-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_401269-588289

-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 96410, 96742
Sorry, prediction pasa_asmbl_13922.p2 fails validation.
(ATG)	 AA	96410-96742	GG	CAG
Valid prediction for GeneMark_model.62351_t
Valid prediction for GlimmerHMM_glimmerT_36236-T1
Valid prediction for GeneMark_model.62344_t
Valid prediction for Augustus_model.g24367.t1
Valid prediction for GeneMark_model.62349_t
Valid prediction for GeneMark_model.62337_t
Valid prediction for snap_scaffold_15-snap.129-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.92-T1
Valid prediction for GlimmerHMM_glimmerT_36229-T1
Valid prediction for GeneMark_model.62314_t
Valid prediction for GeneMark_model.62329_t
Valid prediction for pasa_asmbl_14841.p1
Valid prediction for GeneMark_model.62339_t
Valid prediction for snap_scaffold_15-snap.118-T1
Valid prediction for GeneMark_model.62318_t
Valid prediction for snap_scaffold_15-snap.113-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_36243-T1
Valid prediction for GeneMark_model.62343_t
Valid prediction for GlimmerHMM_glimmerT_36223-T1
Couldn't classify 88443, 88472
Sorry, prediction pasa_asmbl_13921.p1 fails validation.
(GAG)	 CC	88443-88472	GT	GTG
(ATG)	 AG	88677-88769	GT	ACG
(GGA)	 AG	88893-89048	GT	AGG
(AGC)	 AG	89172-89315	GG	GAG
-recovered pasa_asmbl_13921.p1, initial, 88677, 88769
-recovered pasa_asmbl_13921.p1, terminal, 89172, 89315
-recovered pasa_asmbl_13921.p1, internal, 88677, 88769
-recovered pasa_asmbl_13921.p1, internal, 88893, 89048
Valid prediction for snap_scaffold_15-snap.126-T1
Valid prediction for snap_scaffold_15-snap.86-T1
Valid prediction for GlimmerHMM_glimmerT_36239-T1
Couldn't classify 108841, 108989
Couldn't classify 109665, 110040
Sorry, prediction pasa_asmbl_14820.p1 fails validation.
(ACA)	 CT	108841-108989	GT	ACG
(GTC)	 AG	109665-110040	GC	GGG
-recovered pasa_asmbl_14820.p1, internal, 109665, 110040
Valid prediction for snap_scaffold_15-snap.102-T1
Valid prediction for snap_scaffold_15-snap.110-T1
Valid prediction for Augustus_model.g24369.t1
Valid prediction for GeneMark_model.62334_t
Valid prediction for snap_scaffold_15-snap.95-T1
Valid prediction for GeneMark_model.62325_t
Valid prediction for snap_scaffold_15-snap.119-T1
Valid prediction for HiQ_model.g24370.t1
Valid prediction for snap_scaffold_15-snap.96-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.112-T1
Valid prediction for Augustus_model.g24368.t1
Valid prediction for pasa_asmbl_13926.p1
Valid prediction for GeneMark_model.62328_t
Valid prediction for GlimmerHMM_glimmerT_36232-T1
Valid prediction for snap_scaffold_15-snap.115-T1
Valid prediction for snap_scaffold_15-snap.106-T1
Valid prediction for snap_scaffold_15-snap.89-T1
Valid prediction for snap_scaffold_15-snap.108-T1
Valid prediction for Augustus_model.g24366.t1
Valid prediction for Augustus_model.g24359.t1
Valid prediction for CodingQuarry_transcript_17850-T1
Valid prediction for GeneMark_model.62333_t
Valid prediction for GlimmerHMM_glimmerT_36234-T1
Valid prediction for GlimmerHMM_glimmerT_36245-T1
Valid prediction for GeneMark_model.62331_t
Valid prediction for snap_scaffold_15-snap.116-T1
Valid prediction for GeneMark_model.62335_t
Valid prediction for GlimmerHMM_glimmerT_36225-T1
Valid prediction for CodingQuarry_transcript_17851-T1
Valid prediction for GlimmerHMM_glimmerT_36238-T1
Valid prediction for snap_scaffold_15-snap.111-T1
Valid prediction for snap_scaffold_15-snap.90-T1
Valid prediction for GeneMark_model.62321_t
Valid prediction for GeneMark_model.62309_t
Valid prediction for Augustus_model.g24371.t1
Valid prediction for pasa_asmbl_13918.p1
Valid prediction for snap_scaffold_15-snap.125-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g24372.t1
Valid prediction for GlimmerHMM_glimmerT_36242-T1
Valid prediction for snap_scaffold_15-snap.87-T1
Valid prediction for snap_scaffold_15-snap.124-T1
Valid prediction for CodingQuarry_transcript_17853-T1
Valid prediction for GeneMark_model.62347_t
Valid prediction for snap_scaffold_15-snap.120-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.62327_t
Valid prediction for snap_scaffold_15-snap.104-T1
Couldn't classify 124668, 125216
Sorry, prediction pasa_asmbl_13925.p1 fails validation.
(TAC)	 TG	124668-125216	CT	TGC
Valid prediction for snap_scaffold_15-snap.131-T1
Valid prediction for GeneMark_model.62326_t
Valid prediction for snap_scaffold_15-snap.105-T1
Valid prediction for GeneMark_model.62316_t
Valid prediction for snap_scaffold_15-snap.128-T1
Valid prediction for GeneMark_model.62306_t
Valid prediction for GlimmerHMM_glimmerT_36237-T1
Valid prediction for snap_scaffold_15-snap.122-T1
Valid prediction for snap_scaffold_15-snap.107-T1
Valid prediction for snap_scaffold_15-snap.100-T1
Valid prediction for GeneMark_model.62324_t
Valid prediction for GeneMark_model.62311_t
Valid prediction for GlimmerHMM_glimmerT_36244-T1
Valid prediction for GlimmerHMM_glimmerT_36222-T1
Valid prediction for snap_scaffold_15-snap.123-T1
Valid prediction for snap_scaffold_15-snap.109-T1
Valid prediction for GeneMark_model.62341_t
Valid prediction for GeneMark_model.62305_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 Augustus_model.g24364.t1
Valid prediction for GeneMark_model.62319_t
Valid prediction for GlimmerHMM_glimmerT_36248-T1
Valid prediction for GeneMark_model.62307_t
Valid prediction for GeneMark_model.62317_t
Valid prediction for GlimmerHMM_glimmerT_36235-T1
Valid prediction for GeneMark_model.62322_t
Valid prediction for snap_scaffold_15-snap.103-T1
Couldn't classify 36495, 36974
Sorry, prediction pasa_asmbl_14943.p1 fails validation.
(GAC)	 CG	36495-36974	AT	ACA
Valid prediction for snap_scaffold_15-snap.117-T1
Valid prediction for GeneMark_model.62342_t
Valid prediction for GeneMark_model.62310_t
Couldn't classify 39192, 39355
Couldn't classify 39849, 40605
Sorry, prediction pasa_asmbl_14941.p1 fails validation.
(AGC)	 CC	39192-39355	GT	AGG
(GGA)	 AG	39849-40605	GA	GGG
Valid prediction for Augustus_model.g24360.t1
Valid prediction for GlimmerHMM_glimmerT_36247-T1
Couldn't classify 42806, 42909
Couldn't classify 46844, 46858
Sorry, prediction pasa_asmbl_14940.p1 fails validation.
(GAA)	 GA	42806-42909	GT	AAG
(GTA)	 AG	43706-43821	GT	AGG
(GAG)	 AG	44251-44369	GT	AGG
(GCG)	 AG	44491-44609	GT	AGG
(GTG)	 AG	45048-45189	GT	AGG
(TAC)	 AG	46844-46858	AT	CCA
-recovered pasa_asmbl_14940.p1, internal, 43706, 43821
-recovered pasa_asmbl_14940.p1, internal, 44251, 44369
-recovered pasa_asmbl_14940.p1, internal, 44491, 44609
-recovered pasa_asmbl_14940.p1, internal, 45048, 45189
Valid prediction for GeneMark_model.62338_t
Valid prediction for GlimmerHMM_glimmerT_36227-T1
Valid prediction for GeneMark_model.62350_t
Valid prediction for GlimmerHMM_glimmerT_36226-T1
Couldn't classify 173562, 173655
Sorry, prediction pasa_asmbl_15946.p1 fails validation.
(ATT)	 AG	173562-173655	GT	AGG
(GAC)	 AG	175562-175657	GT	TGG
(AGT)	 AG	176310-176449	GC	GAG
-recovered pasa_asmbl_15946.p1, terminal, 176310, 176449
-recovered pasa_asmbl_15946.p1, internal, 173562, 173655
-recovered pasa_asmbl_15946.p1, internal, 175562, 175657
-recovered pasa_asmbl_15946.p1, internal, 176310, 176449
Valid prediction for GeneMark_model.62340_t
Valid prediction for Augustus_model.g24361.t1
Valid prediction for GlimmerHMM_glimmerT_36246-T1
Valid prediction for snap_scaffold_15-snap.93-T1
Valid prediction for GeneMark_model.62312_t
Valid prediction for snap_scaffold_15-snap.88-T1
Valid prediction for snap_scaffold_15-snap.94-T1
Valid prediction for GeneMark_model.62348_t
Valid prediction for GeneMark_model.62332_t
Valid prediction for GeneMark_model.62313_t
Couldn't classify 46964, 47088
Sorry, prediction pasa_asmbl_14939.p1 fails validation.
(CCT)	 AG	46964-47088	GT	ACG
(GTC)	 AG	47446-47554	GT	AGG
(CCG)	 AG	47972-48178	GT	AGG
(GTG)	 AG	48440-48549	GT	AGG
(CAT)	 AG	49083-49197	GT	AGG
(GTG)	 AG	49739-49876	GT	AGG
(ATC)	 AG	50033-50223	GT	AGG
(GCG)	 AG	51487-51733	GT	GGG
(GTC)	 AG	52349-52564	GT	AGG
(ATC)	 AG	53215-53355	AC	GAA
-recovered pasa_asmbl_14939.p1, terminal, 53215, 53355
-recovered pasa_asmbl_14939.p1, internal, 46964, 47088
-recovered pasa_asmbl_14939.p1, internal, 47446, 47554
-recovered pasa_asmbl_14939.p1, internal, 47972, 48178
-recovered pasa_asmbl_14939.p1, internal, 48440, 48549
-recovered pasa_asmbl_14939.p1, internal, 49083, 49197
-recovered pasa_asmbl_14939.p1, internal, 49739, 49876
-recovered pasa_asmbl_14939.p1, internal, 50033, 50223
-recovered pasa_asmbl_14939.p1, internal, 51487, 51733
-recovered pasa_asmbl_14939.p1, internal, 52349, 52564
Valid prediction for snap_scaffold_15-snap.99-T1
Valid prediction for snap_scaffold_15-snap.91-T1
Valid prediction for GeneMark_model.62346_t
Valid prediction for GlimmerHMM_glimmerT_36230-T1
Valid prediction for Augustus_model.g24362.t1
Valid prediction for GeneMark_model.62345_t
Valid prediction for GeneMark_model.62320_t
Valid prediction for GlimmerHMM_glimmerT_36224-T1
Valid prediction for snap_scaffold_15-snap.101-T1
Valid prediction for snap_scaffold_15-snap.97-T1
Couldn't classify 38331, 39095
Sorry, prediction pasa_asmbl_14942.p1 fails validation.
(TCA)	 TG	38331-39095	GG	AAG
Valid prediction for GlimmerHMM_glimmerT_36228-T1
Valid prediction for snap_scaffold_15-snap.85-T1
Valid prediction for snap_scaffold_15-snap.121-T1
Valid prediction for GeneMark_model.62330_t
Valid prediction for Augustus_model.g24363.t1
Valid prediction for GlimmerHMM_glimmerT_36241-T1
Valid prediction for snap_scaffold_15-snap.98-T1
Valid prediction for snap_scaffold_15-snap.127-T1
Valid prediction for GeneMark_model.62315_t
Valid prediction for Augustus_model.g24374.t1
Valid prediction for GlimmerHMM_glimmerT_36231-T1
Valid prediction for GeneMark_model.62336_t
Valid prediction for snap_scaffold_15-snap.130-T1
Valid prediction for GlimmerHMM_glimmerT_36233-T1
Valid prediction for Augustus_model.g24373.t1
Couldn't classify 168349, 169998
Sorry, prediction pasa_asmbl_14935.p1 fails validation.
(ATG)	 GA	167877-167978	GT	AGG
(AAC)	 AG	168349-169998	GG	AGG
-recovered pasa_asmbl_14935.p1, initial, 167877, 167978
Valid prediction for Augustus_model.g24365.t1
Couldn't classify 29942, 30006
Sorry, prediction pasa_asmbl_15889.p1 fails validation.
(ATG)	 AC	26365-26410	GT	AGG
(ATC)	 AG	28264-28396	GT	TGG
(CTC)	 AG	28711-28805	GT	GAG
(ATC)	 AG	29942-30006	TT	AGT
-recovered pasa_asmbl_15889.p1, initial, 26365, 26410
-recovered pasa_asmbl_15889.p1, internal, 28264, 28396
-recovered pasa_asmbl_15889.p1, internal, 28711, 28805
Valid prediction for GeneMark_model.62323_t
Valid prediction for snap_scaffold_15-snap.114-T1
Valid prediction for CodingQuarry_transcript_17849-T1
Valid prediction for GlimmerHMM_glimmerT_36240-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19145, rend_intergenic: 12171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30132, rend_intergenic: 23024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38213, rend_intergenic: 35594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59134, rend_intergenic: 54351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71134, rend_intergenic: 68274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119094, rend_intergenic: 117488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147248, rend_intergenic: 134169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169313, rend_intergenic: 151860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172553, rend_intergenic: 169631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184072, rend_intergenic: 182587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187021
-exon list size: 713


building trellis

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71.2    
71.3    
71.5    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.1    
73.3    
73.4    
73.6    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.5    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 19145, rend_intergenic: 12171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30132, rend_intergenic: 23024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38213, rend_intergenic: 35594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59134, rend_intergenic: 54351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71134, rend_intergenic: 68274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119094, rend_intergenic: 117488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147248, rend_intergenic: 134169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169313, rend_intergenic: 151860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172553, rend_intergenic: 169631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184072, rend_intergenic: 182587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support