-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_298620-620610

-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_48843-T1
Valid prediction for pasa_asmbl_29858.p1
Valid prediction for snap_scaffold_22-snap.84-T1
Valid prediction for Augustus_model.g32591.t1
Valid prediction for GlimmerHMM_glimmerT_48823-T1
Valid prediction for GlimmerHMM_glimmerT_48842-T1
Valid prediction for GlimmerHMM_glimmerT_48813-T1
Valid prediction for snap_scaffold_22-snap.87-T1
Valid prediction for CodingQuarry_transcript_34073-T1
Valid prediction for HiQ_model.g32610.t1
Valid prediction for snap_scaffold_22-snap.97-T1
Valid prediction for Augustus_model.g32626.t1
Couldn't classify 294472, 294623
Sorry, prediction pasa_asmbl_29867.p1 fails validation.
(ATC)	 AA	294472-294623	GT	AGG
(TAT)	 AG	294884-295073	GT	AGG
(CTG)	 AG	295228-295389	GT	CGG
(TTT)	 AG	295492-295651	GT	CGG
(AAA)	 AG	295753-295895	GT	AGG
(GAA)	 AG	296063-296258	GT	AGG
(ATG)	 AG	296366-296502	AA	AAA
-recovered pasa_asmbl_29867.p1, terminal, 296366, 296502
-recovered pasa_asmbl_29867.p1, internal, 294884, 295073
-recovered pasa_asmbl_29867.p1, internal, 295228, 295389
-recovered pasa_asmbl_29867.p1, internal, 295492, 295651
-recovered pasa_asmbl_29867.p1, internal, 295753, 295895
-recovered pasa_asmbl_29867.p1, internal, 296063, 296258
Valid prediction for GlimmerHMM_glimmerT_48833-T1
Valid prediction for GlimmerHMM_glimmerT_48841-T1
Couldn't classify 7895, 7926
Sorry, prediction pasa_asmbl_29836.p1 fails validation.
(GTG)	 GG	7895-7926	GT	AGG
(CCC)	 AG	8583-8722	GT	CGG
(TCC)	 AG	9255-9395	GT	CAG
(AGG)	 AG	9658-9800	GT	AGG
(GGG)	 AG	10106-10276	TG	AAT
-recovered pasa_asmbl_29836.p1, terminal, 10106, 10276
-recovered pasa_asmbl_29836.p1, internal, 8583, 8722
-recovered pasa_asmbl_29836.p1, internal, 9255, 9395
-recovered pasa_asmbl_29836.p1, internal, 9658, 9800
Valid prediction for Augustus_model.g32625.t1
Valid prediction for CodingQuarry_transcript_34084-T1
Valid prediction for CodingQuarry_transcript_34074-T1
Valid prediction for snap_scaffold_22-snap.102-T1
Valid prediction for snap_scaffold_22-snap.75-T1
Couldn't classify 17542, 17659
Sorry, prediction pasa_asmbl_29838.p1 fails validation.
(GCC)	 GG	17542-17659	GT	AGG
(ACC)	 AG	19802-19900	GT	AGG
(CCT)	 AG	20132-20901	GT	AGG
(GGA)	 AG	22212-22260	GT	AGG
(ACA)	 AG	23947-24035	GT	AGG
(ACA)	 AG	24819-24932	CT	AAC
-recovered pasa_asmbl_29838.p1, terminal, 24819, 24932
-recovered pasa_asmbl_29838.p1, internal, 19802, 19900
-recovered pasa_asmbl_29838.p1, internal, 20132, 20901
-recovered pasa_asmbl_29838.p1, internal, 22212, 22260
-recovered pasa_asmbl_29838.p1, internal, 23947, 24035
Valid prediction for GlimmerHMM_glimmerT_48809-T1
Valid prediction for GlimmerHMM_glimmerT_48840-T1
Valid prediction for Augustus_model.g32623.t1
Valid prediction for HiQ_model.g32624.t1
Valid prediction for Augustus_model.g32592.t1
Valid prediction for CodingQuarry_transcript_34080-T1
Valid prediction for CodingQuarry_transcript_34079-T1
Valid prediction for Augustus_model.g32614.t1
Valid prediction for GlimmerHMM_glimmerT_48818-T1
Valid prediction for GlimmerHMM_glimmerT_48828-T1
Valid prediction for snap_scaffold_22-snap.123-T1
Valid prediction for snap_scaffold_22-snap.95-T1
Valid prediction for snap_scaffold_22-snap.83-T1
Valid prediction for pasa_asmbl_29873.p1
Valid prediction for GlimmerHMM_glimmerT_48844-T1
Valid prediction for Augustus_model.g32586.t1
Valid prediction for Augustus_model.g32596.t1
Couldn't classify 283531, 283893
Sorry, prediction pasa_asmbl_29866.p6 fails validation.
(GTT)	 TT	283531-283893	AG	AAA
Valid prediction for pasa_asmbl_29862.p1
Valid prediction for GlimmerHMM_glimmerT_48806-T1
Couldn't classify 308789, 308847
Couldn't classify 311127, 311158
Sorry, prediction pasa_asmbl_29871.p1 fails validation.
(ACC)	 GC	308789-308847	GT	AGG
(GTG)	 AG	308952-309028	GT	AGG
(GCG)	 AG	309261-309339	GT	AGG
(TGG)	 AG	309920-310095	GT	AGG
(AGG)	 AG	310559-310687	GT	AGG
(TGA)	 AG	311127-311158	CA	AAC
-recovered pasa_asmbl_29871.p1, internal, 308952, 309028
-recovered pasa_asmbl_29871.p1, internal, 309261, 309339
-recovered pasa_asmbl_29871.p1, internal, 309920, 310095
-recovered pasa_asmbl_29871.p1, internal, 310559, 310687
Valid prediction for GlimmerHMM_glimmerT_48820-T1
Valid prediction for snap_scaffold_22-snap.78-T1
Valid prediction for CodingQuarry_transcript_34078-T1
Valid prediction for CodingQuarry_transcript_34081-T1
Valid prediction for snap_scaffold_22-snap.86-T1
Valid prediction for snap_scaffold_22-snap.126-T1
Valid prediction for Augustus_model.g32621.t1
Valid prediction for Augustus_model.g32587.t1
Valid prediction for GlimmerHMM_glimmerT_48805-T1
Valid prediction for GlimmerHMM_glimmerT_48808-T1
Valid prediction for pasa_asmbl_29850.p1
Couldn't classify 312844, 312948
Couldn't classify 313515, 313664
Sorry, prediction pasa_asmbl_30496.p1 fails validation.
(GCC)	 CG	312844-312948	GT	CGG
(GTG)	 AG	313201-313365	GT	AGG
(TTT)	 AG	313515-313664	TC	ACT
-recovered pasa_asmbl_30496.p1, internal, 313201, 313365
Valid prediction for CodingQuarry_transcript_34088-T1
Valid prediction for snap_scaffold_22-snap.82-T1
Valid prediction for CodingQuarry_transcript_34082-T1
Valid prediction for GlimmerHMM_glimmerT_48825-T1
Valid prediction for CodingQuarry_transcript_34072-T1
Valid prediction for snap_scaffold_22-snap.76-T1
Valid prediction for snap_scaffold_22-snap.110-T1
Valid prediction for pasa_asmbl_29857.p1
Valid prediction for Augustus_model.g32619.t1
Valid prediction for Augustus_model.g32604.t1
Valid prediction for Augustus_model.g32595.t1
Valid prediction for HiQ_model.g32589.t1
Couldn't classify 22919, 23284
Sorry, prediction pasa_asmbl_29841.p1 fails validation.
(AAG)	 GT	22919-23284	AC	GGA
Valid prediction for Augustus_model.g32588.t1
Valid prediction for snap_scaffold_22-snap.99-T1
Valid prediction for Augustus_model.g32602.t1
Valid prediction for CodingQuarry_transcript_34071-T1
Valid prediction for snap_scaffold_22-snap.81-T1
Valid prediction for Augustus_model.g32622.t1
Valid prediction for snap_scaffold_22-snap.117-T1
Valid prediction for HiQ_model.g32607.t1
Valid prediction for snap_scaffold_22-snap.122-T1
Valid prediction for snap_scaffold_22-snap.101-T1
Valid prediction for snap_scaffold_22-snap.109-T1
Valid prediction for snap_scaffold_22-snap.121-T1
Valid prediction for GlimmerHMM_glimmerT_48837-T1
Valid prediction for snap_scaffold_22-snap.125-T1
Valid prediction for snap_scaffold_22-snap.104-T1
Valid prediction for snap_scaffold_22-snap.74-T1
Valid prediction for snap_scaffold_22-snap.80-T1
Valid prediction for HiQ_model.g32613.t1
Valid prediction for snap_scaffold_22-snap.79-T1
Valid prediction for snap_scaffold_22-snap.124-T1
Valid prediction for GlimmerHMM_glimmerT_48822-T1
Valid prediction for HiQ_model.g32608.t1
Valid prediction for pasa_asmbl_29837.p1
Valid prediction for snap_scaffold_22-snap.108-T1
Valid prediction for GlimmerHMM_glimmerT_48810-T1
Valid prediction for pasa_asmbl_29854.p2
Valid prediction for CodingQuarry_transcript_34090-T1
Valid prediction for pasa_asmbl_29846.p1
Valid prediction for snap_scaffold_22-snap.88-T1
Valid prediction for snap_scaffold_22-snap.77-T1
Valid prediction for GlimmerHMM_glimmerT_48839-T1
Valid prediction for HiQ_model.g32606.t1
Valid prediction for GlimmerHMM_glimmerT_48817-T1
Valid prediction for Augustus_model.g32601.t1
Valid prediction for GlimmerHMM_glimmerT_48807-T1
Couldn't classify 816, 1127
Sorry, prediction pasa_asmbl_29834.p1 fails validation.
(GAG)	 CA	816-1127	TC	GAT
Valid prediction for GlimmerHMM_glimmerT_48829-T1
Valid prediction for Augustus_model.g32590.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 HiQ_model.g32620.t1
Valid prediction for snap_scaffold_22-snap.111-T1
Valid prediction for Augustus_model.g32594.t1
Valid prediction for CodingQuarry_transcript_34075-T1
Valid prediction for Augustus_model.g32615.t1
Valid prediction for Augustus_model.g32618.t1
Valid prediction for Augustus_model.g32616.t1
Valid prediction for snap_scaffold_22-snap.91-T1
Valid prediction for snap_scaffold_22-snap.89-T1
Valid prediction for CodingQuarry_transcript_34086-T1
Valid prediction for pasa_asmbl_29084.p1
Valid prediction for Augustus_model.g32593.t1
Valid prediction for Augustus_model.g32597.t1
Valid prediction for HiQ_model.g32605.t1
Valid prediction for GlimmerHMM_glimmerT_48811-T1
Couldn't classify 64400, 64467
Sorry, prediction pasa_asmbl_29108.p1 fails validation.
(ATG)	 GG	53575-53661	GT	TTG
(AAA)	 AG	54317-54449	GT	AGG
(GTA)	 AG	54594-54730	GT	CGG
(AAT)	 AG	54874-55047	GT	AGG
(GGC)	 AG	55439-55720	GT	AGG
(GAC)	 AG	55851-56012	GT	GGG
(GCG)	 AG	56097-56317	GT	AGG
(GTT)	 AG	56404-56536	GT	AGG
(GTG)	 AG	56631-56755	GT	AGG
(TGT)	 AG	57071-57281	GT	GGG
(GGT)	 AG	57537-57746	GT	AGG
(GTG)	 AG	57839-58007	GT	GGG
(GTC)	 AG	58146-58240	GT	AGG
(GTG)	 AG	58412-58615	GT	AGG
(GTT)	 AG	58819-59041	GT	TGG
(GTT)	 AG	59299-59482	GT	AAG
(GTT)	 AG	59714-59885	GT	AGG
(GTG)	 AG	60055-60160	GT	GGG
(GTG)	 AG	60776-60981	GT	TCG
(GCT)	 AG	61080-61343	GT	AAG
(GTG)	 AG	61475-61682	GT	TGG
(GTT)	 AG	61818-61918	GT	AGG
(GAC)	 AG	62018-62122	GT	AGG
(GTG)	 AG	62327-62509	GT	CGG
(GTG)	 AG	62744-62947	GT	CGG
(GTG)	 AG	63368-63554	GT	ACG
(CCA)	 AG	63708-63821	GT	GGG
(GTA)	 AG	63940-64089	GT	AGG
(GAG)	 AG	64400-64467	CC	CCC
-recovered pasa_asmbl_29108.p1, initial, 53575, 53661
-recovered pasa_asmbl_29108.p1, internal, 54317, 54449
-recovered pasa_asmbl_29108.p1, internal, 54594, 54730
-recovered pasa_asmbl_29108.p1, internal, 54874, 55047
-recovered pasa_asmbl_29108.p1, internal, 55439, 55720
-recovered pasa_asmbl_29108.p1, internal, 55851, 56012
-recovered pasa_asmbl_29108.p1, internal, 56097, 56317
-recovered pasa_asmbl_29108.p1, internal, 56404, 56536
-recovered pasa_asmbl_29108.p1, internal, 56631, 56755
-recovered pasa_asmbl_29108.p1, internal, 57071, 57281
-recovered pasa_asmbl_29108.p1, internal, 57537, 57746
-recovered pasa_asmbl_29108.p1, internal, 57839, 58007
-recovered pasa_asmbl_29108.p1, internal, 58146, 58240
-recovered pasa_asmbl_29108.p1, internal, 58412, 58615
-recovered pasa_asmbl_29108.p1, internal, 58819, 59041
-recovered pasa_asmbl_29108.p1, internal, 59299, 59482
-recovered pasa_asmbl_29108.p1, internal, 59714, 59885
-recovered pasa_asmbl_29108.p1, internal, 60055, 60160
-recovered pasa_asmbl_29108.p1, internal, 60776, 60981
-recovered pasa_asmbl_29108.p1, internal, 61080, 61343
-recovered pasa_asmbl_29108.p1, internal, 61475, 61682
-recovered pasa_asmbl_29108.p1, internal, 61818, 61918
-recovered pasa_asmbl_29108.p1, internal, 62018, 62122
-recovered pasa_asmbl_29108.p1, internal, 62327, 62509
-recovered pasa_asmbl_29108.p1, internal, 62744, 62947
-recovered pasa_asmbl_29108.p1, internal, 63368, 63554
-recovered pasa_asmbl_29108.p1, internal, 63708, 63821
-recovered pasa_asmbl_29108.p1, internal, 63940, 64089
Valid prediction for GlimmerHMM_glimmerT_48830-T1
Valid prediction for GlimmerHMM_glimmerT_48836-T1
Valid prediction for snap_scaffold_22-snap.115-T1
Valid prediction for pasa_asmbl_29089.p1
Valid prediction for CodingQuarry_transcript_34083-T1
Valid prediction for GlimmerHMM_glimmerT_48812-T1
Valid prediction for Augustus_model.g32599.t1
Valid prediction for snap_scaffold_22-snap.92-T1
Valid prediction for snap_scaffold_22-snap.119-T1
Valid prediction for GlimmerHMM_glimmerT_48838-T1
Valid prediction for snap_scaffold_22-snap.105-T1
Valid prediction for HiQ_model.g32603.t1
Valid prediction for snap_scaffold_22-snap.93-T1
Valid prediction for GlimmerHMM_glimmerT_48827-T1
Valid prediction for snap_scaffold_22-snap.90-T1
Valid prediction for pasa_asmbl_29087.p1
Valid prediction for Augustus_model.g32617.t1
Valid prediction for snap_scaffold_22-snap.118-T1
Valid prediction for GlimmerHMM_glimmerT_48835-T1
Valid prediction for Augustus_model.g32609.t1
Valid prediction for GlimmerHMM_glimmerT_48815-T1
Valid prediction for snap_scaffold_22-snap.114-T1
Valid prediction for pasa_asmbl_29092.p1
Valid prediction for GlimmerHMM_glimmerT_48831-T1
Valid prediction for snap_scaffold_22-snap.112-T1
Valid prediction for snap_scaffold_22-snap.103-T1
Valid prediction for GlimmerHMM_glimmerT_48814-T1
Valid prediction for snap_scaffold_22-snap.106-T1
Valid prediction for HiQ_model.g32598.t1
Valid prediction for GlimmerHMM_glimmerT_48834-T1
Valid prediction for snap_scaffold_22-snap.98-T1
Valid prediction for Augustus_model.g32612.t1
Valid prediction for GlimmerHMM_glimmerT_48821-T1
Valid prediction for snap_scaffold_22-snap.113-T1
Valid prediction for pasa_asmbl_29090.p1
Valid prediction for GlimmerHMM_glimmerT_48826-T1
Valid prediction for GlimmerHMM_glimmerT_48832-T1
Valid prediction for pasa_asmbl_29083.p1
Valid prediction for GlimmerHMM_glimmerT_48816-T1
Valid prediction for snap_scaffold_22-snap.116-T1
Valid prediction for CodingQuarry_transcript_34087-T1
Valid prediction for snap_scaffold_22-snap.94-T1
Valid prediction for snap_scaffold_22-snap.85-T1
Valid prediction for GlimmerHMM_glimmerT_48819-T1
Valid prediction for snap_scaffold_22-snap.107-T1
Valid prediction for GlimmerHMM_glimmerT_48824-T1
Valid prediction for CodingQuarry_transcript_34077-T1
Valid prediction for snap_scaffold_22-snap.120-T1
Valid prediction for Augustus_model.g32600.t1
Valid prediction for pasa_asmbl_29085.p1
Couldn't classify 72788, 72849
Sorry, prediction pasa_asmbl_29106.p1 fails validation.
(TGC)	 AC	72788-72849	GT	AGG
(AAT)	 AG	75502-75695	GT	AGG
(GTG)	 AG	77098-77252	GT	AGG
(GAG)	 AG	80102-80263	GT	AGG
(ACT)	 AG	80527-80676	GT	AGG
(GTG)	 AG	80884-80970	GT	AGG
(GTG)	 AG	81108-81240	GT	AGG
(GTA)	 AG	81395-81486	GT	AGG
(GTG)	 AG	81939-82004	AA	GAA
add_exon() Sorry, pasa_asmbl_29106.p1 75502-75695-terminal-2 is invalid.
-recovered pasa_asmbl_29106.p1, terminal, 75502, 75695
-recovered pasa_asmbl_29106.p1, terminal, 81939, 82004
-recovered pasa_asmbl_29106.p1, internal, 75502, 75695
-recovered pasa_asmbl_29106.p1, internal, 77098, 77252
-recovered pasa_asmbl_29106.p1, internal, 80102, 80263
-recovered pasa_asmbl_29106.p1, internal, 80527, 80676
-recovered pasa_asmbl_29106.p1, internal, 80884, 80970
-recovered pasa_asmbl_29106.p1, internal, 81108, 81240
-recovered pasa_asmbl_29106.p1, internal, 81395, 81486
Valid prediction for snap_scaffold_22-snap.100-T1
Valid prediction for CodingQuarry_transcript_34076-T1
Valid prediction for HiQ_model.g32611.t1
Valid prediction for snap_scaffold_22-snap.96-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 155959, rend_intergenic: 152638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252544, rend_intergenic: 248137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 321991
-exon list size: 573


building trellis

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49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
51.0    
51.1    
51.3    
51.5    
51.7    
51.8    
52.0    
52.2    
52.3    
52.5    
52.7    
52.9    
53.0    
53.2    
53.4    
53.6    
53.7    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
55.0    
55.1    
55.3    
55.5    
55.7    
55.8    
56.0    
56.2    
56.3    
56.5    
56.7    
56.9    
57.0    
57.2    
57.4    
57.6    
57.7    
57.9    
58.1    
58.3    
58.4    
58.6    
58.8    
59.0    
59.1    
59.3    
59.5    
59.7    
59.8    
60.0    
60.2    
60.3    
60.5    
60.7    
60.9    
61.0    
61.2    
61.4    
61.6    
61.7    
61.9    
62.1    
62.3    
62.4    
62.6    
62.8    
63.0    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.9    
65.0    
65.2    
65.4    
65.6    
65.7    
65.9    
66.1    
66.3    
66.4    
66.6    
66.8    
67.0    
67.1    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.9    
69.0    
69.2    
69.4    
69.6    
69.7    
69.9    
70.1    
70.3    
70.4    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.6    
73.7    
73.9    
74.1    
74.3    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.1    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
83.0    
83.1    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 155959, rend_intergenic: 152638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252544, rend_intergenic: 248137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 43 predictions persist after filtering for low support