-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_10574270-10755246

-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 snap_scaffold_3-snap.2127-T1
Valid prediction for GlimmerHMM_glimmerT_7414-T1
Valid prediction for snap_scaffold_3-snap.2151-T1
Valid prediction for snap_scaffold_3-snap.2143-T1
Valid prediction for GeneMark_model.12288_t
Valid prediction for Augustus_model.g4858.t1
Valid prediction for GeneMark_model.12264_t
Valid prediction for snap_scaffold_3-snap.2131-T1
Valid prediction for GlimmerHMM_glimmerT_7410-T1
Valid prediction for snap_scaffold_3-snap.2138-T1
Valid prediction for snap_scaffold_3-snap.2123-T1
Valid prediction for snap_scaffold_3-snap.2146-T1
Valid prediction for GeneMark_model.12256_t
Valid prediction for Augustus_model.g4849.t1
Valid prediction for GlimmerHMM_glimmerT_7396-T1
Valid prediction for GlimmerHMM_glimmerT_7415-T1
Valid prediction for snap_scaffold_3-snap.2149-T1
Valid prediction for GeneMark_model.12272_t
Valid prediction for GlimmerHMM_glimmerT_7395-T1
Valid prediction for Augustus_model.g4855.t1
Valid prediction for GeneMark_model.12268_t
Valid prediction for GlimmerHMM_glimmerT_7406-T1
Couldn't classify 1624, 1881
Sorry, prediction pasa_asmbl_40231.p1 fails validation.
(CTC)	 TT	1624-1881	GT	TGG
(TCC)	 AG	2074-2281	GT	AGG
(ACG)	 AG	2394-2475	GT	CGG
(GTC)	 AG	2564-2819	CG	GAC
-recovered pasa_asmbl_40231.p1, terminal, 2564, 2819
-recovered pasa_asmbl_40231.p1, internal, 2074, 2281
-recovered pasa_asmbl_40231.p1, internal, 2394, 2475
Couldn't classify 9072, 9132
Sorry, prediction pasa_asmbl_40232.p1 fails validation.
(GGC)	 AT	9072-9132	GT	AGG
(GGG)	 AG	9264-9420	GT	AGG
(GTT)	 AG	11601-11709	GT	AGG
(GCC)	 AG	13958-14083	GT	AGG
(CTC)	 AG	14542-14700	GT	AGG
(TAT)	 AG	15813-15911	GT	AGG
(AAC)	 AG	16036-16274	GT	AGG
(ACT)	 AG	16872-16980	GA	GAG
-recovered pasa_asmbl_40232.p1, terminal, 16872, 16980
-recovered pasa_asmbl_40232.p1, internal, 9264, 9420
-recovered pasa_asmbl_40232.p1, internal, 11601, 11709
-recovered pasa_asmbl_40232.p1, internal, 13958, 14083
-recovered pasa_asmbl_40232.p1, internal, 14542, 14700
-recovered pasa_asmbl_40232.p1, internal, 15813, 15911
-recovered pasa_asmbl_40232.p1, internal, 16036, 16274
Valid prediction for snap_scaffold_3-snap.2135-T1
Valid prediction for GlimmerHMM_glimmerT_7421-T1
Valid prediction for GeneMark_model.12260_t
Valid prediction for GeneMark_model.12286_t
Valid prediction for snap_scaffold_3-snap.2126-T1
Valid prediction for GeneMark_model.12284_t
Valid prediction for CodingQuarry_transcript_46153-T1
Valid prediction for GeneMark_model.12253_t
Valid prediction for snap_scaffold_3-snap.2148-T1
Valid prediction for snap_scaffold_3-snap.2154-T1
Valid prediction for snap_scaffold_3-snap.2116-T1
Valid prediction for snap_scaffold_3-snap.2133-T1
Valid prediction for snap_scaffold_3-snap.2152-T1
Valid prediction for snap_scaffold_3-snap.2137-T1
Valid prediction for GeneMark_model.12280_t
Valid prediction for GeneMark_model.12282_t
Valid prediction for GlimmerHMM_glimmerT_7419-T1
Valid prediction for snap_scaffold_3-snap.2136-T1
Valid prediction for GeneMark_model.12249_t
Valid prediction for GeneMark_model.12261_t
Valid prediction for GeneMark_model.12258_t
Valid prediction for GeneMark_model.12273_t
Valid prediction for snap_scaffold_3-snap.2124-T1
Valid prediction for GlimmerHMM_glimmerT_7398-T1
Valid prediction for GeneMark_model.12276_t
Valid prediction for snap_scaffold_3-snap.2141-T1
Valid prediction for snap_scaffold_3-snap.2119-T1
Valid prediction for GeneMark_model.12252_t
Valid prediction for GlimmerHMM_glimmerT_7417-T1
Valid prediction for CodingQuarry_transcript_46152-T1
Valid prediction for Augustus_model.g4850.t1
Valid prediction for HiQ_model.g4853.t1
Valid prediction for CodingQuarry_transcript_46154-T1
Valid prediction for pasa_asmbl_40235.p1
Valid prediction for GeneMark_model.12265_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 GeneMark_model.12274_t
Valid prediction for snap_scaffold_3-snap.2129-T1
Valid prediction for snap_scaffold_3-snap.2147-T1
Valid prediction for GlimmerHMM_glimmerT_7405-T1
Valid prediction for snap_scaffold_3-snap.2155-T1
Valid prediction for snap_scaffold_3-snap.2121-T1
Valid prediction for snap_scaffold_3-snap.2153-T1
Valid prediction for GeneMark_model.12285_t
Valid prediction for GeneMark_model.12275_t
Valid prediction for snap_scaffold_3-snap.2132-T1
Valid prediction for GeneMark_model.12263_t
Valid prediction for snap_scaffold_3-snap.2150-T1
Couldn't classify 141663, 141845
Sorry, prediction pasa_asmbl_39059.p1 fails validation.
(TTC)	 AG	141663-141845	GT	AGG
(GTG)	 AG	142110-142256	AA	GAA
-recovered pasa_asmbl_39059.p1, terminal, 142110, 142256
-recovered pasa_asmbl_39059.p1, internal, 141663, 141845
Valid prediction for CodingQuarry_transcript_46156-T1
Valid prediction for snap_scaffold_3-snap.2120-T1
Valid prediction for Augustus_model.g4860.t1
Valid prediction for GeneMark_model.12250_t
Valid prediction for snap_scaffold_3-snap.2145-T1
Valid prediction for GeneMark_model.12254_t
Valid prediction for GlimmerHMM_glimmerT_7397-T1
Valid prediction for GeneMark_model.12255_t
Valid prediction for snap_scaffold_3-snap.2125-T1
Valid prediction for GlimmerHMM_glimmerT_7400-T1
Valid prediction for GeneMark_model.12277_t
Valid prediction for GlimmerHMM_glimmerT_7403-T1
Valid prediction for snap_scaffold_3-snap.2144-T1
Valid prediction for GeneMark_model.12259_t
Valid prediction for GlimmerHMM_glimmerT_7412-T1
Valid prediction for Augustus_model.g4859.t1
Valid prediction for GlimmerHMM_glimmerT_7402-T1
Couldn't classify 20652, 21056
Sorry, prediction pasa_asmbl_39063.p1 fails validation.
(ACC)	 AC	20652-21056	GC	CAG
Valid prediction for GeneMark_model.12267_t
Valid prediction for GeneMark_model.12271_t
Valid prediction for GlimmerHMM_glimmerT_7420-T1
Valid prediction for snap_scaffold_3-snap.2118-T1
Valid prediction for GeneMark_model.12287_t
Couldn't classify 22156, 22240
Sorry, prediction pasa_asmbl_39062.p1 fails validation.
(TTC)	 CC	22156-22240	GT	GGG
(ACC)	 AG	22848-23053	GT	GGG
(GAG)	 AG	23149-23195	GT	AAG
(TGC)	 AG	23325-23399	GT	AAG
(GTG)	 AG	23602-23750	GT	AGG
(GCC)	 AG	23950-24064	GT	AAG
(GAA)	 AG	24371-24558	GT	TGG
(CAC)	 AG	25713-25854	GT	AAG
(GTA)	 AG	26076-26202	GT	AGG
(GTG)	 AG	26817-26987	GT	TCG
(GCT)	 AG	27672-27695	CA	GAC
-recovered pasa_asmbl_39062.p1, terminal, 27672, 27695
-recovered pasa_asmbl_39062.p1, internal, 22848, 23053
-recovered pasa_asmbl_39062.p1, internal, 23149, 23195
-recovered pasa_asmbl_39062.p1, internal, 23325, 23399
-recovered pasa_asmbl_39062.p1, internal, 23602, 23750
-recovered pasa_asmbl_39062.p1, internal, 23950, 24064
-recovered pasa_asmbl_39062.p1, internal, 24371, 24558
-recovered pasa_asmbl_39062.p1, internal, 25713, 25854
-recovered pasa_asmbl_39062.p1, internal, 26076, 26202
-recovered pasa_asmbl_39062.p1, internal, 26817, 26987
Valid prediction for GlimmerHMM_glimmerT_7408-T1
Valid prediction for GeneMark_model.12278_t
Valid prediction for snap_scaffold_3-snap.2115-T1
Valid prediction for GeneMark_model.12248_t
Valid prediction for snap_scaffold_3-snap.2122-T1
Couldn't classify 23602, 23750
Sorry, prediction Augustus_model.g4861.t1 fails validation.
(ATG)	 CC	1925-2094	GT	AGG
(TTC)	 AG	2229-2292	GT	AGG
(GCA)	 AG	4836-4944	GT	AGG
(CAT)	 AG	5436-5485	GT	AGG
(TTT)	 AG	5699-5835	GT	TGG
(GGC)	 AG	7674-7794	GT	AGG
(GAT)	 AG	7986-8198	GT	TGG
(CAT)	 AG	10615-10669	GT	GAG
(TTC)	 AG	11227-11261	GT	AGG
(AAG)	 AG	12261-12354	GT	AGG
(GCT)	 AG	13848-13974	GT	AGG
(GTG)	 AG	14724-14822	GT	GGG
(GGT)	 AG	15268-15487	GT	AGG
(GCT)	 AG	15997-16143	GT	AGG
(GCC)	 AG	18369-18461	GT	AGG
(AGT)	 AG	18777-18854	GT	AGG
(CTC)	 AG	19062-19169	GT	AGG
(ATG)	 AG	19316-19714	GT	AGG
(CAG)	 AG	19949-20056	GT	AGG
(GGG)	 AG	20409-21316	GT	AGG
(GAA)	 AG	21642-21771	GT	ACG
(CTG)	 AG	22135-22240	GT	GGG
(ACC)	 AG	22848-23053	GT	GGG
(GAG)	 AG	23149-23195	GT	AAG
(TGC)	 AG	23325-23399	GT	AAG
(GTG)	 AG	23602-23750	GT	AGG
-recovered Augustus_model.g4861.t1, initial, 1925, 2094
-recovered Augustus_model.g4861.t1, initial, 19316, 19714
add_exon() Sorry, Augustus_model.g4861.t1 12261-12354-terminal-3 is invalid.
-recovered Augustus_model.g4861.t1, terminal, 12261, 12354
-recovered Augustus_model.g4861.t1, internal, 2229, 2292
-recovered Augustus_model.g4861.t1, internal, 4836, 4944
-recovered Augustus_model.g4861.t1, internal, 5436, 5485
-recovered Augustus_model.g4861.t1, internal, 5699, 5835
-recovered Augustus_model.g4861.t1, internal, 7674, 7794
-recovered Augustus_model.g4861.t1, internal, 7986, 8198
-recovered Augustus_model.g4861.t1, internal, 10615, 10669
-recovered Augustus_model.g4861.t1, internal, 11227, 11261
-recovered Augustus_model.g4861.t1, internal, 12261, 12354
-recovered Augustus_model.g4861.t1, internal, 13848, 13974
-recovered Augustus_model.g4861.t1, internal, 14724, 14822
-recovered Augustus_model.g4861.t1, internal, 15268, 15487
-recovered Augustus_model.g4861.t1, internal, 15997, 16143
-recovered Augustus_model.g4861.t1, internal, 18369, 18461
-recovered Augustus_model.g4861.t1, internal, 18777, 18854
-recovered Augustus_model.g4861.t1, internal, 19062, 19169
-recovered Augustus_model.g4861.t1, internal, 19316, 19714
-recovered Augustus_model.g4861.t1, internal, 19949, 20056
-recovered Augustus_model.g4861.t1, internal, 20409, 21316
-recovered Augustus_model.g4861.t1, internal, 21642, 21771
-recovered Augustus_model.g4861.t1, internal, 22135, 22240
-recovered Augustus_model.g4861.t1, internal, 22848, 23053
-recovered Augustus_model.g4861.t1, internal, 23149, 23195
-recovered Augustus_model.g4861.t1, internal, 23325, 23399
-recovered Augustus_model.g4861.t1, internal, 23602, 23750
Valid prediction for Augustus_model.g4854.t1
Valid prediction for GeneMark_model.12289_t
Valid prediction for GlimmerHMM_glimmerT_7407-T1
Valid prediction for snap_scaffold_3-snap.2139-T1
Valid prediction for snap_scaffold_3-snap.2113-T1
Valid prediction for CodingQuarry_transcript_46151-T1
Valid prediction for CodingQuarry_transcript_46150-T1
Valid prediction for Augustus_model.g4852.t1
Valid prediction for snap_scaffold_3-snap.2142-T1
Valid prediction for GeneMark_model.12262_t
Valid prediction for GlimmerHMM_glimmerT_7418-T1
Valid prediction for CodingQuarry_transcript_46149-T1
Valid prediction for GeneMark_model.12257_t
Valid prediction for GlimmerHMM_glimmerT_7413-T1
Valid prediction for Augustus_model.g4857.t1
Valid prediction for snap_scaffold_3-snap.2130-T1
Valid prediction for GlimmerHMM_glimmerT_7411-T1
Valid prediction for snap_scaffold_3-snap.2140-T1
Valid prediction for snap_scaffold_3-snap.2117-T1
Valid prediction for pasa_asmbl_39053.p2
Valid prediction for GeneMark_model.12279_t
Valid prediction for GlimmerHMM_glimmerT_7404-T1
Valid prediction for GeneMark_model.12281_t
Valid prediction for GeneMark_model.12269_t
Valid prediction for GlimmerHMM_glimmerT_7423-T1
Valid prediction for GeneMark_model.12283_t
Valid prediction for GlimmerHMM_glimmerT_7399-T1
Valid prediction for GlimmerHMM_glimmerT_7422-T1
Valid prediction for snap_scaffold_3-snap.2128-T1
Valid prediction for GlimmerHMM_glimmerT_7401-T1
Valid prediction for HiQ_model.g4851.t1
Couldn't classify 16039, 16143
Couldn't classify 19316, 19432
Sorry, prediction pasa_asmbl_39064.p1 fails validation.
(AGT)	 AC	16039-16143	GT	AGG
(GCC)	 AG	18369-18461	GT	AGG
(AGT)	 AG	18777-18854	GT	AGG
(CTC)	 AG	19062-19169	GT	AGG
(ATG)	 AG	19316-19432	CC	CCC
-recovered pasa_asmbl_39064.p1, internal, 18369, 18461
-recovered pasa_asmbl_39064.p1, internal, 18777, 18854
-recovered pasa_asmbl_39064.p1, internal, 19062, 19169
Valid prediction for GlimmerHMM_glimmerT_7416-T1
Valid prediction for snap_scaffold_3-snap.2114-T1
Valid prediction for GlimmerHMM_glimmerT_7409-T1
Valid prediction for snap_scaffold_3-snap.2156-T1
Valid prediction for GeneMark_model.12266_t
Valid prediction for CodingQuarry_transcript_46148-T1
Valid prediction for snap_scaffold_3-snap.2134-T1
Valid prediction for GeneMark_model.12251_t
Valid prediction for Augustus_model.g4856.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30914, rend_intergenic: 28051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36817, rend_intergenic: 31939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67924, rend_intergenic: 63517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74501, rend_intergenic: 71868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91453, rend_intergenic: 87600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97596, rend_intergenic: 95105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122767, rend_intergenic: 118483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129972, rend_intergenic: 124064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137016, rend_intergenic: 130615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163044, rend_intergenic: 154096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172998, rend_intergenic: 165335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173085, rend_intergenic: 173082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180977
-exon list size: 645


building trellis

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59.8    
60.0    
60.1    
60.3    
60.4    
60.6    
60.7    
60.9    
61.1    
61.2    
61.4    
61.5    
61.7    
61.8    
62.0    
62.1    
62.3    
62.4    
62.6    
62.8    
62.9    
63.1    
63.2    
63.4    
63.5    
63.7    
63.8    
64.0    
64.1    
64.3    
64.5    
64.6    
64.8    
64.9    
65.1    
65.2    
65.4    
65.5    
65.7    
65.8    
66.0    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.5    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.5    
70.6    
70.8    
70.9    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.5    
72.6    
72.8    
73.0    
73.1    
73.3    
73.4    
73.6    
73.7    
73.9    
74.0    
74.2    
74.3    
74.5    
74.7    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.0    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 30914, rend_intergenic: 28051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36817, rend_intergenic: 31939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67924, rend_intergenic: 63517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74501, rend_intergenic: 71868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91453, rend_intergenic: 87600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97596, rend_intergenic: 95105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122767, rend_intergenic: 118483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129972, rend_intergenic: 124064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137016, rend_intergenic: 130615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163044, rend_intergenic: 154096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172998, rend_intergenic: 165335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173085, rend_intergenic: 173082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support