-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_369

-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 63, 125
Sorry, prediction GeneMark_model.107445_t fails validation.
(AGA)	 AG	63-125	GT	GAG
(TAA)	 AG	147-155	GT	AGG
(GAG)	 AG	183-189	GT	GGG
(TCC)	 AG	1261-1404	GT	AGG
(ATC)	 AG	1716-1727	GT	AGG
(GTC)	 AG	1752-1763	GT	AGG
(GTC)	 AG	1788-1799	GT	AGG
(ATC)	 AG	1824-1835	GT	AGG
(GTC)	 AG	1860-1871	GT	AGG
(GTC)	 AG	1896-1975	GT	ATG
(CTC)	 AG	2024-2143	GT	AGG
(GCA)	 AG	2174-2263	GT	AGG
(GCA)	 AG	2294-2423	GT	AGG
(GTG)	 AG	2595-2632	GT	AGG
(GTG)	 AG	2747-2884	GT	AGG
(AGA)	 AG	2925-2990	GT	GAG
(GAA)	 AG	3014-3043	GT	TTG
(AAA)	 AG	3066-3101	GT	GTG
(AGA)	 AG	3127-3135	GT	AGG
(GGG)	 AG	3364-3390	GT	AGG
(GGA)	 AG	3846-3879	GA	AAG
add_exon() Sorry, GeneMark_model.107445_t 2747-2884-terminal-1 is invalid.
-recovered GeneMark_model.107445_t, terminal, 2747, 2884
-recovered GeneMark_model.107445_t, terminal, 3127, 3135
-recovered GeneMark_model.107445_t, terminal, 3846, 3879
-recovered GeneMark_model.107445_t, internal, 63, 125
-recovered GeneMark_model.107445_t, internal, 147, 155
-recovered GeneMark_model.107445_t, internal, 183, 189
-recovered GeneMark_model.107445_t, internal, 1261, 1404
-recovered GeneMark_model.107445_t, internal, 1716, 1727
-recovered GeneMark_model.107445_t, internal, 1752, 1763
-recovered GeneMark_model.107445_t, internal, 1788, 1799
-recovered GeneMark_model.107445_t, internal, 1824, 1835
-recovered GeneMark_model.107445_t, internal, 1860, 1871
-recovered GeneMark_model.107445_t, internal, 1896, 1975
-recovered GeneMark_model.107445_t, internal, 2024, 2143
-recovered GeneMark_model.107445_t, internal, 2174, 2263
-recovered GeneMark_model.107445_t, internal, 2294, 2423
-recovered GeneMark_model.107445_t, internal, 2595, 2632
-recovered GeneMark_model.107445_t, internal, 2747, 2884
-recovered GeneMark_model.107445_t, internal, 2925, 2990
-recovered GeneMark_model.107445_t, internal, 3014, 3043
-recovered GeneMark_model.107445_t, internal, 3066, 3101
-recovered GeneMark_model.107445_t, internal, 3127, 3135
-recovered GeneMark_model.107445_t, internal, 3364, 3390
Valid prediction for snap_scaffold_369-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_61758-T1
Valid prediction for GeneMark_model.107447_t
Valid prediction for snap_scaffold_369-snap.2-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: -)Couldn't classify 5452, 5886
Sorry, prediction pasa_asmbl_41004.p2 fails validation.
(CCT)	 GA	5452-5886	AC	GAA
Valid prediction for GeneMark_model.107446_t
Couldn't classify 500, 520
Sorry, prediction GeneMark_model.107448_t fails validation.
(GGA)	 AG	500-520	GT	GAG
(AGG)	 AG	543-725	GT	GAG
(TCA)	 AG	753-771	AA	GAA
-recovered GeneMark_model.107448_t, terminal, 753, 771
-recovered GeneMark_model.107448_t, internal, 500, 520
-recovered GeneMark_model.107448_t, internal, 543, 725
Valid prediction for GlimmerHMM_glimmerT_61759-T1
add_exon() Sorry, GlimmerHMM_glimmerT_61759-T1 4787-4959-terminal-1 is invalid.
Couldn't classify 30, 83
Sorry, prediction snap_scaffold_369-snap.3-T1 fails validation.
(AGG)	 AG	30-83	GT	CGG
(TCA)	 AG	441-803	GT	AGG
(GGT)	 AG	3162-3470	GT	AGG
(CGG)	 AG	4787-4921	AA	AGA
-recovered snap_scaffold_369-snap.3-T1, terminal, 4787, 4921
-recovered snap_scaffold_369-snap.3-T1, internal, 30, 83
-recovered snap_scaffold_369-snap.3-T1, internal, 441, 803
-recovered snap_scaffold_369-snap.3-T1, internal, 3162, 3470
Couldn't classify 5203, 5432
Couldn't classify 5453, 5532
Couldn't classify 5573, 6030
Sorry, prediction CodingQuarry_transcript_46455-T1 fails validation.
(ATG)	 CT	5203-5432	CT	ACC
(CTC)	 AC	5453-5532	CT	ACC
(CTC)	 AC	5573-6030	CG	AAC
Couldn't classify 5203, 5432
Couldn't classify 5453, 5532
Couldn't classify 5573, 5844
Couldn't classify 5905, 5928
Couldn't classify 5977, 6030
Sorry, prediction CodingQuarry_transcript_46456-T1 fails validation.
(ATG)	 CT	5203-5432	CT	ACC
(CTC)	 AC	5453-5532	CT	ACC
(CTC)	 AC	5573-5844	CT	ATC
(CTG)	 AC	5905-5928	CT	ACC
(CTG)	 AC	5977-6030	CG	AAC

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6469, rend_intergenic: 2735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 7655
-exon list size: 83


building trellis

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94.1    
95.3    
96.5    
97.6    
98.8    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 6469, rend_intergenic: 2735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support