-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_2901550-3194138

-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 158955, 159007
Sorry, prediction pasa_asmbl_39887.p1 fails validation.
(GGT)	 AT	158955-159007	GT	AAG
(GAG)	 AG	159143-159269	GT	CTG
(ACG)	 AG	159608-159761	GT	GGG
(GCT)	 AG	159852-159912	GT	AAG
(CTG)	 AG	160605-160671	GT	TGG
(GTA)	 AG	161122-161340	GT	AGG
(GGG)	 AG	161870-161911	GT	AGG
(GTT)	 AG	162210-162428	AG	GAA
-recovered pasa_asmbl_39887.p1, terminal, 162210, 162428
-recovered pasa_asmbl_39887.p1, internal, 159143, 159269
-recovered pasa_asmbl_39887.p1, internal, 159608, 159761
-recovered pasa_asmbl_39887.p1, internal, 159852, 159912
-recovered pasa_asmbl_39887.p1, internal, 160605, 160671
-recovered pasa_asmbl_39887.p1, internal, 161122, 161340
-recovered pasa_asmbl_39887.p1, internal, 161870, 161911
Valid prediction for GlimmerHMM_glimmerT_6371-T1
Valid prediction for snap_scaffold_3-snap.667-T1
Valid prediction for snap_scaffold_3-snap.695-T1
Valid prediction for GeneMark_model.10446_t
Valid prediction for GeneMark_model.10465_t
Valid prediction for snap_scaffold_3-snap.678-T1
Valid prediction for GeneMark_model.10452_t
Valid prediction for GlimmerHMM_glimmerT_6366-T1
Valid prediction for HiQ_model.g4167.t1
Valid prediction for GlimmerHMM_glimmerT_6374-T1
Valid prediction for Augustus_model.g4172.t1
Valid prediction for GlimmerHMM_glimmerT_6379-T1
Valid prediction for snap_scaffold_3-snap.664-T1
Valid prediction for GeneMark_model.10441_t
Valid prediction for Augustus_model.g4169.t1
Valid prediction for GeneMark_model.10467_t
Valid prediction for snap_scaffold_3-snap.684-T1
Valid prediction for GeneMark_model.10447_t
Valid prediction for GeneMark_model.10451_t
Valid prediction for snap_scaffold_3-snap.671-T1
Valid prediction for snap_scaffold_3-snap.663-T1
Valid prediction for GlimmerHMM_glimmerT_6368-T1
Valid prediction for GeneMark_model.10450_t
Valid prediction for Augustus_model.g4170.t1
Valid prediction for Augustus_model.g4166.t1
Valid prediction for snap_scaffold_3-snap.660-T1
Valid prediction for GeneMark_model.10468_t
Valid prediction for GeneMark_model.10442_t
Valid prediction for snap_scaffold_3-snap.673-T1
Valid prediction for snap_scaffold_3-snap.675-T1
Valid prediction for snap_scaffold_3-snap.662-T1
Valid prediction for snap_scaffold_3-snap.672-T1
Valid prediction for GeneMark_model.10454_t
Valid prediction for GeneMark_model.10443_t
Valid prediction for snap_scaffold_3-snap.661-T1
Valid prediction for Augustus_model.g4171.t1
Valid prediction for snap_scaffold_3-snap.687-T1
Valid prediction for GlimmerHMM_glimmerT_6376-T1
Valid prediction for snap_scaffold_3-snap.679-T1
Valid prediction for pasa_asmbl_39882.p1
Valid prediction for GeneMark_model.10471_t
Valid prediction for snap_scaffold_3-snap.683-T1
Valid prediction for GeneMark_model.10457_t
Couldn't classify 141198, 141375
Sorry, prediction pasa_asmbl_39885.p1 fails validation.
(GCT)	 CA	141198-141375	GT	AGG
(GAA)	 AG	142450-142521	GT	CGG
(GTG)	 AG	144025-144078	GT	CCG
(GCT)	 AG	144335-144523	GT	GGG
(ACA)	 AG	144906-144967	AC	GAA
-recovered pasa_asmbl_39885.p1, terminal, 144906, 144967
-recovered pasa_asmbl_39885.p1, internal, 142450, 142521
-recovered pasa_asmbl_39885.p1, internal, 144025, 144078
-recovered pasa_asmbl_39885.p1, internal, 144335, 144523
Valid prediction for snap_scaffold_3-snap.674-T1
Valid prediction for snap_scaffold_3-snap.670-T1
Couldn't classify 156681, 156831
Couldn't classify 158544, 158611
Sorry, prediction pasa_asmbl_39886.p1 fails validation.
(TTT)	 TC	156681-156831	GT	CGG
(CCT)	 AG	157831-157965	GT	AGG
(AAA)	 AG	158544-158611	AC	GGA
-recovered pasa_asmbl_39886.p1, internal, 157831, 157965
Valid prediction for GeneMark_model.10462_t
Valid prediction for Augustus_model.g4177.t1
Valid prediction for GeneMark_model.10449_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 CodingQuarry_transcript_45990-T1
Valid prediction for GlimmerHMM_glimmerT_6377-T1
Valid prediction for GeneMark_model.10448_t
Valid prediction for snap_scaffold_3-snap.694-T1
Valid prediction for snap_scaffold_3-snap.659-T1
Valid prediction for snap_scaffold_3-snap.685-T1
Valid prediction for GeneMark_model.10455_t
Valid prediction for GeneMark_model.10464_t
Couldn't classify 10073, 10145
Couldn't classify 12299, 12325
Sorry, prediction pasa_asmbl_38713.p1 fails validation.
(CCT)	 CA	10073-10145	GT	AGG
(GAG)	 AG	11168-11289	GT	AGG
(GGT)	 AG	11750-11776	GT	AGG
(GGT)	 AG	11931-12128	GT	CTG
(GGA)	 AG	12299-12325	GT	CAG
-recovered pasa_asmbl_38713.p1, internal, 11168, 11289
-recovered pasa_asmbl_38713.p1, internal, 11750, 11776
-recovered pasa_asmbl_38713.p1, internal, 11931, 12128
-recovered pasa_asmbl_38713.p1, internal, 12299, 12325
Valid prediction for Augustus_model.g4173.t1
Valid prediction for GlimmerHMM_glimmerT_6372-T1
Valid prediction for GeneMark_model.10438_t
Valid prediction for GeneMark_model.10469_t
Valid prediction for snap_scaffold_3-snap.657-T1
Valid prediction for Augustus_model.g4175.t1
Valid prediction for snap_scaffold_3-snap.686-T1
Valid prediction for snap_scaffold_3-snap.666-T1
Valid prediction for GeneMark_model.10470_t
Valid prediction for snap_scaffold_3-snap.669-T1
Valid prediction for HiQ_model.g4178.t1
Valid prediction for Augustus_model.g4174.t1
Valid prediction for HiQ_model.g4168.t1
Couldn't classify 1975, 2283
Sorry, prediction pasa_asmbl_38714.p1 fails validation.
(GAC)	 CA	1975-2283	GA	CCG
Valid prediction for GeneMark_model.10439_t
Valid prediction for GlimmerHMM_glimmerT_6370-T1
Valid prediction for GeneMark_model.10463_t
Valid prediction for snap_scaffold_3-snap.668-T1
Valid prediction for Augustus_model.g4164.t1
Valid prediction for GeneMark_model.10440_t
Valid prediction for snap_scaffold_3-snap.680-T1
Valid prediction for GeneMark_model.10453_t
Valid prediction for snap_scaffold_3-snap.681-T1
Valid prediction for GeneMark_model.10460_t
Couldn't classify 95929, 95953
Couldn't classify 97389, 97908
Sorry, prediction pasa_asmbl_38708.p1 fails validation.
(GCC)	 CA	95929-95953	GT	TGG
(GGG)	 AG	96266-96379	GT	GGG
(GTG)	 AG	96520-96643	GT	AGG
(AGC)	 AG	97389-97908	AC	CCA
add_exon() Sorry, pasa_asmbl_38708.p1 96520-96643-terminal-3 is invalid.
-recovered pasa_asmbl_38708.p1, terminal, 96520, 96643
-recovered pasa_asmbl_38708.p1, internal, 96266, 96379
-recovered pasa_asmbl_38708.p1, internal, 96520, 96643
Valid prediction for Augustus_model.g4179.t1
Valid prediction for Augustus_model.g4176.t1
Valid prediction for GeneMark_model.10445_t
Couldn't classify 98005, 98412
Sorry, prediction pasa_asmbl_38707.p1 fails validation.
(GGT)	 GG	98005-98412	AC	GAA
Valid prediction for GlimmerHMM_glimmerT_6380-T1
Valid prediction for snap_scaffold_3-snap.689-T1
Couldn't classify 224832, 224894
Sorry, prediction pasa_asmbl_38704.p1 fails validation.
(GAT)	 CA	224832-224894	GT	AGG
(TTC)	 AG	226922-226993	GT	AGG
(TTT)	 AG	228531-228629	GT	AAG
(GAT)	 AG	229313-229450	GT	GTG
(GCA)	 AG	229808-229924	GT	GGG
(ATT)	 AG	230372-230458	GT	CGG
(GGA)	 AG	231156-231294	GT	AAG
(GGA)	 AG	231611-231705	GT	AGG
(GAG)	 AG	232709-232780	TG	GAT
add_exon() Sorry, pasa_asmbl_38704.p1 231156-231294-terminal-3 is invalid.
-recovered pasa_asmbl_38704.p1, terminal, 231156, 231294
-recovered pasa_asmbl_38704.p1, terminal, 232709, 232780
-recovered pasa_asmbl_38704.p1, internal, 226922, 226993
-recovered pasa_asmbl_38704.p1, internal, 228531, 228629
-recovered pasa_asmbl_38704.p1, internal, 229313, 229450
-recovered pasa_asmbl_38704.p1, internal, 229808, 229924
-recovered pasa_asmbl_38704.p1, internal, 230372, 230458
-recovered pasa_asmbl_38704.p1, internal, 231156, 231294
-recovered pasa_asmbl_38704.p1, internal, 231611, 231705
Valid prediction for snap_scaffold_3-snap.677-T1
Valid prediction for Augustus_model.g4165.t1
Valid prediction for snap_scaffold_3-snap.696-T1
Valid prediction for GeneMark_model.10458_t
Valid prediction for snap_scaffold_3-snap.690-T1
Valid prediction for snap_scaffold_3-snap.691-T1
Valid prediction for snap_scaffold_3-snap.676-T1
Valid prediction for snap_scaffold_3-snap.682-T1
Valid prediction for GeneMark_model.10466_t
Valid prediction for GeneMark_model.10456_t
Valid prediction for GlimmerHMM_glimmerT_6382-T1
Valid prediction for GlimmerHMM_glimmerT_6369-T1
Valid prediction for GlimmerHMM_glimmerT_6381-T1
Valid prediction for GlimmerHMM_glimmerT_6367-T1
Valid prediction for GlimmerHMM_glimmerT_6375-T1
Valid prediction for snap_scaffold_3-snap.692-T1
Valid prediction for snap_scaffold_3-snap.688-T1
Couldn't classify 13158, 13208
Sorry, prediction pasa_asmbl_38712.p1 fails validation.
(ACA)	 AG	13158-13208	GT	GGG
(GGC)	 AG	13708-13827	GT	CGG
(GGT)	 AG	13983-14045	GT	AGG
(GGG)	 AG	14495-14539	GT	AGG
(GGT)	 AG	15274-15405	GT	TTG
(GAT)	 AG	15656-15724	GT	AGG
(GGT)	 AG	15802-15828	GT	CAG
(GGC)	 AG	15960-16058	GT	AGG
(GGA)	 AG	16224-16259	GT	GAG
(GGA)	 AG	16398-16487	GT	GTG
(TAT)	 AG	16714-16746	GT	AGG
(GGT)	 AG	17169-17204	GT	CTG
(GGC)	 AG	17312-17371	GT	AGG
(GGA)	 AG	17538-17615	GT	AGG
(GGC)	 AG	17805-17840	GT	CTG
(GGT)	 AG	17964-18017	GT	CTG
(GGA)	 AG	18431-18502	GT	CAG
(GGT)	 AG	18726-18791	GT	ACG
(CGA)	 AG	18895-18925	GT	AGG
(CCA)	 AG	19326-19379	GT	AGG
(GTA)	 AG	19491-19525	GT	AAG
(AAC)	 AG	19730-19861	GT	CAG
(GGT)	 AG	20112-20271	GT	CCG
(CCA)	 AG	20385-20449	GT	GGG
(GTG)	 AG	20658-20786	GT	TGG
(CTT)	 AG	20906-20938	GT	TGG
(GAC)	 AG	21134-21478	GT	GAG
(CTG)	 AG	21804-22001	GT	AGG
(GAC)	 AG	22331-22446	GT	TGG
(GCC)	 AG	22734-22947	AG	AGA
-recovered pasa_asmbl_38712.p1, terminal, 22734, 22947
-recovered pasa_asmbl_38712.p1, internal, 13158, 13208
-recovered pasa_asmbl_38712.p1, internal, 13708, 13827
-recovered pasa_asmbl_38712.p1, internal, 13983, 14045
-recovered pasa_asmbl_38712.p1, internal, 14495, 14539
-recovered pasa_asmbl_38712.p1, internal, 15274, 15405
-recovered pasa_asmbl_38712.p1, internal, 15656, 15724
-recovered pasa_asmbl_38712.p1, internal, 15802, 15828
-recovered pasa_asmbl_38712.p1, internal, 15960, 16058
-recovered pasa_asmbl_38712.p1, internal, 16224, 16259
-recovered pasa_asmbl_38712.p1, internal, 16398, 16487
-recovered pasa_asmbl_38712.p1, internal, 16714, 16746
-recovered pasa_asmbl_38712.p1, internal, 17169, 17204
-recovered pasa_asmbl_38712.p1, internal, 17312, 17371
-recovered pasa_asmbl_38712.p1, internal, 17538, 17615
-recovered pasa_asmbl_38712.p1, internal, 17805, 17840
-recovered pasa_asmbl_38712.p1, internal, 17964, 18017
-recovered pasa_asmbl_38712.p1, internal, 18431, 18502
-recovered pasa_asmbl_38712.p1, internal, 18726, 18791
-recovered pasa_asmbl_38712.p1, internal, 18895, 18925
-recovered pasa_asmbl_38712.p1, internal, 19326, 19379
-recovered pasa_asmbl_38712.p1, internal, 19491, 19525
-recovered pasa_asmbl_38712.p1, internal, 19730, 19861
-recovered pasa_asmbl_38712.p1, internal, 20112, 20271
-recovered pasa_asmbl_38712.p1, internal, 20385, 20449
-recovered pasa_asmbl_38712.p1, internal, 20658, 20786
-recovered pasa_asmbl_38712.p1, internal, 20906, 20938
-recovered pasa_asmbl_38712.p1, internal, 21134, 21478
-recovered pasa_asmbl_38712.p1, internal, 21804, 22001
-recovered pasa_asmbl_38712.p1, internal, 22331, 22446
Valid prediction for snap_scaffold_3-snap.665-T1
Valid prediction for GeneMark_model.10461_t
Valid prediction for GeneMark_model.10444_t
Valid prediction for GlimmerHMM_glimmerT_6383-T1
Valid prediction for GlimmerHMM_glimmerT_6373-T1
Valid prediction for snap_scaffold_3-snap.693-T1
Valid prediction for GlimmerHMM_glimmerT_6378-T1
Valid prediction for GlimmerHMM_glimmerT_6384-T1
Valid prediction for snap_scaffold_3-snap.658-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 117537, rend_intergenic: 114947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199074, rend_intergenic: 195949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235941, rend_intergenic: 234338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248898, rend_intergenic: 245773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252699, rend_intergenic: 251321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 288233, rend_intergenic: 286753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 292589
-exon list size: 601


building trellis

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73.5    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.6    
76.8    
76.9    
77.1    
77.3    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 117537, rend_intergenic: 114947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199074, rend_intergenic: 195949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235941, rend_intergenic: 234338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248898, rend_intergenic: 245773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252699, rend_intergenic: 251321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 288233, rend_intergenic: 286753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support