-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_337

-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 223, 312
Sorry, prediction Augustus_model.g41028.t1 fails validation.
(GCC)	 AG	223-312	GT	AGG
(ATG)	 AG	689-777	GT	AAG
(TCC)	 AG	1461-1680	GT	TGG
(GTA)	 AG	1817-1939	GT	CTG
(TAT)	 AG	2107-2272	GT	AGG
(GGG)	 AG	4713-4798	GT	TGG
(AAT)	 AG	5023-5117	CT	GAC
-recovered Augustus_model.g41028.t1, initial, 689, 777
-recovered Augustus_model.g41028.t1, terminal, 5023, 5117
-recovered Augustus_model.g41028.t1, internal, 223, 312
-recovered Augustus_model.g41028.t1, internal, 689, 777
-recovered Augustus_model.g41028.t1, internal, 1461, 1680
-recovered Augustus_model.g41028.t1, internal, 1817, 1939
-recovered Augustus_model.g41028.t1, internal, 2107, 2272
-recovered Augustus_model.g41028.t1, internal, 4713, 4798
Couldn't classify 223, 312
Sorry, prediction snap_scaffold_337-snap.1-T1 fails validation.
(GCC)	 AG	223-312	GT	AGG
(CCA)	 AG	489-620	GT	AGG
(ATG)	 AG	689-777	GT	AAG
(TCC)	 AG	1461-1680	GT	TGG
(GTA)	 AG	1817-1914	GT	TAG
(TAC)	 AG	2130-2237	GT	CCG
(ATG)	 AG	2848-2967	GG	AAG
-recovered snap_scaffold_337-snap.1-T1, initial, 689, 777
-recovered snap_scaffold_337-snap.1-T1, terminal, 2848, 2967
-recovered snap_scaffold_337-snap.1-T1, internal, 223, 312
-recovered snap_scaffold_337-snap.1-T1, internal, 489, 620
-recovered snap_scaffold_337-snap.1-T1, internal, 689, 777
-recovered snap_scaffold_337-snap.1-T1, internal, 1461, 1680
-recovered snap_scaffold_337-snap.1-T1, internal, 1817, 1914
-recovered snap_scaffold_337-snap.1-T1, internal, 2130, 2237
Couldn't classify 222, 312
Sorry, prediction pasa_asmbl_40949.p1 fails validation.
(GGC)	 CA	222-312	GT	AGG
(ATG)	 AG	689-777	GT	AAG
(TCC)	 AG	1461-1680	GT	TGG
(GTA)	 AG	1817-1939	GT	CTG
(TAT)	 AG	2107-2272	GT	AGG
(GGG)	 AG	4713-4798	GT	TGG
(AAT)	 AG	5023-5117	CT	GAC
-recovered pasa_asmbl_40949.p1, initial, 689, 777
-recovered pasa_asmbl_40949.p1, terminal, 5023, 5117
-recovered pasa_asmbl_40949.p1, internal, 689, 777
-recovered pasa_asmbl_40949.p1, internal, 1461, 1680
-recovered pasa_asmbl_40949.p1, internal, 1817, 1939
-recovered pasa_asmbl_40949.p1, internal, 2107, 2272
-recovered pasa_asmbl_40949.p1, internal, 4713, 4798
Valid prediction for GeneMark_model.107346_t
Valid prediction for GlimmerHMM_glimmerT_61724-T1
Couldn't classify 7074, 7540
Sorry, prediction snap_scaffold_337-snap.4-T1 fails validation.
(ATG)	 TG	5466-5548	GT	ATG
(AGA)	 AG	6730-6849	GT	ATG
(CTC)	 AG	7074-7540	GT	GGG
-recovered snap_scaffold_337-snap.4-T1, initial, 5466, 5548
-recovered snap_scaffold_337-snap.4-T1, internal, 6730, 6849
-recovered snap_scaffold_337-snap.4-T1, internal, 7074, 7540
Valid prediction for snap_scaffold_337-snap.3-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_61725-T1
Valid prediction for Augustus_model.g41029.t1
Couldn't classify 223, 312
Sorry, prediction GeneMark_model.107344_t fails validation.
(GCC)	 AG	223-312	GT	AGG
(CCA)	 AG	489-578	GT	AGG
(ATG)	 AG	689-826	GT	GGG
(TCC)	 AG	1461-1497	GT	GGG
(GAC)	 AG	1518-1605	CC	GAC
add_exon() Sorry, GeneMark_model.107344_t 689-826-initial-1 is invalid.
-recovered GeneMark_model.107344_t, initial, 689, 826
-recovered GeneMark_model.107344_t, terminal, 1518, 1605
-recovered GeneMark_model.107344_t, internal, 223, 312
-recovered GeneMark_model.107344_t, internal, 489, 578
-recovered GeneMark_model.107344_t, internal, 689, 826
-recovered GeneMark_model.107344_t, internal, 1461, 1497

-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 GeneMark_model.107345_t
Couldn't classify 490, 621
Sorry, prediction GeneMark_model.107347_t fails validation.
(CAG)	 AG	490-621	GT	TGG
(GTG)	 AG	679-908	GT	TCG
(AGA)	 AG	956-991	GT	ACG
(TCA)	 AG	1022-1036	GT	GAG
(AGA)	 AG	1334-1348	GT	GAG
(AGA)	 AG	1376-1390	GT	GTG
(AGC)	 AG	1892-1957	GT	ATG
(AGA)	 AG	1990-2025	GT	CAG
(GAG)	 AG	2246-2327	GG	GAG
-recovered GeneMark_model.107347_t, terminal, 2246, 2327
-recovered GeneMark_model.107347_t, internal, 490, 621
-recovered GeneMark_model.107347_t, internal, 679, 908
-recovered GeneMark_model.107347_t, internal, 956, 991
-recovered GeneMark_model.107347_t, internal, 1022, 1036
-recovered GeneMark_model.107347_t, internal, 1334, 1348
-recovered GeneMark_model.107347_t, internal, 1376, 1390
-recovered GeneMark_model.107347_t, internal, 1892, 1957
-recovered GeneMark_model.107347_t, internal, 1990, 2025
Couldn't classify 727, 901
Couldn't classify 7418, 7532
Sorry, prediction snap_scaffold_337-snap.2-T1 fails validation.
(GGG)	 AG	727-901	GT	CGG
(GAG)	 AG	2246-2374	GT	GGG
(CGG)	 AG	5793-5869	GT	AGG
(CCA)	 AG	6364-6481	GT	AGG
(GCT)	 AG	7418-7532	GT	AGG
-recovered snap_scaffold_337-snap.2-T1, internal, 727, 901
-recovered snap_scaffold_337-snap.2-T1, internal, 2246, 2374
-recovered snap_scaffold_337-snap.2-T1, internal, 5793, 5869
-recovered snap_scaffold_337-snap.2-T1, internal, 6364, 6481
-recovered snap_scaffold_337-snap.2-T1, internal, 7418, 7532

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 2967, rend_intergenic: 470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7275, rend_intergenic: 4692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 8001
-exon list size: 85


building trellis

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77.0    
78.2    
79.3    
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82.8    
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88.5    
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90.8    
92.0    
93.1    
94.3    
95.4    
96.6    
97.7    
98.9    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 2967, rend_intergenic: 470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7275, rend_intergenic: 4692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support