-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_2631533-2973935

-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_1-snap.452-T1
Valid prediction for snap_scaffold_1-snap.478-T1
Valid prediction for snap_scaffold_1-snap.477-T1
Valid prediction for GlimmerHMM_glimmerT_378-T1
Valid prediction for GeneMark_model.423_t
Valid prediction for snap_scaffold_1-snap.475-T1
Valid prediction for Augustus_model.g271.t1
Valid prediction for Augustus_model.g302.t1
Couldn't classify 325749, 325852
Sorry, prediction pasa_asmbl_1560.p1 fails validation.
(CAG)	 GC	325749-325852	GT	ATG
(TTG)	 AG	326997-327120	GT	AGG
(CTG)	 AG	327497-327650	GT	AGG
(GGG)	 AG	328561-328664	GA	AAG
-recovered pasa_asmbl_1560.p1, terminal, 328561, 328664
-recovered pasa_asmbl_1560.p1, internal, 326997, 327120
-recovered pasa_asmbl_1560.p1, internal, 327497, 327650
Valid prediction for snap_scaffold_1-snap.480-T1
Valid prediction for GlimmerHMM_glimmerT_366-T1
Valid prediction for GlimmerHMM_glimmerT_367-T1
Couldn't classify 165628, 165692
Sorry, prediction pasa_asmbl_1553.p1 fails validation.
(ATG)	 CA	164739-164858	GT	AGG
(GGT)	 AG	165006-165116	GT	TGG
(GTG)	 AG	165208-165268	GT	CTG
(CAT)	 AG	165628-165692	AT	ACA
-recovered pasa_asmbl_1553.p1, initial, 164739, 164858
-recovered pasa_asmbl_1553.p1, internal, 165006, 165116
-recovered pasa_asmbl_1553.p1, internal, 165208, 165268
Valid prediction for GeneMark_model.436_t
Valid prediction for Augustus_model.g304.t1
Valid prediction for Augustus_model.g303.t1
Valid prediction for Augustus_model.g270.t1
Valid prediction for GlimmerHMM_glimmerT_353-T1
Valid prediction for GlimmerHMM_glimmerT_383-T1
Valid prediction for GeneMark_model.399_t
Valid prediction for GlimmerHMM_glimmerT_377-T1
Valid prediction for snap_scaffold_1-snap.448-T1
Valid prediction for Augustus_model.g272.t1
Valid prediction for Augustus_model.g295.t1
Valid prediction for snap_scaffold_1-snap.443-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_365-T1
Valid prediction for GlimmerHMM_glimmerT_352-T1
Valid prediction for Augustus_model.g300.t1
Valid prediction for GeneMark_model.414_t
Valid prediction for GlimmerHMM_glimmerT_357-T1
Valid prediction for GlimmerHMM_glimmerT_370-T1
Valid prediction for snap_scaffold_1-snap.453-T1
Valid prediction for GlimmerHMM_glimmerT_369-T1
Valid prediction for HiQ_model.g293.t1
Valid prediction for Augustus_model.g296.t1
Valid prediction for Augustus_model.g278.t1
Valid prediction for GeneMark_model.421_t
Valid prediction for GeneMark_model.406_t
Valid prediction for GlimmerHMM_glimmerT_362-T1
Valid prediction for Augustus_model.g283.t1
Valid prediction for snap_scaffold_1-snap.447-T1
Valid prediction for GeneMark_model.409_t
Valid prediction for snap_scaffold_1-snap.476-T1
Valid prediction for GeneMark_model.426_t
Valid prediction for GlimmerHMM_glimmerT_361-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g282.t1
Valid prediction for GeneMark_model.432_t
Valid prediction for GeneMark_model.410_t
Valid prediction for snap_scaffold_1-snap.445-T1
Valid prediction for Augustus_model.g284.t1
Valid prediction for CodingQuarry_transcript_2550-T1
Valid prediction for GeneMark_model.427_t
Valid prediction for Augustus_model.g294.t1
Valid prediction for snap_scaffold_1-snap.479-T1
Valid prediction for GeneMark_model.417_t
Valid prediction for snap_scaffold_1-snap.444-T1
Valid prediction for GeneMark_model.403_t
Valid prediction for GeneMark_model.408_t
Valid prediction for GlimmerHMM_glimmerT_379-T1
Valid prediction for GeneMark_model.398_t
Valid prediction for GeneMark_model.429_t
Valid prediction for CodingQuarry_transcript_2551-T1
Valid prediction for Augustus_model.g281.t1
Valid prediction for snap_scaffold_1-snap.458-T1
Valid prediction for snap_scaffold_1-snap.472-T1
Valid prediction for snap_scaffold_1-snap.442-T1
Valid prediction for HiQ_model.g292.t1
Valid prediction for Augustus_model.g301.t1
Couldn't classify 276163, 276630
Sorry, prediction pasa_asmbl_1559.p1 fails validation.
(GAC)	 TT	276163-276630	GT	CGG
Valid prediction for GlimmerHMM_glimmerT_381-T1
Valid prediction for GlimmerHMM_glimmerT_354-T1
Valid prediction for GlimmerHMM_glimmerT_368-T1
Valid prediction for GlimmerHMM_glimmerT_384-T1
Valid prediction for GeneMark_model.411_t
Valid prediction for GlimmerHMM_glimmerT_382-T1
Valid prediction for snap_scaffold_1-snap.482-T1
Valid prediction for snap_scaffold_1-snap.459-T1
Couldn't classify 156705, 156892
Sorry, prediction pasa_asmbl_1547.p1 fails validation.
(GGC)	 TA	156705-156892	GT	AGG
(AGT)	 AG	158096-158228	GT	TGG
(GTG)	 AG	159932-160018	GT	AGG
(GTT)	 AG	161118-161204	TT	GAT
-recovered pasa_asmbl_1547.p1, terminal, 161118, 161204
-recovered pasa_asmbl_1547.p1, internal, 158096, 158228
-recovered pasa_asmbl_1547.p1, internal, 159932, 160018
Valid prediction for snap_scaffold_1-snap.484-T1
Valid prediction for snap_scaffold_1-snap.471-T1
Valid prediction for GeneMark_model.434_t
Valid prediction for snap_scaffold_1-snap.470-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: -)Couldn't classify 214610, 214739
Couldn't classify 215384, 215497
Sorry, prediction pasa_asmbl_1330.p1 fails validation.
(TTA)	 TG	214610-214739	GT	TGG
(CCA)	 AG	214967-215109	GT	AGG
(GCA)	 AG	215384-215497	AG	CCA
-recovered pasa_asmbl_1330.p1, internal, 214967, 215109
Valid prediction for snap_scaffold_1-snap.455-T1
Valid prediction for GlimmerHMM_glimmerT_371-T1
Valid prediction for snap_scaffold_1-snap.483-T1
Valid prediction for snap_scaffold_1-snap.464-T1
Valid prediction for GlimmerHMM_glimmerT_380-T1
Valid prediction for Augustus_model.g287.t1
Valid prediction for GlimmerHMM_glimmerT_375-T1
Valid prediction for GeneMark_model.430_t
Valid prediction for snap_scaffold_1-snap.469-T1
Valid prediction for Augustus_model.g277.t1
Valid prediction for snap_scaffold_1-snap.463-T1
Valid prediction for snap_scaffold_1-snap.461-T1
Valid prediction for GeneMark_model.402_t
Valid prediction for snap_scaffold_1-snap.449-T1
Valid prediction for GeneMark_model.435_t
Valid prediction for GeneMark_model.416_t
Valid prediction for snap_scaffold_1-snap.465-T1
Valid prediction for GlimmerHMM_glimmerT_374-T1
Valid prediction for HiQ_model.g286.t1
Valid prediction for GlimmerHMM_glimmerT_359-T1
Valid prediction for GlimmerHMM_glimmerT_355-T1
Valid prediction for snap_scaffold_1-snap.462-T1
Valid prediction for GeneMark_model.404_t
Valid prediction for snap_scaffold_1-snap.451-T1
Valid prediction for GeneMark_model.413_t
Couldn't classify 224398, 224643
Sorry, prediction pasa_asmbl_128.p1 fails validation.
(ACA)	 AC	224398-224643	GT	AGG
(GTG)	 AG	227326-227418	GT	CTG
(GTT)	 AG	227874-227950	GT	AAG
(GAA)	 AG	229271-229427	GT	AGG
(TGT)	 AG	229626-229733	GT	AGG
(GTG)	 AG	232110-232205	GT	ACG
(GAC)	 AG	232318-232452	GT	AGG
(ATT)	 AG	232681-232743	GG	GAG
-recovered pasa_asmbl_128.p1, terminal, 232681, 232743
-recovered pasa_asmbl_128.p1, internal, 227326, 227418
-recovered pasa_asmbl_128.p1, internal, 227874, 227950
-recovered pasa_asmbl_128.p1, internal, 229271, 229427
-recovered pasa_asmbl_128.p1, internal, 229626, 229733
-recovered pasa_asmbl_128.p1, internal, 232110, 232205
-recovered pasa_asmbl_128.p1, internal, 232318, 232452
Valid prediction for GlimmerHMM_glimmerT_373-T1
Valid prediction for GeneMark_model.433_t
Valid prediction for Augustus_model.g289.t1
Valid prediction for snap_scaffold_1-snap.467-T1
Valid prediction for GlimmerHMM_glimmerT_360-T1
Valid prediction for Augustus_model.g273.t1
Valid prediction for snap_scaffold_1-snap.460-T1
Valid prediction for snap_scaffold_1-snap.456-T1
Valid prediction for GeneMark_model.407_t
Valid prediction for Augustus_model.g297.t1
Valid prediction for GeneMark_model.418_t
Valid prediction for Augustus_model.g290.t1
Valid prediction for GlimmerHMM_glimmerT_376-T1
Valid prediction for Augustus_model.g288.t1
Valid prediction for snap_scaffold_1-snap.454-T1
Valid prediction for GeneMark_model.425_t
Valid prediction for GeneMark_model.424_t
Valid prediction for GeneMark_model.431_t
Valid prediction for Augustus_model.g276.t1
Valid prediction for Augustus_model.g280.t1
Valid prediction for snap_scaffold_1-snap.450-T1
Valid prediction for Augustus_model.g299.t1
Valid prediction for Augustus_model.g298.t1
Valid prediction for GlimmerHMM_glimmerT_356-T1
Valid prediction for Augustus_model.g279.t1
Valid prediction for snap_scaffold_1-snap.473-T1
Valid prediction for GeneMark_model.415_t
Valid prediction for snap_scaffold_1-snap.468-T1
Valid prediction for GeneMark_model.412_t
Valid prediction for Augustus_model.g274.t1
Valid prediction for GlimmerHMM_glimmerT_372-T1
Valid prediction for GeneMark_model.419_t
Valid prediction for GlimmerHMM_glimmerT_358-T1
Valid prediction for Augustus_model.g291.t1
Valid prediction for snap_scaffold_1-snap.466-T1
Valid prediction for GlimmerHMM_glimmerT_363-T1
Valid prediction for snap_scaffold_1-snap.446-T1
Valid prediction for snap_scaffold_1-snap.481-T1
Valid prediction for snap_scaffold_1-snap.474-T1
Valid prediction for GlimmerHMM_glimmerT_364-T1
Valid prediction for Augustus_model.g285.t1
Valid prediction for GeneMark_model.400_t
Valid prediction for GeneMark_model.428_t
Valid prediction for snap_scaffold_1-snap.457-T1
Valid prediction for GeneMark_model.405_t
Valid prediction for Augustus_model.g275.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 312088, rend_intergenic: 304130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 327107, rend_intergenic: 323793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 342403
-exon list size: 431


building trellis

0.2    
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3.9    
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6.9    
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8.8    
9.0    
9.2    
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9.9    
10.2    
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10.6    
10.9    
11.1    
11.3    
11.5    
11.8    
12.0    
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13.2    
13.4    
13.6    
13.9    
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14.3    
14.5    
14.8    
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15.5    
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16.2    
16.4    
16.6    
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17.6    
17.8    
18.0    
18.2    
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18.7    
18.9    
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19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.0    
21.2    
21.5    
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21.9    
22.2    
22.4    
22.6    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
30.9    
31.2    
31.4    
31.6    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.4    
37.6    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.6    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.7    
55.0    
55.2    
55.4    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
61.0    
61.2    
61.4    
61.7    
61.9    
62.1    
62.4    
62.6    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.7    
67.9    
68.1    
68.4    
68.6    
68.8    
69.1    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.4    
77.6    
77.8    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.8    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 312088, rend_intergenic: 304130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 327107, rend_intergenic: 323793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14917
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 2073 - 14917
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 2073 - 13186

-building DP trellis

-building trellis in range 328665 - 342403
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 329415 - 342403