-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_5350042-5563629

-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_9-snap.1152-T1
Couldn't classify 41309, 41479
Couldn't classify 43055, 43117
Sorry, prediction pasa_asmbl_54019.p1 fails validation.
(CTC)	 TC	41309-41479	GT	AGG
(GGG)	 AG	41591-41748	GT	GGG
(AGA)	 AG	41868-41989	GT	TGG
(ACA)	 AG	42158-42289	GT	AGG
(AGA)	 AG	42477-42588	GT	CGG
(CCC)	 AG	42813-42912	GT	AGG
(GTG)	 AG	43055-43117	AG	ACA
-recovered pasa_asmbl_54019.p1, internal, 41591, 41748
-recovered pasa_asmbl_54019.p1, internal, 41868, 41989
-recovered pasa_asmbl_54019.p1, internal, 42158, 42289
-recovered pasa_asmbl_54019.p1, internal, 42477, 42588
-recovered pasa_asmbl_54019.p1, internal, 42813, 42912
Valid prediction for GlimmerHMM_glimmerT_22650-T1
Valid prediction for Augustus_model.g15141.t1
Valid prediction for Augustus_model.g15144.t1
Valid prediction for snap_scaffold_9-snap.1173-T1
Valid prediction for GeneMark_model.38931_t
Valid prediction for GeneMark_model.38920_t
Valid prediction for snap_scaffold_9-snap.1158-T1
Valid prediction for snap_scaffold_9-snap.1166-T1
Valid prediction for GlimmerHMM_glimmerT_22631-T1
Valid prediction for snap_scaffold_9-snap.1171-T1
Valid prediction for snap_scaffold_9-snap.1178-T1
Couldn't classify 3660, 3956
Sorry, prediction pasa_asmbl_54666.p2 fails validation.
(ATG)	 CC	3660-3956	CA	AGC
Valid prediction for snap_scaffold_9-snap.1150-T1
Valid prediction for GeneMark_model.38930_t
Valid prediction for snap_scaffold_9-snap.1145-T1
Valid prediction for GeneMark_model.38933_t
Valid prediction for GlimmerHMM_glimmerT_22632-T1
Valid prediction for Augustus_model.g15140.t1
Valid prediction for Augustus_model.g15146.t1
Valid prediction for snap_scaffold_9-snap.1164-T1
Valid prediction for snap_scaffold_9-snap.1165-T1
Valid prediction for CodingQuarry_transcript_62018-T1
Valid prediction for GeneMark_model.38935_t
Valid prediction for Augustus_model.g15134.t1
Valid prediction for snap_scaffold_9-snap.1161-T1
Valid prediction for Augustus_model.g15148.t1
Couldn't classify 31475, 31623
Sorry, prediction pasa_asmbl_54018.p1 fails validation.
(GCA)	 AC	31475-31623	GT	AAG
(GTT)	 AG	31818-32001	GT	AGG
(AAA)	 AG	32153-32922	GT	CGG
(CTA)	 AG	33027-33213	GT	GGG
(GCC)	 AG	33403-33555	AA	GAA
-recovered pasa_asmbl_54018.p1, terminal, 33403, 33555
-recovered pasa_asmbl_54018.p1, internal, 31818, 32001
-recovered pasa_asmbl_54018.p1, internal, 32153, 32922
-recovered pasa_asmbl_54018.p1, internal, 33027, 33213
Valid prediction for snap_scaffold_9-snap.1162-T1
Valid prediction for GlimmerHMM_glimmerT_22634-T1
Valid prediction for GlimmerHMM_glimmerT_22637-T1
Valid prediction for GlimmerHMM_glimmerT_22644-T1
Couldn't classify 123270, 123430
Couldn't classify 123705, 123839
Sorry, prediction CodingQuarry_transcript_62020-T1 fails validation.
(ATG)	 AG	122500-122538	GT	AAG
(TGG)	 AG	123093-123176	GT	AGG
(GTC)	 AG	123270-123430	AT	TCA
(ATA)	 AC	123705-123839	GT	AGG
(GTT)	 AG	123927-124113	TT	AAT
-recovered CodingQuarry_transcript_62020-T1, initial, 122500, 122538
-recovered CodingQuarry_transcript_62020-T1, terminal, 123927, 124113
-recovered CodingQuarry_transcript_62020-T1, internal, 122500, 122538
-recovered CodingQuarry_transcript_62020-T1, internal, 123093, 123176
Valid prediction for GlimmerHMM_glimmerT_22642-T1
Valid prediction for GeneMark_model.38922_t
Valid prediction for GlimmerHMM_glimmerT_22635-T1
Valid prediction for GlimmerHMM_glimmerT_22628-T1
Valid prediction for GlimmerHMM_glimmerT_22633-T1
Couldn't classify 23902, 23989
Sorry, prediction pasa_asmbl_54678.p1 fails validation.
(CAC)	 CG	23902-23989	GT	AGG
(AGA)	 AG	25111-25352	GT	CGG
(GTT)	 AG	26191-26338	GT	GAG
(TGA)	 AG	26537-26658	GT	AGG
(ATT)	 AG	26761-26826	GT	AGG
(ACT)	 AG	26936-27034	GT	ACG
(CTG)	 AG	28208-28313	GT	AGG
(GTA)	 AG	28420-28562	GT	TGG
(GTG)	 AG	28658-28745	GT	TGG
(GTC)	 AG	28831-28871	GT	AGG
(AAT)	 AG	28979-29157	GT	TGG
(TGA)	 AG	29585-29666	GT	TGG
(CCT)	 AG	29787-29849	AG	AGA
add_exon() Sorry, pasa_asmbl_54678.p1 26191-26338-terminal-3 is invalid.
-recovered pasa_asmbl_54678.p1, terminal, 26191, 26338
-recovered pasa_asmbl_54678.p1, terminal, 29787, 29849
-recovered pasa_asmbl_54678.p1, internal, 25111, 25352
-recovered pasa_asmbl_54678.p1, internal, 26191, 26338
-recovered pasa_asmbl_54678.p1, internal, 26537, 26658
-recovered pasa_asmbl_54678.p1, internal, 26761, 26826
-recovered pasa_asmbl_54678.p1, internal, 26936, 27034
-recovered pasa_asmbl_54678.p1, internal, 28208, 28313
-recovered pasa_asmbl_54678.p1, internal, 28420, 28562
-recovered pasa_asmbl_54678.p1, internal, 28658, 28745
-recovered pasa_asmbl_54678.p1, internal, 28831, 28871
-recovered pasa_asmbl_54678.p1, internal, 28979, 29157
-recovered pasa_asmbl_54678.p1, internal, 29585, 29666
Valid prediction for GeneMark_model.38910_t
Valid prediction for GeneMark_model.38925_t
Valid prediction for GeneMark_model.38926_t
Valid prediction for GlimmerHMM_glimmerT_22645-T1
Valid prediction for CodingQuarry_transcript_62025-T1
Valid prediction for Augustus_model.g15142.t1
Valid prediction for CodingQuarry_transcript_62023-T1
Valid prediction for HiQ_model.g15145.t1
Valid prediction for snap_scaffold_9-snap.1151-T1
Valid prediction for snap_scaffold_9-snap.1154-T1
Valid prediction for pasa_asmbl_54041.p1
Valid prediction for CodingQuarry_transcript_62022-T1
Valid prediction for snap_scaffold_9-snap.1172-T1
Valid prediction for GeneMark_model.38924_t
Valid prediction for GeneMark_model.38929_t
Valid prediction for snap_scaffold_9-snap.1177-T1
Valid prediction for pasa_asmbl_54029.p1
Valid prediction for GlimmerHMM_glimmerT_22629-T1
Valid prediction for HiQ_model.g15137.t1
Valid prediction for GeneMark_model.38902_t
Valid prediction for snap_scaffold_9-snap.1169-T1
Couldn't classify 51385, 51456
Sorry, prediction pasa_asmbl_54023.p1 fails validation.
(GGC)	 CA	51385-51456	GT	CGG
(GGG)	 AG	51685-51756	GT	AGG
(CTC)	 AG	52375-52495	GT	GTG
(GTG)	 AG	52640-52745	GT	AGG
(GGC)	 AG	54730-54879	GT	AGG
(AGC)	 AG	55351-55398	GT	AGG
(TCC)	 AG	57116-57217	GT	AGG
(CTC)	 AG	57778-57871	AC	GAA
add_exon() Sorry, pasa_asmbl_54023.p1 52640-52745-terminal-3 is invalid.
-recovered pasa_asmbl_54023.p1, terminal, 52640, 52745
-recovered pasa_asmbl_54023.p1, terminal, 57778, 57871
-recovered pasa_asmbl_54023.p1, internal, 51685, 51756
-recovered pasa_asmbl_54023.p1, internal, 52375, 52495
-recovered pasa_asmbl_54023.p1, internal, 52640, 52745
-recovered pasa_asmbl_54023.p1, internal, 54730, 54879
-recovered pasa_asmbl_54023.p1, internal, 55351, 55398
-recovered pasa_asmbl_54023.p1, internal, 57116, 57217
Valid prediction for GlimmerHMM_glimmerT_22643-T1
Valid prediction for GlimmerHMM_glimmerT_22638-T1
Valid prediction for CodingQuarry_transcript_62024-T1
Valid prediction for GeneMark_model.38915_t
Valid prediction for CodingQuarry_transcript_62017-T1
Valid prediction for snap_scaffold_9-snap.1179-T1
Valid prediction for GeneMark_model.38904_t
Valid prediction for GeneMark_model.38913_t
Valid prediction for GeneMark_model.38918_t
Valid prediction for HiQ_model.g15138.t1
Valid prediction for snap_scaffold_9-snap.1163-T1
Couldn't classify 176994, 177076
Sorry, prediction pasa_asmbl_54036.p1 fails validation.
(TGG)	 CC	176994-177076	GT	GGG
(ACC)	 AG	178926-179113	GT	AGG
(GGT)	 AG	179210-179274	GT	CTG
(CTG)	 AG	179381-179474	GT	AGG
(GCC)	 AG	180592-180663	GT	AGG
(GAT)	 AG	181047-181199	GT	CGG
(AGG)	 AG	181422-181537	GT	AGG
(AGT)	 AG	182627-182638	CT	AAC
-recovered pasa_asmbl_54036.p1, terminal, 182627, 182638
-recovered pasa_asmbl_54036.p1, internal, 178926, 179113
-recovered pasa_asmbl_54036.p1, internal, 179210, 179274
-recovered pasa_asmbl_54036.p1, internal, 179381, 179474
-recovered pasa_asmbl_54036.p1, internal, 180592, 180663
-recovered pasa_asmbl_54036.p1, internal, 181047, 181199
-recovered pasa_asmbl_54036.p1, internal, 181422, 181537
Valid prediction for GeneMark_model.38919_t
Valid prediction for snap_scaffold_9-snap.1156-T1
Valid prediction for GlimmerHMM_glimmerT_22636-T1
Valid prediction for Augustus_model.g15135.t1
Valid prediction for GeneMark_model.38936_t
Valid prediction for snap_scaffold_9-snap.1157-T1
Valid prediction for GlimmerHMM_glimmerT_22641-T1
Valid prediction for pasa_asmbl_54709.p1
Valid prediction for GeneMark_model.38908_t
Valid prediction for HiQ_model.g15147.t1
Couldn't classify 49941, 49980
Sorry, prediction pasa_asmbl_54021.p1 fails validation.
(ATG)	 TT	46458-46614	GT	ATG
(ATA)	 AG	47012-47081	GT	AGG
(ATT)	 AG	47185-47266	GT	AGG
(TTG)	 AG	47506-47579	GT	AGG
(ATT)	 AG	47835-48086	GT	AGG
(AGC)	 AG	48471-48536	GT	GTG
(AGG)	 AG	48898-48987	GT	AGG
(GTC)	 AG	49123-49176	GT	GAG
(AAG)	 AG	49941-49980	GA	AGG
-recovered pasa_asmbl_54021.p1, initial, 46458, 46614
add_exon() Sorry, pasa_asmbl_54021.p1 47012-47081-terminal-3 is invalid.
-recovered pasa_asmbl_54021.p1, terminal, 47012, 47081
add_exon() Sorry, pasa_asmbl_54021.p1 49123-49176-terminal-1 is invalid.
-recovered pasa_asmbl_54021.p1, terminal, 49123, 49176
-recovered pasa_asmbl_54021.p1, internal, 47012, 47081
-recovered pasa_asmbl_54021.p1, internal, 47185, 47266
-recovered pasa_asmbl_54021.p1, internal, 47506, 47579
-recovered pasa_asmbl_54021.p1, internal, 47835, 48086
-recovered pasa_asmbl_54021.p1, internal, 48471, 48536
-recovered pasa_asmbl_54021.p1, internal, 48898, 48987
-recovered pasa_asmbl_54021.p1, internal, 49123, 49176
Valid prediction for Augustus_model.g15139.t1
Valid prediction for snap_scaffold_9-snap.1168-T1
Valid prediction for snap_scaffold_9-snap.1146-T1
Valid prediction for GeneMark_model.38937_t
Couldn't classify 123270, 123430
Couldn't classify 123705, 123839
Sorry, prediction CodingQuarry_transcript_62021-T1 fails validation.
(ATG)	 AG	122500-122547	GT	TTG
(TGG)	 AG	123093-123176	GT	AGG
(GTC)	 AG	123270-123430	AT	TCA
(ATA)	 AC	123705-123839	GT	AGG
(GTT)	 AG	123927-124113	TT	AAT
-recovered CodingQuarry_transcript_62021-T1, initial, 122500, 122547
-recovered CodingQuarry_transcript_62021-T1, terminal, 123927, 124113
-recovered CodingQuarry_transcript_62021-T1, internal, 122500, 122547
-recovered CodingQuarry_transcript_62021-T1, internal, 123093, 123176
Valid prediction for GeneMark_model.38906_t
Couldn't classify 123270, 123430
Couldn't classify 123705, 123839
Sorry, prediction pasa_asmbl_54030.p1 fails validation.
(ATG)	 AG	122500-122538	GT	AAG
(TGG)	 AG	123093-123176	GT	AGG
(GTC)	 AG	123270-123430	AT	TCA
(ATA)	 AC	123705-123839	GT	AGG
(GTT)	 AG	123927-124113	TT	AAT
-recovered pasa_asmbl_54030.p1, initial, 122500, 122538
-recovered pasa_asmbl_54030.p1, terminal, 123927, 124113
-recovered pasa_asmbl_54030.p1, internal, 122500, 122538
-recovered pasa_asmbl_54030.p1, internal, 123093, 123176

-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 GlimmerHMM_glimmerT_22639-T1
Valid prediction for snap_scaffold_9-snap.1155-T1
Valid prediction for snap_scaffold_9-snap.1147-T1
Valid prediction for GlimmerHMM_glimmerT_22647-T1
Valid prediction for Augustus_model.g15149.t1
Valid prediction for GlimmerHMM_glimmerT_22651-T1
Valid prediction for GlimmerHMM_glimmerT_22640-T1
Valid prediction for CodingQuarry_transcript_62026-T1
Valid prediction for GeneMark_model.38907_t
Valid prediction for snap_scaffold_9-snap.1176-T1
Valid prediction for snap_scaffold_9-snap.1159-T1
Valid prediction for snap_scaffold_9-snap.1174-T1
Valid prediction for GeneMark_model.38905_t
Valid prediction for GlimmerHMM_glimmerT_22646-T1
Valid prediction for GlimmerHMM_glimmerT_22653-T1
Valid prediction for Augustus_model.g15150.t1
Valid prediction for GeneMark_model.38909_t
Valid prediction for snap_scaffold_9-snap.1160-T1
Valid prediction for GeneMark_model.38903_t
Valid prediction for GeneMark_model.38914_t
Valid prediction for GeneMark_model.38916_t
Valid prediction for GlimmerHMM_glimmerT_22652-T1
Valid prediction for GeneMark_model.38921_t
Valid prediction for GeneMark_model.38934_t
Valid prediction for CodingQuarry_transcript_62019-T1
Valid prediction for GeneMark_model.38932_t
Valid prediction for GeneMark_model.38911_t
Valid prediction for GeneMark_model.38928_t
Valid prediction for pasa_asmbl_54969.p1
Valid prediction for GeneMark_model.38927_t
Valid prediction for GeneMark_model.38923_t
Valid prediction for GlimmerHMM_glimmerT_22649-T1
Valid prediction for GlimmerHMM_glimmerT_22630-T1
Valid prediction for Augustus_model.g15136.t1
Valid prediction for snap_scaffold_9-snap.1148-T1
Valid prediction for snap_scaffold_9-snap.1175-T1
Couldn't classify 7339, 7468
Sorry, prediction pasa_asmbl_54972.p1 fails validation.
(GCC)	 CA	7339-7468	GT	AGG
(GTT)	 AG	10098-10196	GT	GCG
(AAT)	 AG	10882-11069	GT	GGG
(ATC)	 AG	11225-11275	GT	AGG
(AGA)	 AG	14248-14334	GT	ATG
(CCC)	 AG	14667-14834	GG	AGG
-recovered pasa_asmbl_54972.p1, terminal, 14667, 14834
-recovered pasa_asmbl_54972.p1, internal, 10098, 10196
-recovered pasa_asmbl_54972.p1, internal, 10882, 11069
-recovered pasa_asmbl_54972.p1, internal, 11225, 11275
-recovered pasa_asmbl_54972.p1, internal, 14248, 14334
Valid prediction for GeneMark_model.38938_t
Valid prediction for snap_scaffold_9-snap.1167-T1
Valid prediction for GlimmerHMM_glimmerT_22648-T1
Valid prediction for snap_scaffold_9-snap.1170-T1
Valid prediction for snap_scaffold_9-snap.1149-T1
Valid prediction for snap_scaffold_9-snap.1153-T1
Valid prediction for HiQ_model.g15143.t1
Valid prediction for GeneMark_model.38917_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10819, rend_intergenic: 7688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45397, rend_intergenic: 41201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55647, rend_intergenic: 50299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188348, rend_intergenic: 186417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197532, rend_intergenic: 194367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210186, rend_intergenic: 204410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213588
-exon list size: 598


building trellis

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53.7    
53.8    
54.0    
54.2    
54.3    
54.5    
54.7    
54.8    
55.0    
55.2    
55.3    
55.5    
55.7    
55.8    
56.0    
56.2    
56.3    
56.5    
56.7    
56.8    
57.0    
57.2    
57.3    
57.5    
57.7    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.8    
59.0    
59.2    
59.3    
59.5    
59.7    
59.8    
60.0    
60.2    
60.3    
60.5    
60.7    
60.8    
61.0    
61.2    
61.3    
61.5    
61.7    
61.8    
62.0    
62.2    
62.3    
62.5    
62.7    
62.8    
63.0    
63.2    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.8    
65.0    
65.2    
65.3    
65.5    
65.7    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.8    
77.0    
77.2    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
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 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 10819, rend_intergenic: 7688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45397, rend_intergenic: 41201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55647, rend_intergenic: 50299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188348, rend_intergenic: 186417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197532, rend_intergenic: 194367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210186, rend_intergenic: 204410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support