-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_7833421-8143338

-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: +)Couldn't classify 303205, 303223
Sorry, prediction pasa_asmbl_24649.p1 fails validation.
(GTC)	 AT	303205-303223	GT	AGG
(ATG)	 AG	303333-303448	GT	AGG
(GGG)	 AG	304060-304217	GT	AGG
(CTA)	 AG	304311-304402	GT	ACG
(GTA)	 AG	304650-305422	GG	GAG
add_exon() Sorry, pasa_asmbl_24649.p1 303333-303448-initial-1 is invalid.
-recovered pasa_asmbl_24649.p1, initial, 303333, 303448
-recovered pasa_asmbl_24649.p1, terminal, 304650, 305422
-recovered pasa_asmbl_24649.p1, internal, 303333, 303448
-recovered pasa_asmbl_24649.p1, internal, 304060, 304217
-recovered pasa_asmbl_24649.p1, internal, 304311, 304402
Valid prediction for GeneMark_model.6811_t
Valid prediction for pasa_asmbl_24641.p1
Valid prediction for Augustus_model.g2859.t1
Valid prediction for GeneMark_model.6816_t
Valid prediction for snap_scaffold_2-snap.1682-T1
Valid prediction for GlimmerHMM_glimmerT_4227-T1
Valid prediction for GeneMark_model.6827_t
Valid prediction for HiQ_model.g2843.t1
Valid prediction for GlimmerHMM_glimmerT_4229-T1
Valid prediction for snap_scaffold_2-snap.1686-T1
Valid prediction for GeneMark_model.6825_t
Valid prediction for snap_scaffold_2-snap.1676-T1
Valid prediction for HiQ_model.g2848.t1
Valid prediction for GeneMark_model.6801_t
Valid prediction for GlimmerHMM_glimmerT_4221-T1
Valid prediction for GeneMark_model.6807_t
Valid prediction for GeneMark_model.6797_t
Valid prediction for CodingQuarry_transcript_28559-T1
Valid prediction for GlimmerHMM_glimmerT_4241-T1
Valid prediction for GlimmerHMM_glimmerT_4230-T1
Couldn't classify 60715, 60939
Sorry, prediction pasa_asmbl_24629.p1 fails validation.
(AAG)	 GT	60715-60939	GT	AGG
(AAT)	 AG	61072-61189	GT	AGG
(GGC)	 AG	61289-61446	AT	AAA
add_exon() Sorry, pasa_asmbl_24629.p1 61072-61189-terminal-3 is invalid.
-recovered pasa_asmbl_24629.p1, terminal, 61072, 61189
-recovered pasa_asmbl_24629.p1, terminal, 61289, 61446
-recovered pasa_asmbl_24629.p1, internal, 61072, 61189
Couldn't classify 297124, 297141
Couldn't classify 298733, 298830
Sorry, prediction pasa_asmbl_24648.p1 fails validation.
(CCC)	 GT	297124-297141	GT	TAG
(AAC)	 AG	297889-298000	GT	CGG
(AGG)	 AG	298234-298350	GT	AGG
(ACC)	 AG	298733-298830	GG	CGG
-recovered pasa_asmbl_24648.p1, internal, 297889, 298000
-recovered pasa_asmbl_24648.p1, internal, 298234, 298350
Valid prediction for snap_scaffold_2-snap.1661-T1
Valid prediction for HiQ_model.g2856.t1
Valid prediction for snap_scaffold_2-snap.1660-T1
Valid prediction for CodingQuarry_transcript_28562-T1
Valid prediction for snap_scaffold_2-snap.1689-T1
Valid prediction for snap_scaffold_2-snap.1670-T1
Valid prediction for snap_scaffold_2-snap.1690-T1
Valid prediction for GlimmerHMM_glimmerT_4243-T1
Valid prediction for GlimmerHMM_glimmerT_4245-T1
Valid prediction for Augustus_model.g2849.t1
Valid prediction for CodingQuarry_transcript_28570-T1
Valid prediction for snap_scaffold_2-snap.1684-T1
Valid prediction for CodingQuarry_transcript_28558-T1
Valid prediction for snap_scaffold_2-snap.1680-T1
Valid prediction for pasa_asmbl_24639.p1
Valid prediction for snap_scaffold_2-snap.1668-T1
Valid prediction for pasa_asmbl_24619.p1
Valid prediction for HiQ_model.g2841.t1
Valid prediction for snap_scaffold_2-snap.1664-T1
Valid prediction for GlimmerHMM_glimmerT_4231-T1
Valid prediction for Augustus_model.g2858.t1
Valid prediction for GeneMark_model.6823_t
Valid prediction for GeneMark_model.6813_t
Valid prediction for pasa_asmbl_24644.p1
Valid prediction for GlimmerHMM_glimmerT_4237-T1
Valid prediction for snap_scaffold_2-snap.1653-T1
Valid prediction for GlimmerHMM_glimmerT_4239-T1
Valid prediction for Augustus_model.g2846.t1
Valid prediction for Augustus_model.g2840.t1
Valid prediction for pasa_asmbl_24625.p1
Valid prediction for pasa_asmbl_24618.p1
Valid prediction for GeneMark_model.6810_t
Valid prediction for snap_scaffold_2-snap.1659-T1
Valid prediction for CodingQuarry_transcript_28566-T1
Valid prediction for snap_scaffold_2-snap.1672-T1
Valid prediction for GeneMark_model.6821_t
Valid prediction for snap_scaffold_2-snap.1669-T1
Valid prediction for CodingQuarry_transcript_28568-T1
Valid prediction for HiQ_model.g2850.t1
Valid prediction for CodingQuarry_transcript_28561-T1
Valid prediction for snap_scaffold_2-snap.1683-T1
Valid prediction for GeneMark_model.6812_t
Valid prediction for snap_scaffold_2-snap.1658-T1
Valid prediction for snap_scaffold_2-snap.1679-T1
Valid prediction for Augustus_model.g2854.t1
Valid prediction for snap_scaffold_2-snap.1657-T1
Valid prediction for GeneMark_model.6830_t
Valid prediction for GeneMark_model.6800_t
Valid prediction for CodingQuarry_transcript_28567-T1
Valid prediction for GlimmerHMM_glimmerT_4223-T1
Valid prediction for GeneMark_model.6824_t
Valid prediction for GeneMark_model.6809_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 GlimmerHMM_glimmerT_4228-T1
Valid prediction for GeneMark_model.6814_t
Valid prediction for pasa_asmbl_23313.p1
Valid prediction for snap_scaffold_2-snap.1688-T1
Valid prediction for snap_scaffold_2-snap.1651-T1
Valid prediction for snap_scaffold_2-snap.1654-T1
Valid prediction for snap_scaffold_2-snap.1655-T1
Valid prediction for GeneMark_model.6804_t
Valid prediction for GlimmerHMM_glimmerT_4232-T1
Valid prediction for Augustus_model.g2852.t1
Valid prediction for GeneMark_model.6806_t
Valid prediction for snap_scaffold_2-snap.1678-T1
Valid prediction for GlimmerHMM_glimmerT_4234-T1
Valid prediction for GeneMark_model.6826_t
Valid prediction for GeneMark_model.6829_t
Valid prediction for pasa_asmbl_23316.p1
Couldn't classify 74900, 75082
Sorry, prediction pasa_asmbl_23332.p2 fails validation.
(CAG)	 AC	74900-75082	GT	AGG
(GGC)	 AG	75784-75975	GT	AGG
(GTG)	 AG	76068-76242	GT	AGG
(AAA)	 AG	76706-76872	AT	GAA
-recovered pasa_asmbl_23332.p2, terminal, 76706, 76872
-recovered pasa_asmbl_23332.p2, internal, 75784, 75975
-recovered pasa_asmbl_23332.p2, internal, 76068, 76242
Valid prediction for GeneMark_model.6808_t
Valid prediction for GlimmerHMM_glimmerT_4233-T1
Valid prediction for snap_scaffold_2-snap.1677-T1
Valid prediction for Augustus_model.g2837.t1
Valid prediction for GlimmerHMM_glimmerT_4236-T1
Valid prediction for snap_scaffold_2-snap.1675-T1
Valid prediction for snap_scaffold_2-snap.1681-T1
Valid prediction for HiQ_model.g2857.t1
Valid prediction for Augustus_model.g2855.t1
Valid prediction for CodingQuarry_transcript_28569-T1
Valid prediction for CodingQuarry_transcript_28564-T1
Couldn't classify 231790, 232269
Sorry, prediction pasa_asmbl_23314.p1 fails validation.
(ATG)	 GC	231790-232269	GA	CCG
Valid prediction for GlimmerHMM_glimmerT_4219-T1
Valid prediction for Augustus_model.g2838.t1
Valid prediction for Augustus_model.g2839.t1
Valid prediction for snap_scaffold_2-snap.1671-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.6815_t
Couldn't classify 149156, 149198
Couldn't classify 149544, 149692
Sorry, prediction pasa_asmbl_23322.p1 fails validation.
(TAC)	 AT	149156-149198	GT	CGG
(AGA)	 AG	149326-149448	GT	TGG
(CAG)	 AG	149544-149692	GC	GAG
-recovered pasa_asmbl_23322.p1, internal, 149326, 149448
-recovered pasa_asmbl_23322.p1, internal, 149544, 149692
Valid prediction for GlimmerHMM_glimmerT_4225-T1
Valid prediction for GeneMark_model.6818_t
Valid prediction for CodingQuarry_transcript_28563-T1
Valid prediction for GlimmerHMM_glimmerT_4244-T1
Valid prediction for snap_scaffold_2-snap.1667-T1
Valid prediction for snap_scaffold_2-snap.1674-T1
Valid prediction for Augustus_model.g2851.t1
Valid prediction for CodingQuarry_transcript_28565-T1
Couldn't classify 303156, 303275
Couldn't classify 309579, 309728
Sorry, prediction pasa_asmbl_23308.p1 fails validation.
(CTC)	 CC	303156-303275	GT	TGG
(CTC)	 AG	304642-304871	GT	AGG
(CTA)	 AG	306462-306617	GT	CGG
(CTC)	 AG	307975-308212	GT	AGG
(TCT)	 AG	309579-309728	GT	AGG
-recovered pasa_asmbl_23308.p1, internal, 304642, 304871
-recovered pasa_asmbl_23308.p1, internal, 306462, 306617
-recovered pasa_asmbl_23308.p1, internal, 307975, 308212
-recovered pasa_asmbl_23308.p1, internal, 309579, 309728
Valid prediction for GeneMark_model.6799_t
Valid prediction for GlimmerHMM_glimmerT_4226-T1
Valid prediction for GlimmerHMM_glimmerT_4242-T1
Couldn't classify 283687, 283794
Sorry, prediction pasa_asmbl_23310.p1 fails validation.
(ATG)	 AA	277916-278089	GT	AGG
(CCC)	 AG	280047-280214	GT	CTG
(ACA)	 AG	280412-280478	GT	TGG
(CTC)	 AG	280651-280768	GT	AGG
(GAC)	 AG	280862-280973	GT	GGG
(GAG)	 AG	281439-281579	GT	AGG
(GTC)	 AG	281691-281846	GT	AGG
(GAG)	 AG	281942-282084	GT	AGG
(AGA)	 AG	282190-282271	GT	AGG
(CAT)	 AG	282371-282523	GT	TGG
(ATC)	 AG	283687-283794	GT	TGG
-recovered pasa_asmbl_23310.p1, initial, 277916, 278089
-recovered pasa_asmbl_23310.p1, internal, 280047, 280214
-recovered pasa_asmbl_23310.p1, internal, 280412, 280478
-recovered pasa_asmbl_23310.p1, internal, 280651, 280768
-recovered pasa_asmbl_23310.p1, internal, 280862, 280973
-recovered pasa_asmbl_23310.p1, internal, 281439, 281579
-recovered pasa_asmbl_23310.p1, internal, 281691, 281846
-recovered pasa_asmbl_23310.p1, internal, 281942, 282084
-recovered pasa_asmbl_23310.p1, internal, 282190, 282271
-recovered pasa_asmbl_23310.p1, internal, 282371, 282523
-recovered pasa_asmbl_23310.p1, internal, 283687, 283794
Valid prediction for GlimmerHMM_glimmerT_4238-T1
Valid prediction for snap_scaffold_2-snap.1665-T1
Valid prediction for snap_scaffold_2-snap.1650-T1
Valid prediction for snap_scaffold_2-snap.1666-T1
Valid prediction for Augustus_model.g2845.t1
Valid prediction for GlimmerHMM_glimmerT_4222-T1
Valid prediction for GeneMark_model.6822_t
Valid prediction for GeneMark_model.6820_t
Valid prediction for snap_scaffold_2-snap.1673-T1
Couldn't classify 276010, 276045
Sorry, prediction pasa_asmbl_23311.p1 fails validation.
(ATG)	 GT	270588-270641	GT	CTG
(GCA)	 AG	272161-272278	GT	AGG
(CAA)	 AG	272964-273040	GT	AGG
(AAT)	 AG	273396-273593	GT	AGG
(GAG)	 AG	276010-276045	TT	ACT
-recovered pasa_asmbl_23311.p1, initial, 270588, 270641
-recovered pasa_asmbl_23311.p1, internal, 272161, 272278
-recovered pasa_asmbl_23311.p1, internal, 272964, 273040
-recovered pasa_asmbl_23311.p1, internal, 273396, 273593
Valid prediction for snap_scaffold_2-snap.1685-T1
Valid prediction for GeneMark_model.6805_t
Valid prediction for GlimmerHMM_glimmerT_4240-T1
Valid prediction for CodingQuarry_transcript_28560-T1
Valid prediction for GeneMark_model.6817_t
Couldn't classify 71760, 71798
Couldn't classify 73583, 74485
Sorry, prediction pasa_asmbl_23334.p1 fails validation.
(TCC)	 GA	71760-71798	GT	TGG
(GAG)	 AG	73583-74485	GT	ATG
-recovered pasa_asmbl_23334.p1, internal, 73583, 74485
Couldn't classify 235091, 235263
Sorry, prediction pasa_asmbl_23984.p1 fails validation.
(TGT)	 GG	235091-235263	GT	CAG
(GTC)	 AG	235353-235512	GT	AGG
(AGT)	 AG	235657-235914	GT	GGG
(TCA)	 AG	236165-236277	GT	TGG
(GTA)	 AG	236816-236957	GT	AGG
(GAG)	 AG	237179-237706	GA	AAG
-recovered pasa_asmbl_23984.p1, terminal, 237179, 237706
-recovered pasa_asmbl_23984.p1, internal, 235353, 235512
-recovered pasa_asmbl_23984.p1, internal, 235657, 235914
-recovered pasa_asmbl_23984.p1, internal, 236165, 236277
-recovered pasa_asmbl_23984.p1, internal, 236816, 236957
Valid prediction for GeneMark_model.6828_t
Valid prediction for GlimmerHMM_glimmerT_4235-T1
Valid prediction for snap_scaffold_2-snap.1656-T1
Valid prediction for snap_scaffold_2-snap.1662-T1
Valid prediction for GeneMark_model.6798_t
Valid prediction for pasa_asmbl_23324.p1
Valid prediction for snap_scaffold_2-snap.1663-T1
Valid prediction for GeneMark_model.6803_t
Valid prediction for GeneMark_model.6802_t
Valid prediction for Augustus_model.g2844.t1
Valid prediction for GlimmerHMM_glimmerT_4224-T1
Valid prediction for snap_scaffold_2-snap.1652-T1
Valid prediction for snap_scaffold_2-snap.1687-T1
Valid prediction for HiQ_model.g2847.t1
Valid prediction for snap_scaffold_2-snap.1649-T1
Valid prediction for Augustus_model.g2853.t1
Valid prediction for HiQ_model.g2842.t1
Valid prediction for GlimmerHMM_glimmerT_4220-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 153166, rend_intergenic: 150145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236363, rend_intergenic: 234526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256953, rend_intergenic: 256271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 309918
-exon list size: 615


building trellis

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73.6    
73.7    
73.9    
74.1    
74.2    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.7    
80.9    
81.0    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.8    
83.0    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.1    
84.3    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 153166, rend_intergenic: 150145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236363, rend_intergenic: 234526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256953, rend_intergenic: 256271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support