-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_14244338-14697343

-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_11-snap.2996-T1
Valid prediction for Augustus_model.g18720.t1
Valid prediction for Augustus_model.g18719.t1
Valid prediction for Augustus_model.g18723.t1
Valid prediction for GlimmerHMM_glimmerT_28285-T1
Valid prediction for GlimmerHMM_glimmerT_28270-T1
Valid prediction for pasa_asmbl_6087.p1
Valid prediction for snap_scaffold_11-snap.2997-T1
Couldn't classify 307309, 307351
Couldn't classify 329813, 329922
Sorry, prediction pasa_asmbl_6094.p1 fails validation.
(AGG)	 AC	307309-307351	GT	ACG
(TGT)	 AG	307601-307793	GT	AGG
(GGC)	 AG	308030-308154	GT	AGG
(ATG)	 AG	310181-310330	GT	TGG
(GTC)	 AG	310487-310606	GT	AGG
(GTC)	 AG	310743-310907	GT	CGG
(GTG)	 AG	311135-311281	GT	AGG
(GAG)	 AG	312361-312500	GT	AGG
(GTC)	 AG	313522-313651	GT	CCG
(TGC)	 AG	313931-314076	GT	AGG
(ATA)	 AG	314603-314732	GT	GCG
(TGC)	 AG	314930-315066	GT	AGG
(CTG)	 AG	316472-316601	GT	GGG
(ATG)	 AG	316849-316988	GT	ACG
(GCC)	 AG	317211-317343	GT	ACG
(TGT)	 AG	317488-317508	GT	TGG
(CAC)	 AG	317645-317784	GT	CGG
(ACT)	 AG	318947-319076	GT	CAG
(AAC)	 AG	319338-319477	GT	CGG
(GTG)	 AG	319625-319754	GT	ATG
(TGG)	 AG	321393-321535	GT	CGG
(GTT)	 AG	322962-323091	GT	ACG
(TTC)	 AG	323176-323318	GT	ATG
(ACT)	 AG	323514-323643	GT	AGG
(TGG)	 AG	324214-324333	GT	AGG
(GTA)	 AG	324559-324705	GT	ATG
(TGT)	 AG	324899-325015	GT	CTG
(CAT)	 AG	325608-325760	GT	ATG
(TGG)	 AG	326010-326084	GT	TGG
(TGT)	 AG	326427-326566	GT	AGG
(GTG)	 AG	326764-326887	GT	AGG
(GCG)	 AG	327194-327337	GT	TGG
(GGT)	 AG	327534-327698	GT	TAG
(CTT)	 AG	327866-327904	GT	TGG
(GCT)	 AG	328017-328155	GT	AAG
(GGA)	 AG	329190-329332	GT	CCG
(CTT)	 AG	329813-329922	GT	AGG
add_exon() Sorry, pasa_asmbl_6094.p1 310181-310330-initial-1 is invalid.
-recovered pasa_asmbl_6094.p1, initial, 310181, 310330
add_exon() Sorry, pasa_asmbl_6094.p1 316849-316988-initial-1 is invalid.
-recovered pasa_asmbl_6094.p1, initial, 316849, 316988
-recovered pasa_asmbl_6094.p1, internal, 307601, 307793
-recovered pasa_asmbl_6094.p1, internal, 308030, 308154
-recovered pasa_asmbl_6094.p1, internal, 310181, 310330
-recovered pasa_asmbl_6094.p1, internal, 310487, 310606
-recovered pasa_asmbl_6094.p1, internal, 310743, 310907
-recovered pasa_asmbl_6094.p1, internal, 311135, 311281
-recovered pasa_asmbl_6094.p1, internal, 312361, 312500
-recovered pasa_asmbl_6094.p1, internal, 313522, 313651
-recovered pasa_asmbl_6094.p1, internal, 313931, 314076
-recovered pasa_asmbl_6094.p1, internal, 314603, 314732
-recovered pasa_asmbl_6094.p1, internal, 314930, 315066
-recovered pasa_asmbl_6094.p1, internal, 316472, 316601
-recovered pasa_asmbl_6094.p1, internal, 316849, 316988
-recovered pasa_asmbl_6094.p1, internal, 317211, 317343
-recovered pasa_asmbl_6094.p1, internal, 317488, 317508
-recovered pasa_asmbl_6094.p1, internal, 317645, 317784
-recovered pasa_asmbl_6094.p1, internal, 318947, 319076
-recovered pasa_asmbl_6094.p1, internal, 319338, 319477
-recovered pasa_asmbl_6094.p1, internal, 319625, 319754
-recovered pasa_asmbl_6094.p1, internal, 321393, 321535
-recovered pasa_asmbl_6094.p1, internal, 322962, 323091
-recovered pasa_asmbl_6094.p1, internal, 323176, 323318
-recovered pasa_asmbl_6094.p1, internal, 323514, 323643
-recovered pasa_asmbl_6094.p1, internal, 324214, 324333
-recovered pasa_asmbl_6094.p1, internal, 324559, 324705
-recovered pasa_asmbl_6094.p1, internal, 324899, 325015
-recovered pasa_asmbl_6094.p1, internal, 325608, 325760
-recovered pasa_asmbl_6094.p1, internal, 326010, 326084
-recovered pasa_asmbl_6094.p1, internal, 326427, 326566
-recovered pasa_asmbl_6094.p1, internal, 326764, 326887
-recovered pasa_asmbl_6094.p1, internal, 327194, 327337
-recovered pasa_asmbl_6094.p1, internal, 327534, 327698
-recovered pasa_asmbl_6094.p1, internal, 327866, 327904
-recovered pasa_asmbl_6094.p1, internal, 328017, 328155
-recovered pasa_asmbl_6094.p1, internal, 329190, 329332
-recovered pasa_asmbl_6094.p1, internal, 329813, 329922
Valid prediction for snap_scaffold_11-snap.2995-T1
Valid prediction for snap_scaffold_11-snap.2992-T1
Couldn't classify 258786, 259178
Sorry, prediction pasa_asmbl_6082.p1 fails validation.
(CAA)	 TG	258786-259178	AA	AAA
Valid prediction for snap_scaffold_11-snap.3010-T1
Valid prediction for GlimmerHMM_glimmerT_28277-T1
Valid prediction for snap_scaffold_11-snap.2994-T1
Valid prediction for pasa_asmbl_6086.p1
Valid prediction for Augustus_model.g18717.t1
Valid prediction for GlimmerHMM_glimmerT_28266-T1
Valid prediction for GlimmerHMM_glimmerT_28273-T1
Couldn't classify 334816, 334974
Sorry, prediction pasa_asmbl_6095.p1 fails validation.
(CTG)	 AG	334816-334974	GT	CCG
(TTC)	 AG	335287-335364	GT	TGG
(AGA)	 AG	336330-336416	GT	CGG
(GGG)	 AG	336925-336978	GT	TTG
(GGT)	 AG	337470-337565	GT	CAG
(GGC)	 AG	338030-338083	GT	AAG
(GGT)	 AG	339070-339123	GT	GGG
(GGA)	 AG	339539-339592	GT	TGG
(GGA)	 AG	340112-340183	GT	CAG
(GGA)	 AG	340467-340502	GT	AGG
(GGA)	 AG	340597-340663	GT	CAG
(GCC)	 AG	340765-340947	GT	AGG
(GTT)	 AG	341405-341482	GT	TGG
(GGC)	 AG	342596-342766	GT	AGG
(CCG)	 AG	344047-344201	AC	AAA
-recovered pasa_asmbl_6095.p1, terminal, 344047, 344201
-recovered pasa_asmbl_6095.p1, internal, 334816, 334974
-recovered pasa_asmbl_6095.p1, internal, 335287, 335364
-recovered pasa_asmbl_6095.p1, internal, 336330, 336416
-recovered pasa_asmbl_6095.p1, internal, 336925, 336978
-recovered pasa_asmbl_6095.p1, internal, 337470, 337565
-recovered pasa_asmbl_6095.p1, internal, 338030, 338083
-recovered pasa_asmbl_6095.p1, internal, 339070, 339123
-recovered pasa_asmbl_6095.p1, internal, 339539, 339592
-recovered pasa_asmbl_6095.p1, internal, 340112, 340183
-recovered pasa_asmbl_6095.p1, internal, 340467, 340502
-recovered pasa_asmbl_6095.p1, internal, 340597, 340663
-recovered pasa_asmbl_6095.p1, internal, 340765, 340947
-recovered pasa_asmbl_6095.p1, internal, 341405, 341482
-recovered pasa_asmbl_6095.p1, internal, 342596, 342766
Valid prediction for GlimmerHMM_glimmerT_28265-T1
Valid prediction for GlimmerHMM_glimmerT_28261-T1
Valid prediction for GlimmerHMM_glimmerT_28276-T1
Valid prediction for snap_scaffold_11-snap.2998-T1
Valid prediction for HiQ_model.g18721.t1
Valid prediction for HiQ_model.g18722.t1
Valid prediction for GlimmerHMM_glimmerT_28279-T1
Couldn't classify 304914, 305184
Couldn't classify 307085, 307170
Sorry, prediction pasa_asmbl_6246.p1 fails validation.
(GTT)	 CA	304914-305184	GT	TGG
(TCT)	 AG	307085-307170	GT	TGG
-recovered pasa_asmbl_6246.p1, internal, 307085, 307170
Valid prediction for GlimmerHMM_glimmerT_28286-T1
Valid prediction for snap_scaffold_11-snap.2991-T1
Couldn't classify 258786, 259110
Sorry, prediction pasa_asmbl_6084.p1 fails validation.
(CAA)	 TG	258786-259110	GT	GGG
(TGA)	 AG	260760-260767	CC	AGC
-recovered pasa_asmbl_6084.p1, terminal, 260760, 260767
Valid prediction for CodingQuarry_transcript_8310-T1
Valid prediction for snap_scaffold_11-snap.2993-T1
Valid prediction for GlimmerHMM_glimmerT_28278-T1
Valid prediction for snap_scaffold_11-snap.3012-T1
Valid prediction for GlimmerHMM_glimmerT_28259-T1
Valid prediction for snap_scaffold_11-snap.2990-T1
Valid prediction for snap_scaffold_11-snap.2976-T1
Valid prediction for GlimmerHMM_glimmerT_28275-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_11-snap.3006-T1
Valid prediction for Augustus_model.g18711.t1
Valid prediction for snap_scaffold_11-snap.3004-T1
Valid prediction for Augustus_model.g18714.t1
Valid prediction for CodingQuarry_transcript_8311-T1
Valid prediction for GlimmerHMM_glimmerT_28283-T1
Valid prediction for GlimmerHMM_glimmerT_28268-T1
Valid prediction for snap_scaffold_11-snap.2985-T1
Valid prediction for Augustus_model.g18730.t1
Valid prediction for HiQ_model.g18710.t1
Valid prediction for snap_scaffold_11-snap.3009-T1
Valid prediction for Augustus_model.g18726.t1
Valid prediction for Augustus_model.g18727.t1
Valid prediction for GlimmerHMM_glimmerT_28282-T1
Valid prediction for snap_scaffold_11-snap.3003-T1
Valid prediction for snap_scaffold_11-snap.2980-T1
Couldn't classify 225799, 225942
Sorry, prediction pasa_asmbl_7167.p1 fails validation.
(ATG)	 TC	224607-224750	GT	AGG
(AAA)	 AG	225087-225259	GT	AGG
(TCG)	 AG	225391-225529	GT	AGG
(GTG)	 AG	225799-225942	TA	CCT
-recovered pasa_asmbl_7167.p1, initial, 224607, 224750
-recovered pasa_asmbl_7167.p1, internal, 225087, 225259
-recovered pasa_asmbl_7167.p1, internal, 225391, 225529
Couldn't classify 266630, 266664
Sorry, prediction pasa_asmbl_7163.p1 fails validation.
(TTA)	 AG	266630-266664	GT	AGG
(GGG)	 AG	266901-266988	GT	GTG
(GAC)	 AG	267072-267127	GT	AGG
(CCG)	 AG	267856-268015	AC	GAA
-recovered pasa_asmbl_7163.p1, terminal, 267856, 268015
-recovered pasa_asmbl_7163.p1, internal, 266630, 266664
-recovered pasa_asmbl_7163.p1, internal, 266901, 266988
-recovered pasa_asmbl_7163.p1, internal, 267072, 267127
Valid prediction for Augustus_model.g18712.t1
Valid prediction for snap_scaffold_11-snap.2982-T1
Valid prediction for GlimmerHMM_glimmerT_28280-T1
Valid prediction for snap_scaffold_11-snap.3008-T1
Couldn't classify 231031, 231213
Sorry, prediction pasa_asmbl_7165.p1 fails validation.
(CGG)	 AG	231031-231213	GT	AGG
(GGT)	 AG	231438-231581	GT	GGG
(GTG)	 AG	232231-232365	GT	GGG
(GTG)	 AG	232508-232669	GT	AGG
(AGG)	 AG	232990-233162	GT	AGG
(ACT)	 AG	233364-234144	GT	AGG
(GGC)	 AG	234238-234396	GT	AGG
(GCC)	 AG	235441-235641	GT	AGG
(GAT)	 AG	235986-236027	GT	AGG
(CAG)	 AG	238546-238734	AC	AGA
-recovered pasa_asmbl_7165.p1, terminal, 238546, 238734
-recovered pasa_asmbl_7165.p1, internal, 231031, 231213
-recovered pasa_asmbl_7165.p1, internal, 231438, 231581
-recovered pasa_asmbl_7165.p1, internal, 232231, 232365
-recovered pasa_asmbl_7165.p1, internal, 232508, 232669
-recovered pasa_asmbl_7165.p1, internal, 232990, 233162
-recovered pasa_asmbl_7165.p1, internal, 233364, 234144
-recovered pasa_asmbl_7165.p1, internal, 234238, 234396
-recovered pasa_asmbl_7165.p1, internal, 235441, 235641
-recovered pasa_asmbl_7165.p1, internal, 235986, 236027
Valid prediction for snap_scaffold_11-snap.2977-T1
Valid prediction for Augustus_model.g18718.t1
Valid prediction for snap_scaffold_11-snap.2984-T1
Valid prediction for CodingQuarry_transcript_8308-T1
Valid prediction for snap_scaffold_11-snap.2999-T1
Valid prediction for GlimmerHMM_glimmerT_28274-T1
Valid prediction for GlimmerHMM_glimmerT_28281-T1
Valid prediction for snap_scaffold_11-snap.2988-T1
Valid prediction for Augustus_model.g18725.t1
Couldn't classify 31739, 31817
Sorry, prediction pasa_asmbl_7171.p1 fails validation.
(GAT)	 AG	31739-31817	GT	GCG
(CAC)	 AG	32585-32773	GT	CGG
(ATG)	 AG	34117-34178	GC	AGG
add_exon() Sorry, pasa_asmbl_7171.p1 34117-34178-initial-1 is invalid.
-recovered pasa_asmbl_7171.p1, initial, 34117, 34178
-recovered pasa_asmbl_7171.p1, terminal, 34117, 34178
-recovered pasa_asmbl_7171.p1, internal, 31739, 31817
-recovered pasa_asmbl_7171.p1, internal, 32585, 32773
-recovered pasa_asmbl_7171.p1, internal, 34117, 34178
Valid prediction for snap_scaffold_11-snap.2986-T1
Valid prediction for snap_scaffold_11-snap.2978-T1
Valid prediction for GlimmerHMM_glimmerT_28263-T1
Valid prediction for snap_scaffold_11-snap.2983-T1
Valid prediction for snap_scaffold_11-snap.3000-T1
Valid prediction for Augustus_model.g18713.t1
Valid prediction for snap_scaffold_11-snap.2979-T1
Valid prediction for snap_scaffold_11-snap.2989-T1
Valid prediction for Augustus_model.g18715.t1
Valid prediction for GlimmerHMM_glimmerT_28262-T1
Valid prediction for GlimmerHMM_glimmerT_28260-T1
Valid prediction for GlimmerHMM_glimmerT_28271-T1
Valid prediction for snap_scaffold_11-snap.3007-T1
Valid prediction for GlimmerHMM_glimmerT_28272-T1
Valid prediction for CodingQuarry_transcript_8307-T1
Valid prediction for Augustus_model.g18729.t1
Couldn't classify 31412, 31759
Sorry, prediction pasa_asmbl_7172.p1 fails validation.
(GAT)	 AT	31412-31759	AG	GGA
Valid prediction for snap_scaffold_11-snap.3005-T1
Couldn't classify 28961, 29107
Sorry, prediction CodingQuarry_transcript_8312-T1 fails validation.
(ATG)	 AC	28365-28383	GT	TGG
(TAT)	 AG	28589-28708	GT	AGG
(CTG)	 CG	28961-29107	GT	TGG
(AGA)	 AG	31383-31588	GT	AGG
(CTG)	 AG	31683-31721	AG	GAA
-recovered CodingQuarry_transcript_8312-T1, initial, 28365, 28383
-recovered CodingQuarry_transcript_8312-T1, terminal, 31683, 31721
-recovered CodingQuarry_transcript_8312-T1, internal, 28589, 28708
-recovered CodingQuarry_transcript_8312-T1, internal, 31383, 31588
Valid prediction for snap_scaffold_11-snap.3011-T1
Valid prediction for snap_scaffold_11-snap.2975-T1
Valid prediction for GlimmerHMM_glimmerT_28267-T1
Valid prediction for HiQ_model.g18716.t1
Valid prediction for snap_scaffold_11-snap.2981-T1
Valid prediction for Augustus_model.g18728.t1
Valid prediction for GlimmerHMM_glimmerT_28269-T1
Valid prediction for snap_scaffold_11-snap.3002-T1
Valid prediction for CodingQuarry_transcript_8306-T1
Couldn't classify 283538, 283726
Sorry, prediction pasa_asmbl_7161.p1 fails validation.
(CAG)	 GG	283538-283726	GT	AGG
(CTT)	 AG	284547-284709	GT	AGG
(AGA)	 AG	284917-284992	GT	AGG
(TCC)	 AG	285262-285427	GC	GAG
add_exon() Sorry, pasa_asmbl_7161.p1 284547-284709-terminal-3 is invalid.
-recovered pasa_asmbl_7161.p1, terminal, 284547, 284709
-recovered pasa_asmbl_7161.p1, terminal, 285262, 285427
-recovered pasa_asmbl_7161.p1, internal, 284547, 284709
-recovered pasa_asmbl_7161.p1, internal, 284917, 284992
-recovered pasa_asmbl_7161.p1, internal, 285262, 285427
Valid prediction for snap_scaffold_11-snap.2987-T1
Couldn't classify 281107, 281253
Couldn't classify 282174, 282371
Sorry, prediction pasa_asmbl_7162.p1 fails validation.
(AAC)	 GC	281107-281253	GT	AGG
(GCC)	 AG	282174-282371	GC	GGG
-recovered pasa_asmbl_7162.p1, internal, 282174, 282371
Valid prediction for GlimmerHMM_glimmerT_28264-T1
Valid prediction for Augustus_model.g18724.t1
Valid prediction for pasa_asmbl_7168.p1
Valid prediction for snap_scaffold_11-snap.3001-T1
Valid prediction for GlimmerHMM_glimmerT_28284-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 450717, rend_intergenic: 447368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 453006
-exon list size: 468


building trellis

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53.8    
54.0    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 450717, rend_intergenic: 447368  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