-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_4635786-4937512

-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 GlimmerHMM_glimmerT_53723-T1
Valid prediction for snap_scaffold_24-snap.978-T1
Valid prediction for GeneMark_model.93720_t
Valid prediction for Augustus_model.g35983.t1
Valid prediction for GlimmerHMM_glimmerT_53722-T1
Valid prediction for GeneMark_model.93704_t
Valid prediction for GlimmerHMM_glimmerT_53710-T1
Valid prediction for GeneMark_model.93725_t
Valid prediction for GeneMark_model.93727_t
Valid prediction for GlimmerHMM_glimmerT_53726-T1
Valid prediction for pasa_asmbl_32218.p1
Valid prediction for GeneMark_model.93714_t
Valid prediction for snap_scaffold_24-snap.976-T1
Valid prediction for snap_scaffold_24-snap.997-T1
Valid prediction for GeneMark_model.93722_t
Valid prediction for HiQ_model.g35981.t1
Valid prediction for snap_scaffold_24-snap.977-T1
Valid prediction for snap_scaffold_24-snap.961-T1
Valid prediction for GlimmerHMM_glimmerT_53709-T1
Valid prediction for GeneMark_model.93730_t
Valid prediction for GlimmerHMM_glimmerT_53720-T1
Valid prediction for GeneMark_model.93709_t
Valid prediction for HiQ_model.g35974.t1
Valid prediction for snap_scaffold_24-snap.979-T1
Valid prediction for snap_scaffold_24-snap.974-T1
Valid prediction for snap_scaffold_24-snap.963-T1
Valid prediction for pasa_asmbl_32217.p1
Valid prediction for snap_scaffold_24-snap.991-T1
Valid prediction for GlimmerHMM_glimmerT_53729-T1
Valid prediction for GlimmerHMM_glimmerT_53739-T1
Valid prediction for CodingQuarry_transcript_37232-T1
Valid prediction for snap_scaffold_24-snap.990-T1
Valid prediction for GeneMark_model.93723_t
Valid prediction for snap_scaffold_24-snap.962-T1
Valid prediction for GlimmerHMM_glimmerT_53708-T1
Valid prediction for GeneMark_model.93729_t
Valid prediction for Augustus_model.g35975.t1
Valid prediction for GlimmerHMM_glimmerT_53715-T1
Valid prediction for GlimmerHMM_glimmerT_53735-T1
Valid prediction for GeneMark_model.93732_t
Valid prediction for GlimmerHMM_glimmerT_53721-T1
Valid prediction for Augustus_model.g35973.t1
Valid prediction for snap_scaffold_24-snap.996-T1
Valid prediction for Augustus_model.g35982.t1
Valid prediction for GeneMark_model.93707_t
Valid prediction for GlimmerHMM_glimmerT_53736-T1
Valid prediction for snap_scaffold_24-snap.960-T1
Valid prediction for GeneMark_model.93737_t
Valid prediction for GeneMark_model.93731_t
Valid prediction for Augustus_model.g35972.t1
Valid prediction for GlimmerHMM_glimmerT_53734-T1
Couldn't classify 151851, 151972
Couldn't classify 152214, 152358
Sorry, prediction CodingQuarry_transcript_37229-T1 fails validation.
(ATG)	 TC	148734-148751	GT	AGG
(GCA)	 AG	149770-149865	GT	TGG
(GCC)	 AG	149983-150112	GT	AGG
(AGG)	 AG	150200-150325	GT	TGG
(ATG)	 AG	150651-150764	GT	GGG
(ATT)	 AG	150947-151096	GT	GGG
(AGG)	 AG	151573-151656	GT	TGG
(GGG)	 AG	151851-151972	CT	CAC
(TCC)	 TT	152214-152358	GT	AGG
(AGA)	 AG	152466-152592	GT	GGG
(CAT)	 AG	152705-152841	GT	AGG
(CTG)	 AG	153116-153248	GT	GGG
(GTT)	 AG	153526-153671	GT	GGG
(GGC)	 AG	153785-153911	GT	GGG
(CTT)	 AG	154205-154485	GT	CGG
(GTG)	 AG	154670-154734	AA	AAA
-recovered CodingQuarry_transcript_37229-T1, initial, 148734, 148751
add_exon() Sorry, CodingQuarry_transcript_37229-T1 150651-150764-initial-1 is invalid.
-recovered CodingQuarry_transcript_37229-T1, initial, 150651, 150764
-recovered CodingQuarry_transcript_37229-T1, terminal, 154670, 154734
-recovered CodingQuarry_transcript_37229-T1, internal, 149770, 149865
-recovered CodingQuarry_transcript_37229-T1, internal, 149983, 150112
-recovered CodingQuarry_transcript_37229-T1, internal, 150200, 150325
-recovered CodingQuarry_transcript_37229-T1, internal, 150651, 150764
-recovered CodingQuarry_transcript_37229-T1, internal, 150947, 151096
-recovered CodingQuarry_transcript_37229-T1, internal, 151573, 151656
-recovered CodingQuarry_transcript_37229-T1, internal, 152466, 152592
-recovered CodingQuarry_transcript_37229-T1, internal, 152705, 152841
-recovered CodingQuarry_transcript_37229-T1, internal, 153116, 153248
-recovered CodingQuarry_transcript_37229-T1, internal, 153526, 153671
-recovered CodingQuarry_transcript_37229-T1, internal, 153785, 153911
-recovered CodingQuarry_transcript_37229-T1, internal, 154205, 154485
Valid prediction for snap_scaffold_24-snap.993-T1
Valid prediction for GlimmerHMM_glimmerT_53730-T1
Valid prediction for GlimmerHMM_glimmerT_53731-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 GlimmerHMM_glimmerT_53718-T1
Valid prediction for snap_scaffold_24-snap.971-T1
Valid prediction for Augustus_model.g35971.t1
Valid prediction for CodingQuarry_transcript_37230-T1
Valid prediction for GeneMark_model.93716_t
Valid prediction for Augustus_model.g35977.t1
Valid prediction for snap_scaffold_24-snap.987-T1
Valid prediction for Augustus_model.g35979.t1
Valid prediction for snap_scaffold_24-snap.965-T1
Valid prediction for snap_scaffold_24-snap.985-T1
Valid prediction for GeneMark_model.93706_t
Valid prediction for snap_scaffold_24-snap.959-T1
Valid prediction for GlimmerHMM_glimmerT_53732-T1
Valid prediction for snap_scaffold_24-snap.989-T1
Valid prediction for snap_scaffold_24-snap.972-T1
Valid prediction for Augustus_model.g35968.t1
Valid prediction for GeneMark_model.93705_t
Valid prediction for GeneMark_model.93708_t
Valid prediction for GeneMark_model.93735_t
Valid prediction for GeneMark_model.93712_t
Valid prediction for snap_scaffold_24-snap.994-T1
Valid prediction for GeneMark_model.93718_t
Valid prediction for snap_scaffold_24-snap.970-T1
Valid prediction for GeneMark_model.93733_t
Valid prediction for snap_scaffold_24-snap.969-T1
Valid prediction for HiQ_model.g35980.t1
Valid prediction for GlimmerHMM_glimmerT_53724-T1
Valid prediction for snap_scaffold_24-snap.967-T1
Valid prediction for GlimmerHMM_glimmerT_53716-T1
Valid prediction for snap_scaffold_24-snap.975-T1
Valid prediction for GeneMark_model.93734_t
Valid prediction for snap_scaffold_24-snap.964-T1
Valid prediction for GlimmerHMM_glimmerT_53728-T1
Valid prediction for GlimmerHMM_glimmerT_53738-T1
Valid prediction for GeneMark_model.93726_t
Valid prediction for snap_scaffold_24-snap.986-T1
Valid prediction for Augustus_model.g35976.t1
Valid prediction for GeneMark_model.93713_t
Couldn't classify 110411, 110536
Sorry, prediction pasa_asmbl_32868.p1 fails validation.
(ATG)	 AC	109312-109386	GT	AGG
(TAT)	 AG	109552-109677	GT	AGG
(AAG)	 AG	109765-109935	GT	ATG
(GAT)	 AG	110411-110536	GT	CGG
-recovered pasa_asmbl_32868.p1, initial, 109312, 109386
-recovered pasa_asmbl_32868.p1, internal, 109552, 109677
-recovered pasa_asmbl_32868.p1, internal, 109765, 109935
-recovered pasa_asmbl_32868.p1, internal, 110411, 110536
Valid prediction for snap_scaffold_24-snap.968-T1
Valid prediction for GlimmerHMM_glimmerT_53733-T1
Valid prediction for snap_scaffold_24-snap.980-T1
Valid prediction for snap_scaffold_24-snap.981-T1
Valid prediction for Augustus_model.g35970.t1
Valid prediction for GlimmerHMM_glimmerT_53714-T1
Valid prediction for GlimmerHMM_glimmerT_53719-T1
Valid prediction for GlimmerHMM_glimmerT_53713-T1
Valid prediction for GlimmerHMM_glimmerT_53712-T1
Valid prediction for snap_scaffold_24-snap.982-T1
Valid prediction for Augustus_model.g35969.t1
Valid prediction for GlimmerHMM_glimmerT_53711-T1
Valid prediction for GeneMark_model.93719_t
Valid prediction for GeneMark_model.93715_t
Valid prediction for HiQ_model.g35978.t1
Valid prediction for snap_scaffold_24-snap.966-T1
Valid prediction for CodingQuarry_transcript_37231-T1
Valid prediction for GeneMark_model.93736_t
Valid prediction for GeneMark_model.93711_t
Valid prediction for snap_scaffold_24-snap.995-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.93728_t
Valid prediction for snap_scaffold_24-snap.984-T1
Valid prediction for GlimmerHMM_glimmerT_53727-T1
Couldn't classify 114229, 114264
Sorry, prediction pasa_asmbl_32867.p2 fails validation.
(ATG)	 CA	112045-112075	GT	AGG
(ACG)	 AG	112204-112361	GT	TGG
(ATC)	 AG	112590-112688	GT	CTG
(GGA)	 AG	114229-114264	GT	ATG
-recovered pasa_asmbl_32867.p2, initial, 112045, 112075
-recovered pasa_asmbl_32867.p2, internal, 112204, 112361
-recovered pasa_asmbl_32867.p2, internal, 112590, 112688
-recovered pasa_asmbl_32867.p2, internal, 114229, 114264
Valid prediction for snap_scaffold_24-snap.988-T1
Valid prediction for GlimmerHMM_glimmerT_53737-T1
Valid prediction for GlimmerHMM_glimmerT_53717-T1
Valid prediction for GeneMark_model.93710_t
Valid prediction for snap_scaffold_24-snap.983-T1
Valid prediction for pasa_asmbl_32863.p1
Valid prediction for snap_scaffold_24-snap.992-T1
Valid prediction for GeneMark_model.93717_t
Valid prediction for snap_scaffold_24-snap.973-T1
Valid prediction for GlimmerHMM_glimmerT_53725-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11104, rend_intergenic: 9590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 301727
-exon list size: 448


building trellis

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26.7    
26.9    
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27.6    
27.8    
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28.9    
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29.6    
29.8    
30.0    
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30.4    
30.7    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.2    
32.4    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.4    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
45.6    
45.8    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.2    
48.4    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.6    
51.8    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.2    
54.4    
54.7    
54.9    
55.1    
55.3    
55.6    
55.8    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.3    
57.6    
57.8    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.3    
61.6    
61.8    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.3    
63.6    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.3    
65.6    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.3    
67.6    
67.8    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.3    
69.6    
69.8    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.2    
72.4    
72.7    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.6    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.2    
84.4    
84.7    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.7    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 11104, rend_intergenic: 9590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10134
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 2 predictions from path traversal
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support