-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_10745154-10887653

-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.92212_t
Valid prediction for snap_scaffold_23-snap.2100-T1
Valid prediction for GlimmerHMM_glimmerT_53041-T1
Valid prediction for GlimmerHMM_glimmerT_53036-T1
Valid prediction for snap_scaffold_23-snap.2105-T1
Valid prediction for snap_scaffold_23-snap.2103-T1
Valid prediction for pasa_asmbl_31215.p1
Valid prediction for GlimmerHMM_glimmerT_53052-T1
Valid prediction for snap_scaffold_23-snap.2116-T1
Valid prediction for GlimmerHMM_glimmerT_53055-T1
Valid prediction for GlimmerHMM_glimmerT_53050-T1
Valid prediction for GlimmerHMM_glimmerT_53049-T1
Valid prediction for snap_scaffold_23-snap.2130-T1
Valid prediction for snap_scaffold_23-snap.2117-T1
Valid prediction for GeneMark_model.92215_t
Valid prediction for snap_scaffold_23-snap.2126-T1
Valid prediction for snap_scaffold_23-snap.2123-T1
Valid prediction for GeneMark_model.92190_t
Valid prediction for GeneMark_model.92192_t
Valid prediction for snap_scaffold_23-snap.2094-T1
Valid prediction for GlimmerHMM_glimmerT_53056-T1
Valid prediction for GeneMark_model.92201_t
Valid prediction for snap_scaffold_23-snap.2098-T1
Valid prediction for CodingQuarry_transcript_35737-T1
Valid prediction for GeneMark_model.92195_t
Valid prediction for GlimmerHMM_glimmerT_53045-T1
Valid prediction for GeneMark_model.92198_t
Valid prediction for snap_scaffold_23-snap.2106-T1
Valid prediction for snap_scaffold_23-snap.2107-T1
Couldn't classify 110589, 110675
Couldn't classify 113287, 113356
Sorry, prediction pasa_asmbl_31169.p1 fails validation.
(AGT)	 AG	110589-110675	GT	ACG
(GGA)	 AG	111870-111902	GT	AGG
(GAG)	 AG	112514-112635	GT	AGG
(CTA)	 AG	112915-113010	GT	GAG
(TCG)	 AG	113287-113356	GC	ATG
-recovered pasa_asmbl_31169.p1, internal, 110589, 110675
-recovered pasa_asmbl_31169.p1, internal, 111870, 111902
-recovered pasa_asmbl_31169.p1, internal, 112514, 112635
-recovered pasa_asmbl_31169.p1, internal, 112915, 113010
-recovered pasa_asmbl_31169.p1, internal, 113287, 113356
Valid prediction for GeneMark_model.92208_t
Valid prediction for snap_scaffold_23-snap.2109-T1
Couldn't classify 85433, 85464
Sorry, prediction pasa_asmbl_31165.p1 fails validation.
(GAT)	 AG	85433-85464	GT	AGG
(GAT)	 AG	86742-86815	GT	CGG
(GAA)	 AG	86931-86971	GT	AGG
(ATC)	 AG	87220-87281	GT	AGG
(GGA)	 AG	87768-87867	GT	ACG
(CCC)	 AG	88680-88762	GT	CGG
(ACG)	 AG	89417-89576	GT	ATG
(GTG)	 AG	89836-90046	GT	AGG
(AAC)	 AG	90413-90576	GT	TGG
(CAA)	 AG	91000-91160	GT	ACG
(ATT)	 AG	91440-91497	GT	AGG
(GAC)	 AG	91586-91651	CA	AGC
-recovered pasa_asmbl_31165.p1, terminal, 91586, 91651
-recovered pasa_asmbl_31165.p1, internal, 85433, 85464
-recovered pasa_asmbl_31165.p1, internal, 86742, 86815
-recovered pasa_asmbl_31165.p1, internal, 86931, 86971
-recovered pasa_asmbl_31165.p1, internal, 87220, 87281
-recovered pasa_asmbl_31165.p1, internal, 87768, 87867
-recovered pasa_asmbl_31165.p1, internal, 88680, 88762
-recovered pasa_asmbl_31165.p1, internal, 89417, 89576
-recovered pasa_asmbl_31165.p1, internal, 89836, 90046
-recovered pasa_asmbl_31165.p1, internal, 90413, 90576
-recovered pasa_asmbl_31165.p1, internal, 91000, 91160
-recovered pasa_asmbl_31165.p1, internal, 91440, 91497
Valid prediction for CodingQuarry_transcript_35738-T1
Valid prediction for snap_scaffold_23-snap.2113-T1
Valid prediction for snap_scaffold_23-snap.2099-T1
Valid prediction for GeneMark_model.92214_t
Valid prediction for pasa_asmbl_31223.p1
Valid prediction for GlimmerHMM_glimmerT_53057-T1
Valid prediction for GeneMark_model.92220_t
Valid prediction for GeneMark_model.92197_t
Valid prediction for GeneMark_model.92224_t
Valid prediction for GeneMark_model.92217_t
Valid prediction for CodingQuarry_transcript_35736-T1
Valid prediction for GeneMark_model.92221_t
Valid prediction for GeneMark_model.92194_t
Valid prediction for snap_scaffold_23-snap.2120-T1
Valid prediction for snap_scaffold_23-snap.2114-T1
Valid prediction for GeneMark_model.92204_t
Couldn't classify 115417, 115551
Couldn't classify 116539, 116642
Sorry, prediction pasa_asmbl_31170.p1 fails validation.
(CAC)	 CA	115417-115551	GT	TGG
(GTA)	 AG	115675-115789	GT	AGG
(AGT)	 AG	116539-116642	AA	CCA
-recovered pasa_asmbl_31170.p1, internal, 115675, 115789
Valid prediction for GlimmerHMM_glimmerT_53039-T1
Valid prediction for CodingQuarry_transcript_35741-T1
Valid prediction for GeneMark_model.92219_t
Valid prediction for snap_scaffold_23-snap.2128-T1
Valid prediction for snap_scaffold_23-snap.2097-T1
Couldn't classify 77762, 78091
Sorry, prediction pasa_asmbl_31875.p1 fails validation.
(ATG)	 AG	77762-78091	GG	GGG

-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.92222_t
Valid prediction for snap_scaffold_23-snap.2115-T1
Valid prediction for snap_scaffold_23-snap.2110-T1
Couldn't classify 78588, 78896
Sorry, prediction pasa_asmbl_31872.p1 fails validation.
(CCA)	 TA	78588-78896	TG	AAT
Valid prediction for GeneMark_model.92188_t
Valid prediction for GeneMark_model.92225_t
Valid prediction for GlimmerHMM_glimmerT_53037-T1
Valid prediction for GlimmerHMM_glimmerT_53047-T1
Valid prediction for snap_scaffold_23-snap.2118-T1
Valid prediction for snap_scaffold_23-snap.2095-T1
Valid prediction for GeneMark_model.92193_t
Valid prediction for GeneMark_model.92209_t
Valid prediction for GeneMark_model.92189_t
Valid prediction for GeneMark_model.92199_t
Valid prediction for GeneMark_model.92213_t
Valid prediction for snap_scaffold_23-snap.2112-T1
Valid prediction for snap_scaffold_23-snap.2127-T1
Sorry, intron length (9) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 59909, 60038
Couldn't classify 62265, 62307
Sorry, prediction pasa_asmbl_31877.p1 fails validation.
(CAG)	 GG	59909-60038	GT	AGG
(ATG)	 AG	60352-60430	GT	GGG
(CTC)	 AG	60601-60695	GT	AGG
(ACT)	 AG	60925-60998	GT	AGG
(GTT)	 AG	61423-61593	GT	AGG
(AAC)	 AG	61994-62172	GT	GGG
(GGA)	 AG	62265-62307	AC	AGA
add_exon() Sorry, pasa_asmbl_31877.p1 60352-60430-initial-1 is invalid.
-recovered pasa_asmbl_31877.p1, initial, 60352, 60430
-recovered pasa_asmbl_31877.p1, internal, 60352, 60430
-recovered pasa_asmbl_31877.p1, internal, 60601, 60695
-recovered pasa_asmbl_31877.p1, internal, 60925, 60998
-recovered pasa_asmbl_31877.p1, internal, 61423, 61593
-recovered pasa_asmbl_31877.p1, internal, 61994, 62172
Valid prediction for GeneMark_model.92200_t
Couldn't classify 77922, 77966
Sorry, prediction pasa_asmbl_31938.p1 fails validation.
(ATG)	 AC	74311-74358	GT	AGG
(TTC)	 AG	76636-76822	GT	GGG
(GGG)	 AG	77731-77807	GT	AGG
(ACT)	 AG	77922-77966	TA	GGT
-recovered pasa_asmbl_31938.p1, initial, 74311, 74358
-recovered pasa_asmbl_31938.p1, internal, 76636, 76822
-recovered pasa_asmbl_31938.p1, internal, 77731, 77807
Valid prediction for GlimmerHMM_glimmerT_53040-T1
Valid prediction for GlimmerHMM_glimmerT_53054-T1
Valid prediction for GeneMark_model.92205_t
Valid prediction for GlimmerHMM_glimmerT_53043-T1
Valid prediction for GeneMark_model.92226_t
Couldn't classify 120732, 120840
Couldn't classify 125274, 125375
Sorry, prediction pasa_asmbl_31869.p1 fails validation.
(CAG)	 CC	120732-120840	GT	AGG
(TAG)	 AG	123389-123422	GT	AGG
(GGC)	 AG	123622-123671	GT	CAG
(TCA)	 AG	123820-123891	GT	AGG
(ACA)	 AG	124036-124093	GT	GAG
(GCA)	 AG	124224-124386	GT	AGG
(GAG)	 AG	124719-124817	GT	AGG
(CAA)	 AG	125081-125185	GT	ATG
(GTG)	 AG	125274-125375	GG	CAG
-recovered pasa_asmbl_31869.p1, internal, 123389, 123422
-recovered pasa_asmbl_31869.p1, internal, 123622, 123671
-recovered pasa_asmbl_31869.p1, internal, 123820, 123891
-recovered pasa_asmbl_31869.p1, internal, 124036, 124093
-recovered pasa_asmbl_31869.p1, internal, 124224, 124386
-recovered pasa_asmbl_31869.p1, internal, 124719, 124817
-recovered pasa_asmbl_31869.p1, internal, 125081, 125185
Valid prediction for snap_scaffold_23-snap.2119-T1
Valid prediction for GlimmerHMM_glimmerT_53044-T1
Valid prediction for snap_scaffold_23-snap.2124-T1
Valid prediction for GlimmerHMM_glimmerT_53042-T1
Valid prediction for GeneMark_model.92216_t
Valid prediction for snap_scaffold_23-snap.2104-T1
Valid prediction for GeneMark_model.92203_t
Valid prediction for pasa_asmbl_31873.p1
Valid prediction for CodingQuarry_transcript_35733-T1
Valid prediction for GlimmerHMM_glimmerT_53053-T1
Valid prediction for GeneMark_model.92207_t
Valid prediction for snap_scaffold_23-snap.2121-T1
Valid prediction for GlimmerHMM_glimmerT_53048-T1
Valid prediction for GlimmerHMM_glimmerT_53038-T1
Valid prediction for GlimmerHMM_glimmerT_53058-T1
Valid prediction for CodingQuarry_transcript_35734-T1
Valid prediction for GlimmerHMM_glimmerT_53051-T1
Valid prediction for GeneMark_model.92191_t
Valid prediction for snap_scaffold_23-snap.2096-T1
Valid prediction for GeneMark_model.92196_t
Valid prediction for GeneMark_model.92211_t
Valid prediction for snap_scaffold_23-snap.2111-T1
Valid prediction for pasa_asmbl_31868.p1
Valid prediction for GlimmerHMM_glimmerT_53035-T1
Valid prediction for snap_scaffold_23-snap.2122-T1
Valid prediction for snap_scaffold_23-snap.2108-T1
Valid prediction for snap_scaffold_23-snap.2129-T1
Couldn't classify 63135, 63176
Couldn't classify 63937, 64239
Sorry, prediction pasa_asmbl_31905.p1 fails validation.
(GAG)	 AG	63135-63176	GT	AGG
(GTG)	 AG	63288-63360	GT	CGG
(GCT)	 AG	63726-63847	GT	AGG
(ACA)	 AG	63937-64239	AC	ACA
-recovered pasa_asmbl_31905.p1, internal, 63135, 63176
-recovered pasa_asmbl_31905.p1, internal, 63288, 63360
-recovered pasa_asmbl_31905.p1, internal, 63726, 63847
Valid prediction for GlimmerHMM_glimmerT_53034-T1
Valid prediction for snap_scaffold_23-snap.2102-T1
Valid prediction for GeneMark_model.92223_t
Valid prediction for GlimmerHMM_glimmerT_53046-T1
Valid prediction for snap_scaffold_23-snap.2125-T1
Valid prediction for GeneMark_model.92218_t
Valid prediction for CodingQuarry_transcript_35735-T1
Valid prediction for snap_scaffold_23-snap.2101-T1
Couldn't classify 102446, 102551
Sorry, prediction pasa_asmbl_31955.p1 fails validation.
(ATC)	 CC	102446-102551	GT	CGG
(GGT)	 AG	102812-102968	GT	AGG
(CAT)	 AG	104531-104596	GT	AGG
(GCT)	 AG	105112-105160	GA	AAG
-recovered pasa_asmbl_31955.p1, terminal, 105112, 105160
-recovered pasa_asmbl_31955.p1, internal, 102812, 102968
-recovered pasa_asmbl_31955.p1, internal, 104531, 104596

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6305, rend_intergenic: 5048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24286, rend_intergenic: 9307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33852, rend_intergenic: 28608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56008, rend_intergenic: 35035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60162, rend_intergenic: 58380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65934, rend_intergenic: 63925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84428, rend_intergenic: 79577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91651, rend_intergenic: 91059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110528, rend_intergenic: 102871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120770, rend_intergenic: 112215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126675, rend_intergenic: 123048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129301, rend_intergenic: 127079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137885, rend_intergenic: 132453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 142500
-exon list size: 586


building trellis

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81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 6305, rend_intergenic: 5048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24286, rend_intergenic: 9307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33852, rend_intergenic: 28608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56008, rend_intergenic: 35035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60162, rend_intergenic: 58380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65934, rend_intergenic: 63925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84428, rend_intergenic: 79577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91651, rend_intergenic: 91059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110528, rend_intergenic: 102871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120770, rend_intergenic: 112215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126675, rend_intergenic: 123048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129301, rend_intergenic: 127079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137885, rend_intergenic: 132453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support