-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_1-156991

-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 GeneMark_model.37222_t
Valid prediction for GlimmerHMM_glimmerT_21925-T1
Valid prediction for GlimmerHMM_glimmerT_21921-T1
Valid prediction for GlimmerHMM_glimmerT_21916-T1
Valid prediction for GeneMark_model.37217_t
Valid prediction for snap_scaffold_9-snap.27-T1
Valid prediction for GlimmerHMM_glimmerT_21924-T1
Valid prediction for GeneMark_model.37227_t
Valid prediction for snap_scaffold_9-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_21910-T1
Valid prediction for GlimmerHMM_glimmerT_21927-T1
Valid prediction for snap_scaffold_9-snap.21-T1
Valid prediction for Augustus_model.g14676.t1
Valid prediction for GeneMark_model.37242_t
Valid prediction for GeneMark_model.37213_t
Valid prediction for HiQ_model.g14689.t1
Valid prediction for GeneMark_model.37240_t
Valid prediction for Augustus_model.g14679.t1
Valid prediction for GlimmerHMM_glimmerT_21912-T1
Valid prediction for snap_scaffold_9-snap.35-T1
Valid prediction for GlimmerHMM_glimmerT_21914-T1
Valid prediction for snap_scaffold_9-snap.32-T1
Valid prediction for snap_scaffold_9-snap.16-T1
Couldn't classify 45431, 45462
Couldn't classify 47018, 47063
Sorry, prediction pasa_asmbl_53725.p1 fails validation.
(ATG)	 CC	44812-44944	GT	TGG
(TTT)	 AG	45161-45255	GT	GGG
(CTG)	 AG	45431-45462	AT	ACA
(TGT)	 AC	47018-47063	GT	AGG
(GGC)	 AG	50039-50121	GT	AGG
(AGC)	 AG	50289-50425	GT	AGG
(ATA)	 AG	50902-50956	GT	CTG
(GAA)	 AG	51328-51538	GG	AAG
-recovered pasa_asmbl_53725.p1, initial, 44812, 44944
-recovered pasa_asmbl_53725.p1, terminal, 51328, 51538
-recovered pasa_asmbl_53725.p1, internal, 45161, 45255
-recovered pasa_asmbl_53725.p1, internal, 50039, 50121
-recovered pasa_asmbl_53725.p1, internal, 50289, 50425
-recovered pasa_asmbl_53725.p1, internal, 50902, 50956
Valid prediction for HiQ_model.g14683.t1
Valid prediction for CodingQuarry_transcript_61933-T1
Valid prediction for pasa_asmbl_53727.p1
Couldn't classify 88126, 88332
Sorry, prediction pasa_asmbl_53732.p1 fails validation.
(TTC)	 AC	88126-88332	GT	TGG
(GAT)	 AG	90146-90289	GT	ACG
(AAC)	 AG	91347-91529	GT	GGG
(GGT)	 AG	91999-92109	GT	AGG
(AGG)	 AG	92457-92607	GT	CCG
(GCA)	 AG	92868-92953	AT	AAA
-recovered pasa_asmbl_53732.p1, terminal, 92868, 92953
-recovered pasa_asmbl_53732.p1, internal, 90146, 90289
-recovered pasa_asmbl_53732.p1, internal, 91347, 91529
-recovered pasa_asmbl_53732.p1, internal, 91999, 92109
-recovered pasa_asmbl_53732.p1, internal, 92457, 92607
Valid prediction for snap_scaffold_9-snap.34-T1
Valid prediction for HiQ_model.g14677.t1
Valid prediction for snap_scaffold_9-snap.10-T1
Valid prediction for snap_scaffold_9-snap.7-T1
Valid prediction for snap_scaffold_9-snap.36-T1
Valid prediction for GlimmerHMM_glimmerT_21923-T1
Valid prediction for snap_scaffold_9-snap.5-T1
Valid prediction for pasa_asmbl_53730.p1
Valid prediction for snap_scaffold_9-snap.2-T1
Valid prediction for GeneMark_model.37234_t
Valid prediction for GlimmerHMM_glimmerT_21920-T1
Valid prediction for snap_scaffold_9-snap.24-T1
Valid prediction for pasa_asmbl_53733.p1
Valid prediction for snap_scaffold_9-snap.29-T1
Valid prediction for CodingQuarry_transcript_61931-T1
Valid prediction for GeneMark_model.37215_t
Valid prediction for Augustus_model.g14681.t1
Valid prediction for GeneMark_model.37230_t
Valid prediction for Augustus_model.g14688.t1
Valid prediction for GlimmerHMM_glimmerT_21906-T1
Valid prediction for GeneMark_model.37243_t
Valid prediction for GlimmerHMM_glimmerT_21902-T1
Valid prediction for Augustus_model.g14691.t1
Valid prediction for snap_scaffold_9-snap.14-T1
Valid prediction for snap_scaffold_9-snap.6-T1
Valid prediction for CodingQuarry_transcript_61934-T1
Valid prediction for Augustus_model.g14692.t1
Valid prediction for snap_scaffold_9-snap.9-T1
Valid prediction for GlimmerHMM_glimmerT_21907-T1
Valid prediction for HiQ_model.g14684.t1
Valid prediction for GeneMark_model.37219_t
Valid prediction for GeneMark_model.37245_t
Valid prediction for GeneMark_model.37225_t
Valid prediction for snap_scaffold_9-snap.23-T1
Valid prediction for GlimmerHMM_glimmerT_21908-T1
Valid prediction for snap_scaffold_9-snap.30-T1
Valid prediction for snap_scaffold_9-snap.12-T1
Valid prediction for GlimmerHMM_glimmerT_21917-T1
Valid prediction for Augustus_model.g14687.t1
Valid prediction for GeneMark_model.37239_t
Valid prediction for GeneMark_model.37232_t
Valid prediction for GlimmerHMM_glimmerT_21926-T1
Valid prediction for GeneMark_model.37237_t
Valid prediction for CodingQuarry_transcript_61932-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: -)Valid prediction for snap_scaffold_9-snap.19-T1
Valid prediction for GlimmerHMM_glimmerT_21903-T1
Valid prediction for Augustus_model.g14673.t1
Couldn't classify 122291, 122404
Couldn't classify 131530, 131622
Sorry, prediction pasa_asmbl_54764.p1 fails validation.
(CAG)	 TG	122291-122404	GT	AGG
(GAT)	 AG	123901-123948	GT	AGG
(ATT)	 AG	124688-124766	GT	AGG
(ACC)	 AG	124951-125088	GT	GGG
(AGG)	 AG	125562-125685	GT	AGG
(AAA)	 AG	125911-125987	GT	AGG
(CAC)	 AG	126460-126526	GT	AAG
(GGC)	 AG	126934-126982	GT	AGG
(AGA)	 AG	127158-127262	GT	CGG
(ACA)	 AG	127579-127758	GT	GGG
(GAG)	 AG	129713-129771	GT	AAG
(TAT)	 AG	130016-130061	GT	AGG
(GAC)	 AG	131530-131622	GG	ACG
add_exon() Sorry, pasa_asmbl_54764.p1 126460-126526-terminal-3 is invalid.
-recovered pasa_asmbl_54764.p1, terminal, 126460, 126526
-recovered pasa_asmbl_54764.p1, internal, 123901, 123948
-recovered pasa_asmbl_54764.p1, internal, 124688, 124766
-recovered pasa_asmbl_54764.p1, internal, 124951, 125088
-recovered pasa_asmbl_54764.p1, internal, 125562, 125685
-recovered pasa_asmbl_54764.p1, internal, 125911, 125987
-recovered pasa_asmbl_54764.p1, internal, 126460, 126526
-recovered pasa_asmbl_54764.p1, internal, 126934, 126982
-recovered pasa_asmbl_54764.p1, internal, 127158, 127262
-recovered pasa_asmbl_54764.p1, internal, 127579, 127758
-recovered pasa_asmbl_54764.p1, internal, 129713, 129771
-recovered pasa_asmbl_54764.p1, internal, 130016, 130061
Valid prediction for snap_scaffold_9-snap.22-T1
Valid prediction for GeneMark_model.37241_t
Valid prediction for GlimmerHMM_glimmerT_21922-T1
Valid prediction for snap_scaffold_9-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_21918-T1
Valid prediction for Augustus_model.g14690.t1
Couldn't classify 145289, 145509
Couldn't classify 145830, 146004
Sorry, prediction pasa_asmbl_54762.p1 fails validation.
(GAG)	 CG	145289-145509	GT	AGG
(GTC)	 AG	145830-146004	TA	GTT
Valid prediction for GlimmerHMM_glimmerT_21904-T1
Valid prediction for Augustus_model.g14686.t1
Valid prediction for snap_scaffold_9-snap.31-T1
Valid prediction for GeneMark_model.37216_t
Valid prediction for snap_scaffold_9-snap.17-T1
Valid prediction for HiQ_model.g14678.t1
Valid prediction for GlimmerHMM_glimmerT_21913-T1
Valid prediction for GeneMark_model.37212_t
Valid prediction for Augustus_model.g14675.t1
Valid prediction for CodingQuarry_transcript_61930-T1
Valid prediction for GlimmerHMM_glimmerT_21915-T1
Couldn't classify 103807, 104334
Sorry, prediction pasa_asmbl_54766.p1 fails validation.
(ATG)	 CG	102974-103456	GT	AGG
(GTG)	 AG	103807-104334	GG	GGG
-recovered pasa_asmbl_54766.p1, initial, 102974, 103456
Valid prediction for Augustus_model.g14685.t1
Valid prediction for GlimmerHMM_glimmerT_21911-T1
Valid prediction for GeneMark_model.37226_t
Valid prediction for snap_scaffold_9-snap.26-T1
Valid prediction for snap_scaffold_9-snap.18-T1
Valid prediction for snap_scaffold_9-snap.8-T1
Valid prediction for snap_scaffold_9-snap.13-T1
Couldn't classify 88764, 88847
Sorry, prediction pasa_asmbl_54770.p1 fails validation.
(ATG)	 AA	81025-81099	GT	AGG
(ATG)	 AG	81251-81403	GT	AGG
(GTT)	 AG	81527-81659	GT	AGG
(GTC)	 AG	81922-82126	GT	AGG
(GAC)	 AG	82372-82488	GT	GGG
(GCA)	 AG	82688-82838	GT	AGG
(GCT)	 AG	82999-83153	GT	GAG
(GGA)	 AG	83585-83669	GT	AGG
(GCG)	 AG	84356-84493	GT	AGG
(GAC)	 AG	84846-84947	GT	TGG
(GAG)	 AG	86665-86721	GT	AGG
(AAT)	 AG	88131-88268	GT	AGG
(AGG)	 AG	88764-88847	TA	AGT
-recovered pasa_asmbl_54770.p1, initial, 81025, 81099
-recovered pasa_asmbl_54770.p1, initial, 81251, 81403
-recovered pasa_asmbl_54770.p1, internal, 81251, 81403
-recovered pasa_asmbl_54770.p1, internal, 81527, 81659
-recovered pasa_asmbl_54770.p1, internal, 81922, 82126
-recovered pasa_asmbl_54770.p1, internal, 82372, 82488
-recovered pasa_asmbl_54770.p1, internal, 82688, 82838
-recovered pasa_asmbl_54770.p1, internal, 82999, 83153
-recovered pasa_asmbl_54770.p1, internal, 83585, 83669
-recovered pasa_asmbl_54770.p1, internal, 84356, 84493
-recovered pasa_asmbl_54770.p1, internal, 84846, 84947
-recovered pasa_asmbl_54770.p1, internal, 86665, 86721
-recovered pasa_asmbl_54770.p1, internal, 88131, 88268
Valid prediction for GlimmerHMM_glimmerT_21909-T1
Valid prediction for GeneMark_model.37221_t
Valid prediction for GeneMark_model.37235_t
Valid prediction for snap_scaffold_9-snap.28-T1
Valid prediction for snap_scaffold_9-snap.15-T1
Valid prediction for snap_scaffold_9-snap.3-T1
Valid prediction for GeneMark_model.37228_t
Valid prediction for Augustus_model.g14680.t1
Valid prediction for GeneMark_model.37238_t
Valid prediction for GeneMark_model.37244_t
Valid prediction for snap_scaffold_9-snap.4-T1
Valid prediction for snap_scaffold_9-snap.20-T1
Valid prediction for GeneMark_model.37218_t
Valid prediction for GlimmerHMM_glimmerT_21901-T1
Valid prediction for GlimmerHMM_glimmerT_21905-T1
Valid prediction for GeneMark_model.37214_t
Valid prediction for GeneMark_model.37223_t
Valid prediction for GlimmerHMM_glimmerT_21919-T1
Couldn't classify 93514, 93675
Sorry, prediction pasa_asmbl_54767.p2 fails validation.
(TTT)	 GG	93514-93675	GT	GGG
(GGG)	 AG	94190-94334	GT	GGG
(CCA)	 AG	94449-94609	GT	ATG
(GTG)	 AG	94712-94765	GT	AGG
(GGT)	 AG	94890-95021	GC	GAG
-recovered pasa_asmbl_54767.p2, terminal, 94890, 95021
-recovered pasa_asmbl_54767.p2, internal, 94190, 94334
-recovered pasa_asmbl_54767.p2, internal, 94449, 94609
-recovered pasa_asmbl_54767.p2, internal, 94712, 94765
-recovered pasa_asmbl_54767.p2, internal, 94890, 95021
Valid prediction for snap_scaffold_9-snap.25-T1
Valid prediction for GeneMark_model.37231_t
Valid prediction for snap_scaffold_9-snap.38-T1
Valid prediction for GeneMark_model.37224_t
Valid prediction for snap_scaffold_9-snap.33-T1
Valid prediction for GeneMark_model.37236_t
Valid prediction for HiQ_model.g14682.t1
Valid prediction for Augustus_model.g14674.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7630, rend_intergenic: 5997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19266, rend_intergenic: 11841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28089, rend_intergenic: 25253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37822, rend_intergenic: 28738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54046, rend_intergenic: 52400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62517, rend_intergenic: 58165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63519, rend_intergenic: 62738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75069, rend_intergenic: 64264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81387, rend_intergenic: 79589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104259, rend_intergenic: 100378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113971, rend_intergenic: 110012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128687, rend_intergenic: 125740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140145, rend_intergenic: 131922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156991
-exon list size: 550


building trellis

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85.0    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 7630, rend_intergenic: 5997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19266, rend_intergenic: 11841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28089, rend_intergenic: 25253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37822, rend_intergenic: 28738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54046, rend_intergenic: 52400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62517, rend_intergenic: 58165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63519, rend_intergenic: 62738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75069, rend_intergenic: 64264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81387, rend_intergenic: 79589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104259, rend_intergenic: 100378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113971, rend_intergenic: 110012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128687, rend_intergenic: 125740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140145, rend_intergenic: 131922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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