-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_2128651-2248919

-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 Augustus_model.g39723.t1
Valid prediction for snap_scaffold_28-snap.528-T1
Valid prediction for GlimmerHMM_glimmerT_59692-T1
Valid prediction for GlimmerHMM_glimmerT_59685-T1
Valid prediction for GeneMark_model.104166_t
Valid prediction for Augustus_model.g39735.t1
Valid prediction for snap_scaffold_28-snap.542-T1
Couldn't classify 3033, 3086
Sorry, prediction pasa_asmbl_38024.p1 fails validation.
(AAA)	 AA	3033-3086	GT	AAG
(GCC)	 AG	3574-3693	GT	AGG
(GCA)	 AG	3894-4009	GT	AGG
(GAT)	 AG	4103-4181	GT	AGG
(TGT)	 AG	4270-4314	GT	AGG
(GAT)	 AG	4408-4466	GT	AAG
(GAC)	 AG	4603-4632	GT	GGG
(AGC)	 AG	4751-4871	GT	AGG
(ATC)	 AG	5060-5242	TG	GAT
-recovered pasa_asmbl_38024.p1, terminal, 4408, 4466
-recovered pasa_asmbl_38024.p1, terminal, 5060, 5242
-recovered pasa_asmbl_38024.p1, internal, 3574, 3693
-recovered pasa_asmbl_38024.p1, internal, 3894, 4009
-recovered pasa_asmbl_38024.p1, internal, 4103, 4181
-recovered pasa_asmbl_38024.p1, internal, 4270, 4314
-recovered pasa_asmbl_38024.p1, internal, 4408, 4466
-recovered pasa_asmbl_38024.p1, internal, 4603, 4632
-recovered pasa_asmbl_38024.p1, internal, 4751, 4871
Couldn't classify 75363, 75384
Sorry, prediction pasa_asmbl_38045.p1 fails validation.
(ATG)	 CC	74060-74212	GT	TGG
(ATG)	 AG	74388-74473	GT	AGG
(GTT)	 AG	74617-74720	GT	GAG
(GTC)	 AG	74991-75114	GT	GGG
(CAT)	 AG	75363-75384	GC	GCG
-recovered pasa_asmbl_38045.p1, initial, 74060, 74212
-recovered pasa_asmbl_38045.p1, initial, 74388, 74473
add_exon() Sorry, pasa_asmbl_38045.p1 74617-74720-terminal-2 is invalid.
-recovered pasa_asmbl_38045.p1, terminal, 74617, 74720
-recovered pasa_asmbl_38045.p1, internal, 74388, 74473
-recovered pasa_asmbl_38045.p1, internal, 74617, 74720
-recovered pasa_asmbl_38045.p1, internal, 74991, 75114
-recovered pasa_asmbl_38045.p1, internal, 75363, 75384
Valid prediction for snap_scaffold_28-snap.536-T1
Valid prediction for Augustus_model.g39720.t1
Valid prediction for snap_scaffold_28-snap.531-T1
Valid prediction for GlimmerHMM_glimmerT_59691-T1
Valid prediction for Augustus_model.g39726.t1
Valid prediction for GlimmerHMM_glimmerT_59698-T1
Valid prediction for pasa_asmbl_38030.p1
Couldn't classify 70450, 70460
Sorry, prediction pasa_asmbl_38042.p1 fails validation.
(CTC)	 GC	70450-70460	GT	AGG
(GAT)	 AG	70534-70667	GT	AGG
(GTA)	 AG	70763-70971	GT	AGG
(GAG)	 AG	71064-72053	AG	GAA
-recovered pasa_asmbl_38042.p1, terminal, 71064, 72053
-recovered pasa_asmbl_38042.p1, internal, 70534, 70667
-recovered pasa_asmbl_38042.p1, internal, 70763, 70971
Valid prediction for Augustus_model.g39728.t1
Valid prediction for snap_scaffold_28-snap.529-T1
Valid prediction for snap_scaffold_28-snap.538-T1
Valid prediction for GlimmerHMM_glimmerT_59695-T1
Valid prediction for snap_scaffold_28-snap.527-T1
Valid prediction for GlimmerHMM_glimmerT_59681-T1
Couldn't classify 19154, 19314
Couldn't classify 21166, 21296
Sorry, prediction pasa_asmbl_38027.p1 fails validation.
(GGG)	 CA	19154-19314	GT	AGG
(CAA)	 AG	20535-20624	GT	AGG
(ATC)	 AG	20830-21023	GT	AGG
(TCT)	 AG	21166-21296	CC	TAC
-recovered pasa_asmbl_38027.p1, internal, 20535, 20624
-recovered pasa_asmbl_38027.p1, internal, 20830, 21023
Couldn't classify 68405, 68597
Sorry, prediction pasa_asmbl_38037.p1 fails validation.
(GAG)	 CC	68405-68597	GT	TGG
(GTA)	 AG	68729-68860	GT	AGG
(GTA)	 AG	68970-69134	GT	AGG
(AGC)	 AG	69290-69450	TT	AGT
add_exon() Sorry, pasa_asmbl_38037.p1 68729-68860-terminal-1 is invalid.
-recovered pasa_asmbl_38037.p1, terminal, 68729, 68860
-recovered pasa_asmbl_38037.p1, terminal, 69290, 69450
-recovered pasa_asmbl_38037.p1, internal, 68729, 68860
-recovered pasa_asmbl_38037.p1, internal, 68970, 69134
Couldn't classify 111986, 112000
Couldn't classify 113928, 113993
Sorry, prediction pasa_asmbl_38047.p1 fails validation.
(CTT)	 AC	111986-112000	GT	CGG
(ACC)	 AG	112224-112297	GT	CCG
(GAA)	 AG	112402-112453	GT	AGG
(ACA)	 AG	112630-112779	GT	AGG
(AAT)	 AG	113567-113614	GT	CTG
(ACG)	 AG	113928-113993	GC	ACG
-recovered pasa_asmbl_38047.p1, internal, 112224, 112297
-recovered pasa_asmbl_38047.p1, internal, 112402, 112453
-recovered pasa_asmbl_38047.p1, internal, 112630, 112779
-recovered pasa_asmbl_38047.p1, internal, 113567, 113614
-recovered pasa_asmbl_38047.p1, internal, 113928, 113993
Valid prediction for GeneMark_model.104167_t
Valid prediction for GlimmerHMM_glimmerT_59700-T1
Valid prediction for snap_scaffold_28-snap.546-T1
Valid prediction for GlimmerHMM_glimmerT_59701-T1
Valid prediction for snap_scaffold_28-snap.543-T1
Valid prediction for HiQ_model.g39722.t1
Valid prediction for GlimmerHMM_glimmerT_59686-T1
Valid prediction for GeneMark_model.104171_t
Valid prediction for HiQ_model.g39716.t1
Valid prediction for GeneMark_model.104169_t
Valid prediction for GlimmerHMM_glimmerT_59694-T1
Valid prediction for snap_scaffold_28-snap.534-T1
Valid prediction for GeneMark_model.104173_t
Valid prediction for GeneMark_model.104163_t
Valid prediction for GlimmerHMM_glimmerT_59702-T1
Valid prediction for CodingQuarry_transcript_43456-T1
Valid prediction for pasa_asmbl_38032.p1
Valid prediction for HiQ_model.g39721.t1
Valid prediction for snap_scaffold_28-snap.533-T1
Valid prediction for snap_scaffold_28-snap.544-T1
Valid prediction for CodingQuarry_transcript_43457-T1
Valid prediction for snap_scaffold_28-snap.522-T1
Valid prediction for snap_scaffold_28-snap.548-T1
Valid prediction for snap_scaffold_28-snap.539-T1
Valid prediction for Augustus_model.g39732.t1
Valid prediction for GlimmerHMM_glimmerT_59690-T1
Valid prediction for GeneMark_model.104174_t
Valid prediction for GeneMark_model.104168_t
Valid prediction for GlimmerHMM_glimmerT_59688-T1
Valid prediction for GeneMark_model.104170_t
Valid prediction for GeneMark_model.104177_t
Valid prediction for GlimmerHMM_glimmerT_59696-T1
Valid prediction for Augustus_model.g39734.t1
Valid prediction for CodingQuarry_transcript_43460-T1
Couldn't classify 21656, 21710
Sorry, prediction pasa_asmbl_38028.p1 fails validation.
(GGT)	 CA	21656-21710	GT	GGG
(ACC)	 AG	21867-22079	GT	AGG
(GAA)	 AG	22258-22395	GT	AGG
(GTT)	 AG	22520-22664	GT	AGG
(GCG)	 AG	22808-22931	TG	AAT
add_exon() Sorry, pasa_asmbl_38028.p1 21867-22079-terminal-1 is invalid.
-recovered pasa_asmbl_38028.p1, terminal, 21867, 22079
add_exon() Sorry, pasa_asmbl_38028.p1 22520-22664-terminal-3 is invalid.
-recovered pasa_asmbl_38028.p1, terminal, 22520, 22664
-recovered pasa_asmbl_38028.p1, terminal, 22808, 22931
-recovered pasa_asmbl_38028.p1, internal, 21867, 22079
-recovered pasa_asmbl_38028.p1, internal, 22258, 22395
-recovered pasa_asmbl_38028.p1, internal, 22520, 22664
Valid prediction for Augustus_model.g39729.t1
Valid prediction for snap_scaffold_28-snap.530-T1
Valid prediction for GeneMark_model.104179_t
Valid prediction for Augustus_model.g39725.t1
Valid prediction for snap_scaffold_28-snap.526-T1
Valid prediction for snap_scaffold_28-snap.547-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_28-snap.524-T1
Valid prediction for Augustus_model.g39717.t1
Valid prediction for CodingQuarry_transcript_43459-T1
Valid prediction for snap_scaffold_28-snap.535-T1
Valid prediction for GlimmerHMM_glimmerT_59693-T1
Valid prediction for GeneMark_model.104172_t
Valid prediction for CodingQuarry_transcript_43458-T1
Valid prediction for snap_scaffold_28-snap.541-T1
Valid prediction for Augustus_model.g39718.t1
Valid prediction for HiQ_model.g39731.t1
Valid prediction for GeneMark_model.104175_t
Valid prediction for GlimmerHMM_glimmerT_59697-T1
Valid prediction for snap_scaffold_28-snap.540-T1
Valid prediction for snap_scaffold_28-snap.537-T1
Valid prediction for Augustus_model.g39724.t1
Valid prediction for GlimmerHMM_glimmerT_59683-T1
Couldn't classify 58024, 58146
Sorry, prediction pasa_asmbl_37341.p1 fails validation.
(GAG)	 GT	58024-58146	GT	AGG
(CTG)	 AG	58370-58490	GT	TGG
(GTG)	 AG	58832-58920	CA	GAC
-recovered pasa_asmbl_37341.p1, terminal, 58832, 58920
-recovered pasa_asmbl_37341.p1, internal, 58370, 58490
Valid prediction for GlimmerHMM_glimmerT_59684-T1
Couldn't classify 113577, 113894
Sorry, prediction pasa_asmbl_37930.p3 fails validation.
(ACC)	 CG	113577-113894	CC	ACC
Valid prediction for CodingQuarry_transcript_43461-T1
Valid prediction for GlimmerHMM_glimmerT_59687-T1
Valid prediction for Augustus_model.g39730.t1
Valid prediction for GlimmerHMM_glimmerT_59689-T1
Valid prediction for snap_scaffold_28-snap.545-T1
Valid prediction for GlimmerHMM_glimmerT_59682-T1
Valid prediction for GeneMark_model.104176_t
Valid prediction for Augustus_model.g39719.t1
Valid prediction for Augustus_model.g39727.t1
Valid prediction for snap_scaffold_28-snap.523-T1
Valid prediction for pasa_asmbl_37344.p1
Valid prediction for GeneMark_model.104178_t
Valid prediction for snap_scaffold_28-snap.532-T1
Valid prediction for snap_scaffold_28-snap.525-T1
Valid prediction for Augustus_model.g39733.t1
Valid prediction for CodingQuarry_transcript_43455-T1
Valid prediction for GlimmerHMM_glimmerT_59699-T1
Valid prediction for GeneMark_model.104165_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 49647, rend_intergenic: 43264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 120269
-exon list size: 448


building trellis

0.2    
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0.9    
1.1    
1.3    
1.6    
1.8    
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2.7    
2.9    
3.1    
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3.6    
3.8    
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4.4    
4.7    
4.9    
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5.6    
5.8    
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6.9    
7.1    
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7.6    
7.8    
8.0    
8.2    
8.4    
8.7    
8.9    
9.1    
9.3    
9.6    
9.8    
10.0    
10.2    
10.4    
10.7    
10.9    
11.1    
11.3    
11.6    
11.8    
12.0    
12.2    
12.4    
12.7    
12.9    
13.1    
13.3    
13.6    
13.8    
14.0    
14.2    
14.4    
14.7    
14.9    
15.1    
15.3    
15.6    
15.8    
16.0    
16.2    
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16.7    
16.9    
17.1    
17.3    
17.6    
17.8    
18.0    
18.2    
18.4    
18.7    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.2    
20.4    
20.7    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.2    
22.4    
22.7    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.3    
27.6    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.2    
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 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 49647, rend_intergenic: 43264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support