-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_2631533-3032758

-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.477-T1
Valid prediction for GlimmerHMM_glimmerT_364-T1
Valid prediction for snap_scaffold_1-snap.471-T1
Valid prediction for Augustus_model.g309.t1
Valid prediction for HiQ_model.g292.t1
Valid prediction for snap_scaffold_1-snap.447-T1
Valid prediction for GlimmerHMM_glimmerT_339-T1
Valid prediction for snap_scaffold_1-snap.446-T1
Valid prediction for GlimmerHMM_glimmerT_346-T1
Valid prediction for GlimmerHMM_glimmerT_371-T1
Valid prediction for GlimmerHMM_glimmerT_363-T1
Valid prediction for snap_scaffold_1-snap.465-T1
Valid prediction for pasa_asmbl_1565.p1
Valid prediction for snap_scaffold_1-snap.459-T1
Valid prediction for GlimmerHMM_glimmerT_334-T1
Valid prediction for snap_scaffold_1-snap.473-T1
Valid prediction for CodingQuarry_transcript_2553-T1
Valid prediction for HiQ_model.g293.t1
Valid prediction for Augustus_model.g301.t1
Valid prediction for GlimmerHMM_glimmerT_342-T1
Valid prediction for GlimmerHMM_glimmerT_369-T1
Valid prediction for snap_scaffold_1-snap.445-T1
Valid prediction for GlimmerHMM_glimmerT_361-T1
Valid prediction for GlimmerHMM_glimmerT_351-T1
Valid prediction for snap_scaffold_1-snap.458-T1
Valid prediction for snap_scaffold_1-snap.436-T1
Valid prediction for Augustus_model.g270.t1
Valid prediction for Augustus_model.g271.t1
Valid prediction for GlimmerHMM_glimmerT_366-T1
Valid prediction for GlimmerHMM_glimmerT_345-T1
Valid prediction for Augustus_model.g281.t1
Valid prediction for snap_scaffold_1-snap.476-T1
Valid prediction for snap_scaffold_1-snap.472-T1
Valid prediction for GlimmerHMM_glimmerT_359-T1
Valid prediction for Augustus_model.g277.t1
Valid prediction for snap_scaffold_1-snap.478-T1
Valid prediction for snap_scaffold_1-snap.466-T1
Valid prediction for GlimmerHMM_glimmerT_338-T1
Valid prediction for GlimmerHMM_glimmerT_368-T1
Valid prediction for snap_scaffold_1-snap.463-T1
Valid prediction for Augustus_model.g280.t1
Couldn't classify 325749, 325852
Sorry, prediction pasa_asmbl_1566.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_1566.p1, terminal, 328561, 328664
-recovered pasa_asmbl_1566.p1, internal, 326997, 327120
-recovered pasa_asmbl_1566.p1, internal, 327497, 327650
Couldn't classify 156705, 156892
Sorry, prediction pasa_asmbl_1553.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_1553.p1, terminal, 161118, 161204
-recovered pasa_asmbl_1553.p1, internal, 158096, 158228
-recovered pasa_asmbl_1553.p1, internal, 159932, 160018
Valid prediction for CodingQuarry_transcript_2554-T1
Valid prediction for GlimmerHMM_glimmerT_333-T1
Valid prediction for snap_scaffold_1-snap.433-T1
Valid prediction for Augustus_model.g284.t1
Valid prediction for Augustus_model.g305.t1
Valid prediction for GlimmerHMM_glimmerT_360-T1
Valid prediction for GlimmerHMM_glimmerT_372-T1
Valid prediction for Augustus_model.g294.t1
Valid prediction for GlimmerHMM_glimmerT_350-T1
Valid prediction for snap_scaffold_1-snap.470-T1
Valid prediction for Augustus_model.g282.t1
Valid prediction for Augustus_model.g296.t1
Valid prediction for Augustus_model.g304.t1
Valid prediction for snap_scaffold_1-snap.475-T1
Valid prediction for snap_scaffold_1-snap.467-T1
Valid prediction for Augustus_model.g272.t1
Valid prediction for GlimmerHMM_glimmerT_347-T1
Valid prediction for GlimmerHMM_glimmerT_335-T1
Couldn't classify 382631, 382875
Couldn't classify 384639, 384693
Sorry, prediction pasa_asmbl_2823.p1 fails validation.
(GTG)	 AC	382631-382875	GT	AGG
(GAC)	 AG	384639-384693	AA	ACA
Valid prediction for Augustus_model.g303.t1
Valid prediction for Augustus_model.g300.t1
Valid prediction for snap_scaffold_1-snap.431-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.432-T1
Valid prediction for snap_scaffold_1-snap.435-T1
Valid prediction for GlimmerHMM_glimmerT_367-T1
Valid prediction for Augustus_model.g295.t1
Valid prediction for Augustus_model.g310.t1
Valid prediction for snap_scaffold_1-snap.460-T1
Valid prediction for GlimmerHMM_glimmerT_348-T1
Valid prediction for snap_scaffold_1-snap.441-T1
Valid prediction for GlimmerHMM_glimmerT_349-T1
Valid prediction for snap_scaffold_1-snap.442-T1
Valid prediction for GlimmerHMM_glimmerT_370-T1
Valid prediction for snap_scaffold_1-snap.430-T1
Valid prediction for snap_scaffold_1-snap.464-T1
Couldn't classify 386966, 387016
Couldn't classify 389476, 389540
Sorry, prediction pasa_asmbl_1567.p1 fails validation.
(TCC)	 AC	386966-387016	GT	TGG
(ACC)	 AG	387555-387714	GT	GGG
(AGT)	 AG	387975-388078	GC	AGG
(GTG)	 AG	388311-388407	GT	TGG
(AGA)	 AG	389476-389540	GA	CAG
-recovered pasa_asmbl_1567.p1, internal, 387555, 387714
-recovered pasa_asmbl_1567.p1, internal, 387975, 388078
-recovered pasa_asmbl_1567.p1, internal, 388311, 388407
Valid prediction for Augustus_model.g308.t1
Valid prediction for Augustus_model.g302.t1
Valid prediction for snap_scaffold_1-snap.468-T1
Valid prediction for Augustus_model.g283.t1
Couldn't classify 165628, 165692
Sorry, prediction pasa_asmbl_1559.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_1559.p1, initial, 164739, 164858
-recovered pasa_asmbl_1559.p1, internal, 165006, 165116
-recovered pasa_asmbl_1559.p1, internal, 165208, 165268

-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 snap_scaffold_1-snap.450-T1
Valid prediction for snap_scaffold_1-snap.434-T1
Valid prediction for snap_scaffold_1-snap.438-T1
Valid prediction for Augustus_model.g275.t1
Valid prediction for snap_scaffold_1-snap.474-T1
Valid prediction for snap_scaffold_1-snap.451-T1
Valid prediction for GlimmerHMM_glimmerT_356-T1
Valid prediction for GlimmerHMM_glimmerT_352-T1
Valid prediction for GlimmerHMM_glimmerT_336-T1
Valid prediction for Augustus_model.g278.t1
Valid prediction for snap_scaffold_1-snap.453-T1
Valid prediction for snap_scaffold_1-snap.461-T1
Valid prediction for Augustus_model.g306.t1
Valid prediction for GlimmerHMM_glimmerT_354-T1
Valid prediction for snap_scaffold_1-snap.437-T1
Valid prediction for GlimmerHMM_glimmerT_357-T1
Valid prediction for snap_scaffold_1-snap.448-T1
Valid prediction for HiQ_model.g286.t1
Valid prediction for Augustus_model.g288.t1
Valid prediction for snap_scaffold_1-snap.456-T1
Valid prediction for Augustus_model.g274.t1
Valid prediction for Augustus_model.g287.t1
Valid prediction for Augustus_model.g285.t1
Valid prediction for GlimmerHMM_glimmerT_344-T1
Valid prediction for snap_scaffold_1-snap.444-T1
Valid prediction for snap_scaffold_1-snap.457-T1
Valid prediction for Augustus_model.g273.t1
Valid prediction for snap_scaffold_1-snap.440-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_355-T1
Valid prediction for Augustus_model.g291.t1
Valid prediction for snap_scaffold_1-snap.449-T1
Valid prediction for Augustus_model.g297.t1
Valid prediction for GlimmerHMM_glimmerT_341-T1
Valid prediction for snap_scaffold_1-snap.454-T1
Valid prediction for Augustus_model.g276.t1
Valid prediction for Augustus_model.g290.t1
Valid prediction for Augustus_model.g289.t1
Valid prediction for GlimmerHMM_glimmerT_340-T1
Valid prediction for GlimmerHMM_glimmerT_358-T1
Couldn't classify 283221, 283466
Sorry, prediction pasa_asmbl_125.p1 fails validation.
(ACA)	 AC	283221-283466	GT	AGG
(GTG)	 AG	286149-286241	GT	CTG
(GTT)	 AG	286697-286773	GT	AAG
(GAA)	 AG	288094-288250	GT	AGG
(TGT)	 AG	288449-288556	GT	AGG
(GTG)	 AG	290933-291028	GT	ACG
(GAC)	 AG	291141-291275	GT	AGG
(ATT)	 AG	291504-291566	GG	GAG
-recovered pasa_asmbl_125.p1, terminal, 291504, 291566
-recovered pasa_asmbl_125.p1, internal, 286149, 286241
-recovered pasa_asmbl_125.p1, internal, 286697, 286773
-recovered pasa_asmbl_125.p1, internal, 288094, 288250
-recovered pasa_asmbl_125.p1, internal, 288449, 288556
-recovered pasa_asmbl_125.p1, internal, 290933, 291028
-recovered pasa_asmbl_125.p1, internal, 291141, 291275
Valid prediction for snap_scaffold_1-snap.443-T1
Valid prediction for Augustus_model.g307.t1
Valid prediction for snap_scaffold_1-snap.452-T1
Valid prediction for GlimmerHMM_glimmerT_353-T1
Valid prediction for GlimmerHMM_glimmerT_337-T1
Valid prediction for Augustus_model.g299.t1
Valid prediction for Augustus_model.g279.t1
Valid prediction for GlimmerHMM_glimmerT_365-T1
Valid prediction for GlimmerHMM_glimmerT_362-T1
Couldn't classify 273433, 273562
Couldn't classify 274207, 274320
Sorry, prediction pasa_asmbl_1323.p1 fails validation.
(TTA)	 TG	273433-273562	GT	TGG
(CCA)	 AG	273790-273932	GT	AGG
(GCA)	 AG	274207-274320	AG	CCA
-recovered pasa_asmbl_1323.p1, internal, 273790, 273932
Valid prediction for snap_scaffold_1-snap.462-T1
Valid prediction for GlimmerHMM_glimmerT_343-T1
Valid prediction for snap_scaffold_1-snap.439-T1
Valid prediction for Augustus_model.g298.t1
Valid prediction for snap_scaffold_1-snap.469-T1
Valid prediction for snap_scaffold_1-snap.455-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 327107, rend_intergenic: 323793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 379449, rend_intergenic: 379174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 384452, rend_intergenic: 380376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 401226
-exon list size: 381


building trellis

0.3    
0.5    
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1.0    
1.3    
1.6    
1.8    
2.1    
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2.6    
2.9    
3.1    
3.4    
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7.0    
7.3    
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8.1    
8.4    
8.6    
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10.4    
10.7    
11.0    
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11.7    
12.0    
12.3    
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15.7    
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18.0    
18.3    
18.5    
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19.3    
19.6    
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20.4    
20.6    
20.9    
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21.4    
21.7    
21.9    
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22.5    
22.7    
23.0    
23.2    
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23.8    
24.0    
24.3    
24.5    
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25.3    
25.6    
25.8    
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26.4    
26.6    
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27.2    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.2    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.1    
31.3    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.6    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.4    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.4    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.7    
68.9    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.8    
71.0    
71.3    
71.5    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.8    
77.0    
77.3    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.8    
83.0    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.2    
86.4    
86.7    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.7    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 327107, rend_intergenic: 323793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 379449, rend_intergenic: 379174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 384452, rend_intergenic: 380376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 41 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