-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_1-171822

-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 pasa_asmbl_16783.p1
Valid prediction for GeneMark_model.65907_t
Valid prediction for GeneMark_model.65910_t
Valid prediction for HiQ_model.g25795.t1
Valid prediction for snap_scaffold_16-snap.26-T1
Couldn't classify 138725, 138869
Sorry, prediction pasa_asmbl_17535.p1 fails validation.
(ATG)	 AC	137491-137557	GT	CGG
(TTG)	 AG	138105-138177	GT	TGG
(CTG)	 AG	138725-138869	GG	ATG
-recovered pasa_asmbl_17535.p1, initial, 137491, 137557
-recovered pasa_asmbl_17535.p1, internal, 138105, 138177
Valid prediction for snap_scaffold_16-snap.12-T1
Valid prediction for snap_scaffold_16-snap.25-T1
Valid prediction for Augustus_model.g25791.t1
Valid prediction for GlimmerHMM_glimmerT_38477-T1
Valid prediction for Augustus_model.g25782.t1
Valid prediction for GeneMark_model.65915_t
Valid prediction for Augustus_model.g25787.t1
Valid prediction for Augustus_model.g25793.t1
Valid prediction for snap_scaffold_16-snap.20-T1
Valid prediction for Augustus_model.g25784.t1
Valid prediction for GeneMark_model.65903_t
Couldn't classify 104620, 104792
Couldn't classify 105135, 105266
Sorry, prediction pasa_asmbl_17558.p1 fails validation.
(GTT)	 AG	104620-104792	GT	AGG
(CAC)	 AG	104930-105023	GT	AGG
(GTA)	 AG	105135-105266	TG	AGT
-recovered pasa_asmbl_17558.p1, internal, 104620, 104792
-recovered pasa_asmbl_17558.p1, internal, 104930, 105023
Valid prediction for snap_scaffold_16-snap.16-T1
Valid prediction for snap_scaffold_16-snap.30-T1
Valid prediction for CodingQuarry_transcript_19831-T1
Valid prediction for snap_scaffold_16-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_38469-T1
Valid prediction for GeneMark_model.65919_t
Valid prediction for Augustus_model.g25785.t1
Valid prediction for Augustus_model.g25779.t1
Valid prediction for Augustus_model.g25794.t1
Valid prediction for snap_scaffold_16-snap.8-T1
Valid prediction for snap_scaffold_16-snap.19-T1
Valid prediction for pasa_asmbl_16785.p1
Valid prediction for GlimmerHMM_glimmerT_38474-T1
Valid prediction for snap_scaffold_16-snap.22-T1
Valid prediction for GlimmerHMM_glimmerT_38464-T1
Valid prediction for GlimmerHMM_glimmerT_38476-T1
Valid prediction for GlimmerHMM_glimmerT_38478-T1
Valid prediction for GeneMark_model.65917_t
Valid prediction for Augustus_model.g25781.t1
Couldn't classify 109020, 109170
Couldn't classify 109555, 109626
Sorry, prediction pasa_asmbl_17562.p1 fails validation.
(AGG)	 TT	109020-109170	GT	AGG
(AGC)	 AG	109344-109432	GT	CGG
(GAT)	 AG	109555-109626	TG	CTT
-recovered pasa_asmbl_17562.p1, internal, 109344, 109432
Valid prediction for snap_scaffold_16-snap.7-T1
Valid prediction for snap_scaffold_16-snap.28-T1
Valid prediction for snap_scaffold_16-snap.3-T1
Valid prediction for Augustus_model.g25796.t1
Valid prediction for Augustus_model.g25780.t1
Valid prediction for snap_scaffold_16-snap.2-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38465-T1
Valid prediction for snap_scaffold_16-snap.14-T1
Valid prediction for GlimmerHMM_glimmerT_38460-T1
Valid prediction for snap_scaffold_16-snap.17-T1
Valid prediction for snap_scaffold_16-snap.1-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.65912_t
Valid prediction for Augustus_model.g25789.t1
Valid prediction for GlimmerHMM_glimmerT_38458-T1
Valid prediction for Augustus_model.g25792.t1
Valid prediction for GeneMark_model.65913_t
Valid prediction for GlimmerHMM_glimmerT_38457-T1
Valid prediction for GlimmerHMM_glimmerT_38471-T1
Couldn't classify 145376, 145465
Sorry, prediction pasa_asmbl_16789.p1 fails validation.
(AGC)	 GT	145376-145465	GT	TAG
(TAC)	 AG	145546-145687	GT	AGG
(GTT)	 AG	145808-145908	TG	GAT
-recovered pasa_asmbl_16789.p1, terminal, 145808, 145908
-recovered pasa_asmbl_16789.p1, internal, 145546, 145687
Valid prediction for GeneMark_model.65904_t
Valid prediction for GlimmerHMM_glimmerT_38481-T1
Valid prediction for GeneMark_model.65906_t
Valid prediction for GlimmerHMM_glimmerT_38459-T1
Valid prediction for CodingQuarry_transcript_19830-T1
Valid prediction for snap_scaffold_16-snap.24-T1
Valid prediction for snap_scaffold_16-snap.27-T1
Valid prediction for GlimmerHMM_glimmerT_38461-T1
Valid prediction for GeneMark_model.65921_t
Valid prediction for Augustus_model.g25798.t1
Valid prediction for GlimmerHMM_glimmerT_38468-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 snap_scaffold_16-snap.9-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.21-T1
Valid prediction for GlimmerHMM_glimmerT_38462-T1
Valid prediction for Augustus_model.g25797.t1
Valid prediction for pasa_asmbl_16005.p1
Valid prediction for GlimmerHMM_glimmerT_38472-T1
Valid prediction for snap_scaffold_16-snap.29-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.65922_t
Valid prediction for Augustus_model.g25802.t1
Valid prediction for GlimmerHMM_glimmerT_38466-T1
Valid prediction for GeneMark_model.65916_t
Valid prediction for snap_scaffold_16-snap.15-T1
Valid prediction for snap_scaffold_16-snap.4-T1
Valid prediction for GeneMark_model.65918_t
Valid prediction for GlimmerHMM_glimmerT_38470-T1
Valid prediction for HiQ_model.g25790.t1
Valid prediction for Augustus_model.g25786.t1
Valid prediction for snap_scaffold_16-snap.5-T1
Valid prediction for snap_scaffold_16-snap.23-T1
Valid prediction for GlimmerHMM_glimmerT_38467-T1
Valid prediction for GeneMark_model.65909_t
Valid prediction for GeneMark_model.65905_t
Valid prediction for GeneMark_model.65923_t
Valid prediction for snap_scaffold_16-snap.6-T1
Valid prediction for GlimmerHMM_glimmerT_38475-T1
Valid prediction for GlimmerHMM_glimmerT_38479-T1
Valid prediction for Augustus_model.g25788.t1
Valid prediction for GlimmerHMM_glimmerT_38463-T1
Valid prediction for snap_scaffold_16-snap.18-T1
Valid prediction for Augustus_model.g25801.t1
Valid prediction for GlimmerHMM_glimmerT_38473-T1
Valid prediction for snap_scaffold_16-snap.10-T1
Valid prediction for Augustus_model.g25800.t1
Couldn't classify 85693, 85789
Sorry, prediction pasa_asmbl_15997.p1 fails validation.
(AAG)	 GA	85693-85789	GT	AGG
(GAA)	 AG	85879-85936	GT	AGG
(TGG)	 AG	86040-86119	GT	AGG
(GAT)	 AG	87210-87252	GT	GGG
(CGT)	 AG	87343-87441	GT	GGG
(CAT)	 AG	90404-90484	GT	AAG
(GGC)	 AG	90600-90790	GT	AGG
(GCA)	 AG	90937-91116	GT	AGG
(GAC)	 AG	91317-91372	GT	AGG
(GCA)	 AG	91471-91616	GT	AGG
(GGC)	 AG	92860-92935	AT	GAA
-recovered pasa_asmbl_15997.p1, terminal, 92860, 92935
-recovered pasa_asmbl_15997.p1, internal, 85879, 85936
-recovered pasa_asmbl_15997.p1, internal, 86040, 86119
-recovered pasa_asmbl_15997.p1, internal, 87210, 87252
-recovered pasa_asmbl_15997.p1, internal, 87343, 87441
-recovered pasa_asmbl_15997.p1, internal, 90404, 90484
-recovered pasa_asmbl_15997.p1, internal, 90600, 90790
-recovered pasa_asmbl_15997.p1, internal, 90937, 91116
-recovered pasa_asmbl_15997.p1, internal, 91317, 91372
-recovered pasa_asmbl_15997.p1, internal, 91471, 91616
Valid prediction for Augustus_model.g25783.t1
Valid prediction for CodingQuarry_transcript_19829-T1
Valid prediction for HiQ_model.g25799.t1
Valid prediction for snap_scaffold_16-snap.13-T1
Valid prediction for GlimmerHMM_glimmerT_38480-T1
Valid prediction for GeneMark_model.65914_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 28336, rend_intergenic: 28333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169141, rend_intergenic: 167222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171822
-exon list size: 364


building trellis

0.3    
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1.1    
1.4    
1.6    
1.9    
2.2    
2.5    
2.7    
3.0    
3.3    
3.6    
3.8    
4.1    
4.4    
4.6    
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5.7    
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6.6    
6.8    
7.1    
7.4    
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9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
12.8    
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13.9    
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14.5    
14.8    
15.0    
15.3    
15.6    
15.8    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.0    
21.3    
21.6    
21.9    
22.1    
22.4    
22.7    
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23.2    
23.5    
23.8    
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24.3    
24.6    
24.9    
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25.4    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
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32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.4    
43.7    
44.0    
44.3    
44.5    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.5    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.5    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.5    
55.7    
56.0    
56.3    
56.6    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.7    
63.9    
64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
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68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.9    
72.1    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.2    
76.5    
76.8    
77.0    
77.3    
77.6    
77.9    
78.1    
78.4    
78.7    
79.0    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.3    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.2    
93.4    
93.7    
94.0    
94.3    
94.5    
94.8    
95.1    
95.4    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 29 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 28336, rend_intergenic: 28333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169141, rend_intergenic: 167222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support