-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_10705389-10914192

-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_2-snap.2147-T1
Valid prediction for snap_scaffold_2-snap.2150-T1
Valid prediction for HiQ_model.g3090.t1
Valid prediction for GeneMark_model.7353_t
Couldn't classify 164000, 164118
Couldn't classify 167289, 167479
Sorry, prediction pasa_asmbl_24779.p1 fails validation.
(GAG)	 AG	164000-164118	GT	AGG
(GCC)	 AG	164902-164960	GT	AGG
(ACA)	 AG	167289-167479	CT	GCC
-recovered pasa_asmbl_24779.p1, internal, 164000, 164118
-recovered pasa_asmbl_24779.p1, internal, 164902, 164960
Valid prediction for GlimmerHMM_glimmerT_4599-T1
Valid prediction for snap_scaffold_2-snap.2176-T1
Valid prediction for snap_scaffold_2-snap.2153-T1
Valid prediction for snap_scaffold_2-snap.2151-T1
Valid prediction for GeneMark_model.7329_t
Valid prediction for pasa_asmbl_24773.p2
Valid prediction for snap_scaffold_2-snap.2148-T1
Valid prediction for Augustus_model.g3072.t1
Valid prediction for GeneMark_model.7338_t
Valid prediction for GeneMark_model.7335_t
Valid prediction for pasa_asmbl_24767.p1
Valid prediction for GeneMark_model.7360_t
Valid prediction for snap_scaffold_2-snap.2155-T1
Valid prediction for Augustus_model.g3075.t1
Valid prediction for CodingQuarry_transcript_28617-T1
Valid prediction for Augustus_model.g3071.t1
Valid prediction for GeneMark_model.7356_t
Valid prediction for GeneMark_model.7330_t
Valid prediction for snap_scaffold_2-snap.2152-T1
Valid prediction for GeneMark_model.7358_t
Valid prediction for snap_scaffold_2-snap.2156-T1
Valid prediction for HiQ_model.g3068.t1
Valid prediction for GeneMark_model.7333_t
Valid prediction for snap_scaffold_2-snap.2173-T1
Valid prediction for GlimmerHMM_glimmerT_4579-T1
Valid prediction for snap_scaffold_2-snap.2171-T1
Valid prediction for Augustus_model.g3088.t1
Valid prediction for snap_scaffold_2-snap.2149-T1
Valid prediction for GlimmerHMM_glimmerT_4594-T1
Valid prediction for CodingQuarry_transcript_28619-T1
Valid prediction for GlimmerHMM_glimmerT_4596-T1
Couldn't classify 15505, 16105
Sorry, prediction pasa_asmbl_24761.p1 fails validation.
(ATG)	 CC	13539-13551	GT	TGG
(ACA)	 AG	14098-14265	GT	TGG
(ATG)	 AG	14343-14443	GT	AGG
(CTC)	 AG	14807-14890	GT	TGG
(ATT)	 AG	15047-15120	GT	GGG
(TCT)	 AG	15505-16105	CA	AGC
-recovered pasa_asmbl_24761.p1, initial, 13539, 13551
-recovered pasa_asmbl_24761.p1, initial, 14343, 14443
-recovered pasa_asmbl_24761.p1, internal, 14098, 14265
-recovered pasa_asmbl_24761.p1, internal, 14343, 14443
-recovered pasa_asmbl_24761.p1, internal, 14807, 14890
-recovered pasa_asmbl_24761.p1, internal, 15047, 15120
Valid prediction for Augustus_model.g3073.t1
Valid prediction for GeneMark_model.7363_t
Valid prediction for GeneMark_model.7328_t
Valid prediction for snap_scaffold_2-snap.2157-T1
Valid prediction for pasa_asmbl_24760.p1
Valid prediction for GlimmerHMM_glimmerT_4580-T1
Couldn't classify 164000, 164118
Sorry, prediction pasa_asmbl_24778.p1 fails validation.
(GAG)	 AG	164000-164118	GT	AGG
(GCC)	 AG	164902-164960	GT	AGG
(ACA)	 AG	167289-167421	GT	AGG
(GTT)	 AG	170139-170164	GT	AAG
(AGA)	 AG	170360-170451	GT	TTG
(ATC)	 AG	171312-171403	GT	AGG
(AGG)	 AG	171588-171636	GT	AGG
(GAA)	 AG	171902-171973	GT	AGG
(AAC)	 AG	172112-172155	GT	AAG
(CCT)	 AG	172321-172430	GT	GGG
(GTC)	 AG	172759-172913	GT	GGG
(CTC)	 AG	173292-173309	GT	AGG
(ATT)	 AG	174739-174886	GT	TGG
(TGT)	 AG	175118-175211	GT	AAG
(TTA)	 AG	175465-175555	GT	AGG
(TAC)	 AG	175695-175763	GT	AGG
(CCT)	 AG	176047-176154	CC	AGC
add_exon() Sorry, pasa_asmbl_24778.p1 170139-170164-terminal-2 is invalid.
-recovered pasa_asmbl_24778.p1, terminal, 170139, 170164
-recovered pasa_asmbl_24778.p1, terminal, 176047, 176154
-recovered pasa_asmbl_24778.p1, internal, 164000, 164118
-recovered pasa_asmbl_24778.p1, internal, 164902, 164960
-recovered pasa_asmbl_24778.p1, internal, 167289, 167421
-recovered pasa_asmbl_24778.p1, internal, 170139, 170164
-recovered pasa_asmbl_24778.p1, internal, 170360, 170451
-recovered pasa_asmbl_24778.p1, internal, 171312, 171403
-recovered pasa_asmbl_24778.p1, internal, 171588, 171636
-recovered pasa_asmbl_24778.p1, internal, 171902, 171973
-recovered pasa_asmbl_24778.p1, internal, 172112, 172155
-recovered pasa_asmbl_24778.p1, internal, 172321, 172430
-recovered pasa_asmbl_24778.p1, internal, 172759, 172913
-recovered pasa_asmbl_24778.p1, internal, 173292, 173309
-recovered pasa_asmbl_24778.p1, internal, 174739, 174886
-recovered pasa_asmbl_24778.p1, internal, 175118, 175211
-recovered pasa_asmbl_24778.p1, internal, 175465, 175555
-recovered pasa_asmbl_24778.p1, internal, 175695, 175763
Couldn't classify 16229, 16540
Sorry, prediction pasa_asmbl_24764.p2 fails validation.
(CTC)	 CC	16229-16540	CC	AAC
Valid prediction for HiQ_model.g3069.t1
Valid prediction for Augustus_model.g3089.t1
Valid prediction for snap_scaffold_2-snap.2154-T1
Valid prediction for GlimmerHMM_glimmerT_4581-T1
Valid prediction for snap_scaffold_2-snap.2172-T1
Valid prediction for HiQ_model.g3070.t1
Valid prediction for GlimmerHMM_glimmerT_4598-T1
Valid prediction for Augustus_model.g3074.t1
Valid prediction for GlimmerHMM_glimmerT_4577-T1
Couldn't classify 55016, 55126
Sorry, prediction pasa_asmbl_24768.p1 fails validation.
(AGC)	 CC	55016-55126	GT	AAG
(GTG)	 AG	55330-55446	GT	AGG
(TTG)	 AG	55818-55913	GC	AAG
-recovered pasa_asmbl_24768.p1, terminal, 55818, 55913
-recovered pasa_asmbl_24768.p1, internal, 55330, 55446
-recovered pasa_asmbl_24768.p1, internal, 55818, 55913
Valid prediction for GeneMark_model.7332_t
Valid prediction for GeneMark_model.7337_t
Valid prediction for GlimmerHMM_glimmerT_4576-T1
Valid prediction for snap_scaffold_2-snap.2174-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_2-snap.2158-T1
Valid prediction for GeneMark_model.7331_t
Valid prediction for GeneMark_model.7354_t
Valid prediction for GeneMark_model.7348_t
Valid prediction for snap_scaffold_2-snap.2165-T1
Valid prediction for GeneMark_model.7364_t
Valid prediction for snap_scaffold_2-snap.2161-T1
Valid prediction for snap_scaffold_2-snap.2170-T1
Valid prediction for snap_scaffold_2-snap.2177-T1
Valid prediction for Augustus_model.g3084.t1
Valid prediction for GeneMark_model.7361_t
Valid prediction for snap_scaffold_2-snap.2178-T1
Valid prediction for Augustus_model.g3080.t1
Valid prediction for GeneMark_model.7342_t
Valid prediction for snap_scaffold_2-snap.2162-T1
Valid prediction for GlimmerHMM_glimmerT_4582-T1
Valid prediction for GlimmerHMM_glimmerT_4597-T1
Valid prediction for GeneMark_model.7359_t
Valid prediction for Augustus_model.g3076.t1
Valid prediction for GlimmerHMM_glimmerT_4587-T1
Valid prediction for GeneMark_model.7352_t
Valid prediction for GeneMark_model.7343_t
Valid prediction for snap_scaffold_2-snap.2166-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GeneMark_model.7346_t
Valid prediction for GlimmerHMM_glimmerT_4586-T1
Valid prediction for GeneMark_model.7339_t
Valid prediction for GlimmerHMM_glimmerT_4575-T1
Valid prediction for snap_scaffold_2-snap.2164-T1
Valid prediction for snap_scaffold_2-snap.2175-T1
Valid prediction for HiQ_model.g3092.t1
Valid prediction for GeneMark_model.7340_t
Valid prediction for GeneMark_model.7345_t
Valid prediction for snap_scaffold_2-snap.2169-T1
Valid prediction for GeneMark_model.7351_t
Valid prediction for GlimmerHMM_glimmerT_4601-T1
Valid prediction for snap_scaffold_2-snap.2163-T1
Valid prediction for GlimmerHMM_glimmerT_4589-T1
Valid prediction for GlimmerHMM_glimmerT_4578-T1
Valid prediction for GeneMark_model.7362_t
Valid prediction for snap_scaffold_2-snap.2168-T1
Valid prediction for GeneMark_model.7344_t
Valid prediction for snap_scaffold_2-snap.2159-T1
Valid prediction for GeneMark_model.7327_t
Valid prediction for Augustus_model.g3086.t1
Valid prediction for Augustus_model.g3081.t1
Valid prediction for GlimmerHMM_glimmerT_4600-T1
Valid prediction for Augustus_model.g3078.t1
Valid prediction for GlimmerHMM_glimmerT_4592-T1
Valid prediction for Augustus_model.g3091.t1
Valid prediction for GlimmerHMM_glimmerT_4595-T1
Valid prediction for GeneMark_model.7349_t
Valid prediction for Augustus_model.g3079.t1
Valid prediction for GlimmerHMM_glimmerT_4584-T1
Valid prediction for snap_scaffold_2-snap.2167-T1
Valid prediction for GeneMark_model.7355_t
Valid prediction for Augustus_model.g3077.t1
Valid prediction for GlimmerHMM_glimmerT_4583-T1
Valid prediction for pasa_asmbl_23454.p1
Valid prediction for GlimmerHMM_glimmerT_4593-T1
Valid prediction for GlimmerHMM_glimmerT_4590-T1
Valid prediction for Augustus_model.g3083.t1
Valid prediction for GlimmerHMM_glimmerT_4585-T1
Valid prediction for GeneMark_model.7341_t
Valid prediction for GeneMark_model.7357_t
Valid prediction for GeneMark_model.7350_t
Valid prediction for GlimmerHMM_glimmerT_4591-T1
Valid prediction for GeneMark_model.7336_t
Valid prediction for snap_scaffold_2-snap.2160-T1
Valid prediction for Augustus_model.g3082.t1
Valid prediction for GeneMark_model.7334_t
Valid prediction for GlimmerHMM_glimmerT_4588-T1
Valid prediction for Augustus_model.g3085.t1
Valid prediction for Augustus_model.g3087.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 188452, rend_intergenic: 184484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208804
-exon list size: 450


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.5    
1.8    
2.0    
2.2    
2.4    
2.7    
2.9    
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3.3    
3.5    
3.8    
4.0    
4.2    
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4.6    
4.9    
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5.5    
5.8    
6.0    
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6.6    
6.9    
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7.5    
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8.0    
8.2    
8.4    
8.6    
8.8    
9.1    
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9.5    
9.7    
10.0    
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10.4    
10.6    
10.8    
11.1    
11.3    
11.5    
11.7    
11.9    
12.2    
12.4    
12.6    
12.8    
13.1    
13.3    
13.5    
13.7    
13.9    
14.2    
14.4    
14.6    
14.8    
15.0    
15.3    
15.5    
15.7    
15.9    
16.2    
16.4    
16.6    
16.8    
17.0    
17.3    
17.5    
17.7    
17.9    
18.1    
18.4    
18.6    
18.8    
19.0    
19.2    
19.5    
19.7    
19.9    
20.1    
20.4    
20.6    
20.8    
21.0    
21.2    
21.5    
21.7    
21.9    
22.1    
22.3    
22.6    
22.8    
23.0    
23.2    
23.5    
23.7    
23.9    
24.1    
24.3    
24.6    
24.8    
25.0    
25.2    
25.4    
25.7    
25.9    
26.1    
26.3    
26.5    
26.8    
27.0    
27.2    
27.4    
27.7    
27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.4    
29.6    
29.9    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.4    
31.6    
31.9    
32.1    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.8    
34.1    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.6    
35.8    
36.1    
36.3    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
38.9    
39.2    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.8    
42.0    
42.3    
42.5    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.0    
44.2    
44.5    
44.7    
44.9    
45.1    
45.4    
45.6    
45.8    
46.0    
46.2    
46.5    
46.7    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.2    
48.5    
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    
51.5    
51.8    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.3    
53.5    
53.8    
54.0    
54.2    
54.4    
54.6    
54.9    
55.1    
55.3    
55.5    
55.8    
56.0    
56.2    
56.4    
56.6    
56.9    
57.1    
57.3    
57.5    
57.7    
58.0    
58.2    
58.4    
58.6    
58.8    
59.1    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.8    
61.1    
61.3    
61.5    
61.7    
61.9    
62.2    
62.4    
62.6    
62.8    
63.1    
63.3    
63.5    
63.7    
63.9    
64.2    
64.4    
64.6    
64.8    
65.0    
65.3    
65.5    
65.7    
65.9    
66.2    
66.4    
66.6    
66.8    
67.0    
67.3    
67.5    
67.7    
67.9    
68.1    
68.4    
68.6    
68.8    
69.0    
69.2    
69.5    
69.7    
69.9    
70.1    
70.4    
70.6    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.3    
72.6    
72.8    
73.0    
73.2    
73.5    
73.7    
73.9    
74.1    
74.3    
74.6    
74.8    
75.0    
75.2    
75.4    
75.7    
75.9    
76.1    
76.3    
76.5    
76.8    
77.0    
77.2    
77.4    
77.7    
77.9    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.4    
79.6    
79.9    
80.1    
80.3    
80.5    
80.8    
81.0    
81.2    
81.4    
81.6    
81.9    
82.1    
82.3    
82.5    
82.7    
83.0    
83.2    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.7    
85.0    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.3    
92.5    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.1    
95.4    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 188452, rend_intergenic: 184484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support