT)	 CC	90716-90786	GT	AGG
(GTG)	 AG	90889-91049	GT	AGG
(GTG)	 AG	91153-91479	CC	GAC
-recovered CodingQuarry_transcript_13072-T1, initial, 78901, 78975
-recovered CodingQuarry_transcript_13072-T1, initial, 81038, 81123
add_exon() Sorry, CodingQuarry_transcript_13072-T1 79844-80076-terminal-2 is invalid.
-recovered CodingQuarry_transcript_13072-T1, terminal, 79844, 80076
-recovered CodingQuarry_transcript_13072-T1, terminal, 91153, 91479
-recovered CodingQuarry_transcript_13072-T1, internal, 78901, 78975
-recovered CodingQuarry_transcript_13072-T1, internal, 79844, 80076
-recovered CodingQuarry_transcript_13072-T1, internal, 80188, 80285
-recovered CodingQuarry_transcript_13072-T1, internal, 80511, 80620
-recovered CodingQuarry_transcript_13072-T1, internal, 80788, 80898
-recovered CodingQuarry_transcript_13072-T1, internal, 81038, 81123
-recovered CodingQuarry_transcript_13072-T1, internal, 81222, 81309
-recovered CodingQuarry_transcript_13072-T1, internal, 81415, 81583
-recovered CodingQuarry_transcript_13072-T1, internal, 81700, 81767
-recovered CodingQuarry_transcript_13072-T1, internal, 82035, 82178
-recovered CodingQuarry_transcript_13072-T1, internal, 82285, 82454
-recovered CodingQuarry_transcript_13072-T1, internal, 82636, 82725
-recovered CodingQuarry_transcript_13072-T1, internal, 82806, 82962
-recovered CodingQuarry_transcript_13072-T1, internal, 83141, 83260
-recovered CodingQuarry_transcript_13072-T1, internal, 83337, 83506
-recovered CodingQuarry_transcript_13072-T1, internal, 83692, 83809
-recovered CodingQuarry_transcript_13072-T1, internal, 83945, 84040
-recovered CodingQuarry_transcript_13072-T1, internal, 84198, 84301
-recovered CodingQuarry_transcript_13072-T1, internal, 84389, 84520
-recovered CodingQuarry_transcript_13072-T1, internal, 84645, 84807
-recovered CodingQuarry_transcript_13072-T1, internal, 84922, 85035
-recovered CodingQuarry_transcript_13072-T1, internal, 85151, 85249
-recovered CodingQuarry_transcript_13072-T1, internal, 85358, 85473
-recovered CodingQuarry_transcript_13072-T1, internal, 85572, 85718
-recovered CodingQuarry_transcript_13072-T1, internal, 85871, 85960
-recovered CodingQuarry_transcript_13072-T1, internal, 86050, 86185
-recovered CodingQuarry_transcript_13072-T1, internal, 86294, 86350
-recovered CodingQuarry_transcript_13072-T1, internal, 86802, 86934
-recovered CodingQuarry_transcript_13072-T1, internal, 87113, 87182
-recovered CodingQuarry_transcript_13072-T1, internal, 87285, 87474
-recovered CodingQuarry_transcript_13072-T1, internal, 87887, 87976
-recovered CodingQuarry_transcript_13072-T1, internal, 88085, 88171
-recovered CodingQuarry_transcript_13072-T1, internal, 88297, 88356
-recovered CodingQuarry_transcript_13072-T1, internal, 88894, 88965
-recovered CodingQuarry_transcript_13072-T1, internal, 89166, 89300
-recovered CodingQuarry_transcript_13072-T1, internal, 89828, 89960
-recovered CodingQuarry_transcript_13072-T1, internal, 90889, 91049
Valid prediction for Augustus_model.g21146.t1
Valid prediction for snap_scaffold_13-snap.1198-T1
Couldn't classify 29578, 29595
Couldn't classify 33263, 33360
Sorry, prediction pasa_asmbl_10350.p1 fails validation.
(CAG)	 AC	29578-29595	GT	GGG
(GTC)	 AG	30990-31040	GT	AAG
(GTT)	 AG	32241-32333	GT	ACG
(GTC)	 AG	33009-33090	GT	AGG
(GAG)	 AG	33263-33360	GA	GAG
-recovered pasa_asmbl_10350.p1, internal, 30990, 31040
-recovered pasa_asmbl_10350.p1, internal, 32241, 32333
-recovered pasa_asmbl_10350.p1, internal, 33009, 33090
Valid prediction for snap_scaffold_13-snap.1197-T1
Valid prediction for GlimmerHMM_glimmerT_31759-T1
Valid prediction for GlimmerHMM_glimmerT_31768-T1
Valid prediction for pasa_asmbl_9777.p1
Valid prediction for CodingQuarry_transcript_13071-T1
Valid prediction for GlimmerHMM_glimmerT_31762-T1
Valid prediction for GlimmerHMM_glimmerT_31777-T1
Valid prediction for snap_scaffold_13-snap.1174-T1
Valid prediction for HiQ_model.g21137.t1
Valid prediction for GlimmerHMM_glimmerT_31756-T1
Valid prediction for GlimmerHMM_glimmerT_31772-T1
Valid prediction for CodingQuarry_transcript_13068-T1
Valid prediction for GlimmerHMM_glimmerT_31767-T1
Valid prediction for GlimmerHMM_glimmerT_31780-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10341, rend_intergenic: 8848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185314, rend_intergenic: 174106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207881, rend_intergenic: 203166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240826, rend_intergenic: 233368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 255698, rend_intergenic: 250429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256031, rend_intergenic: 255870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258684, rend_intergenic: 256269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 265187
-exon list size: 531


building trellis

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79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 10341, rend_intergenic: 8848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185314, rend_intergenic: 174106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207881, rend_intergenic: 203166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240826, rend_intergenic: 233368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 255698, rend_intergenic: 250429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256031, rend_intergenic: 255870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258684, rend_intergenic: 256269  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