-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_1711362-1965650

-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.315-T1
Valid prediction for GeneMark_model.290_t
Valid prediction for snap_scaffold_1-snap.303-T1
Valid prediction for snap_scaffold_1-snap.313-T1
Valid prediction for snap_scaffold_1-snap.325-T1
Valid prediction for GlimmerHMM_glimmerT_254-T1
Valid prediction for GlimmerHMM_glimmerT_249-T1
Valid prediction for GlimmerHMM_glimmerT_251-T1
Valid prediction for GeneMark_model.260_t
Valid prediction for GlimmerHMM_glimmerT_244-T1
Valid prediction for snap_scaffold_1-snap.309-T1
Valid prediction for snap_scaffold_1-snap.302-T1
Valid prediction for GlimmerHMM_glimmerT_240-T1
Valid prediction for Augustus_model.g184.t1
Valid prediction for GeneMark_model.261_t
Valid prediction for pasa_asmbl_1518.p1
Valid prediction for Augustus_model.g192.t1
Valid prediction for GlimmerHMM_glimmerT_233-T1
Valid prediction for CodingQuarry_transcript_2536-T1
Valid prediction for snap_scaffold_1-snap.312-T1
Couldn't classify 193492, 193559
Couldn't classify 198878, 199030
Sorry, prediction pasa_asmbl_1514.p1 fails validation.
(GTA)	 AG	193492-193559	GT	TGG
(TGA)	 AG	195871-196021	GT	CGG
(AGT)	 AG	196651-196743	GT	GTG
(TTG)	 AG	196857-196936	GT	AGG
(TAA)	 AG	197088-197168	GT	GGG
(GGT)	 AG	198417-198522	GT	AGG
(TTG)	 AG	198878-199030	CT	AGC
-recovered pasa_asmbl_1514.p1, internal, 193492, 193559
-recovered pasa_asmbl_1514.p1, internal, 195871, 196021
-recovered pasa_asmbl_1514.p1, internal, 196651, 196743
-recovered pasa_asmbl_1514.p1, internal, 196857, 196936
-recovered pasa_asmbl_1514.p1, internal, 197088, 197168
-recovered pasa_asmbl_1514.p1, internal, 198417, 198522
Valid prediction for GlimmerHMM_glimmerT_250-T1
Valid prediction for snap_scaffold_1-snap.304-T1
Valid prediction for GeneMark_model.272_t
Valid prediction for GeneMark_model.267_t
Valid prediction for snap_scaffold_1-snap.300-T1
Valid prediction for GeneMark_model.269_t
Valid prediction for GlimmerHMM_glimmerT_255-T1
Valid prediction for GeneMark_model.273_t
Valid prediction for GlimmerHMM_glimmerT_243-T1
Valid prediction for GlimmerHMM_glimmerT_234-T1
Valid prediction for CodingQuarry_transcript_2538-T1
Valid prediction for GlimmerHMM_glimmerT_258-T1
Valid prediction for HiQ_model.g176.t1
Valid prediction for HiQ_model.g173.t1
Valid prediction for GlimmerHMM_glimmerT_229-T1
Valid prediction for CodingQuarry_transcript_2537-T1
Valid prediction for snap_scaffold_1-snap.310-T1
Valid prediction for snap_scaffold_1-snap.306-T1
Valid prediction for GeneMark_model.282_t
Valid prediction for GeneMark_model.291_t
Valid prediction for GlimmerHMM_glimmerT_241-T1
Valid prediction for Augustus_model.g182.t1
Valid prediction for snap_scaffold_1-snap.324-T1
Valid prediction for snap_scaffold_1-snap.305-T1
Valid prediction for Augustus_model.g172.t1
Valid prediction for snap_scaffold_1-snap.322-T1
Valid prediction for Augustus_model.g189.t1
Valid prediction for Augustus_model.g181.t1
Valid prediction for GeneMark_model.265_t
Valid prediction for GeneMark_model.292_t
Valid prediction for Augustus_model.g175.t1
Valid prediction for snap_scaffold_1-snap.332-T1
Valid prediction for snap_scaffold_1-snap.321-T1
Valid prediction for Augustus_model.g197.t1
Valid prediction for snap_scaffold_1-snap.333-T1
Valid prediction for GeneMark_model.293_t
Couldn't classify 179899, 179992
Couldn't classify 189736, 189873
Sorry, prediction pasa_asmbl_1512.p1 fails validation.
(GAA)	 CT	179899-179992	GT	AGG
(AGA)	 AG	180194-180255	GT	AGG
(GAT)	 AG	180988-181033	GT	AGG
(GCC)	 AG	181816-181941	GT	GGG
(GAT)	 AG	182122-182166	GT	GGG
(ATT)	 AG	182518-182561	GT	TAG
(GTG)	 AG	182763-182819	GT	AGG
(ATG)	 AG	183769-183821	GT	GGG
(TCT)	 AG	184826-185028	GT	TGG
(ATG)	 AG	185956-186147	GT	TGG
(ATC)	 AG	186237-186282	GT	AGG
(AGC)	 AG	186457-186570	GT	TGG
(TGC)	 AG	187942-187997	GT	AGG
(GGT)	 AG	189175-189332	GT	GAG
(GGA)	 AG	189736-189873	GT	AAG
-recovered pasa_asmbl_1512.p1, initial, 183769, 183821
add_exon() Sorry, pasa_asmbl_1512.p1 185956-186147-initial-1 is invalid.
-recovered pasa_asmbl_1512.p1, initial, 185956, 186147
-recovered pasa_asmbl_1512.p1, terminal, 187942, 187997
-recovered pasa_asmbl_1512.p1, internal, 180194, 180255
-recovered pasa_asmbl_1512.p1, internal, 180988, 181033
-recovered pasa_asmbl_1512.p1, internal, 181816, 181941
-recovered pasa_asmbl_1512.p1, internal, 182122, 182166
-recovered pasa_asmbl_1512.p1, internal, 182518, 182561
-recovered pasa_asmbl_1512.p1, internal, 182763, 182819
-recovered pasa_asmbl_1512.p1, internal, 183769, 183821
-recovered pasa_asmbl_1512.p1, internal, 184826, 185028
-recovered pasa_asmbl_1512.p1, internal, 185956, 186147
-recovered pasa_asmbl_1512.p1, internal, 186237, 186282
-recovered pasa_asmbl_1512.p1, internal, 186457, 186570
-recovered pasa_asmbl_1512.p1, internal, 187942, 187997
-recovered pasa_asmbl_1512.p1, internal, 189175, 189332
-recovered pasa_asmbl_1512.p1, internal, 189736, 189873
Valid prediction for snap_scaffold_1-snap.329-T1
Valid prediction for pasa_asmbl_1502.p1
Valid prediction for HiQ_model.g193.t1
Valid prediction for GeneMark_model.268_t
Valid prediction for snap_scaffold_1-snap.299-T1
Valid prediction for GlimmerHMM_glimmerT_228-T1
Valid prediction for snap_scaffold_1-snap.326-T1
Valid prediction for GlimmerHMM_glimmerT_232-T1
Valid prediction for GlimmerHMM_glimmerT_261-T1
Valid prediction for snap_scaffold_1-snap.320-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g196.t1
Valid prediction for GlimmerHMM_glimmerT_263-T1
Couldn't classify 35034, 36281
Sorry, prediction pasa_asmbl_1503.p1 fails validation.
(ATG)	 GG	35034-36281	AG	GGA
Valid prediction for Augustus_model.g190.t1
Valid prediction for Augustus_model.g195.t1
Valid prediction for GlimmerHMM_glimmerT_259-T1
Valid prediction for snap_scaffold_1-snap.296-T1
Valid prediction for GeneMark_model.288_t
Valid prediction for GeneMark_model.274_t
Valid prediction for GeneMark_model.264_t
Valid prediction for pasa_asmbl_1506.p1
Valid prediction for GlimmerHMM_glimmerT_260-T1
Valid prediction for GeneMark_model.286_t
Valid prediction for GlimmerHMM_glimmerT_236-T1
Valid prediction for GeneMark_model.276_t

-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 GeneMark_model.280_t
Valid prediction for GeneMark_model.278_t
Valid prediction for Augustus_model.g180.t1
Valid prediction for snap_scaffold_1-snap.330-T1
Valid prediction for GlimmerHMM_glimmerT_256-T1
Valid prediction for snap_scaffold_1-snap.298-T1
Couldn't classify 152948, 153262
Sorry, prediction pasa_asmbl_84.p1 fails validation.
(ATG)	 TG	152948-153262	AA	GAA
Valid prediction for Augustus_model.g188.t1
Valid prediction for snap_scaffold_1-snap.319-T1
Valid prediction for GlimmerHMM_glimmerT_230-T1
Valid prediction for snap_scaffold_1-snap.297-T1
Valid prediction for snap_scaffold_1-snap.318-T1
Valid prediction for GeneMark_model.266_t
Couldn't classify 148423, 149100
Sorry, prediction pasa_asmbl_85.p1 fails validation.
(TGC)	 CC	148423-149100	AG	GAA
Valid prediction for Augustus_model.g177.t1
Valid prediction for HiQ_model.g187.t1
Valid prediction for GeneMark_model.284_t
Valid prediction for snap_scaffold_1-snap.301-T1
Valid prediction for GeneMark_model.262_t
Valid prediction for snap_scaffold_1-snap.327-T1
Valid prediction for GlimmerHMM_glimmerT_238-T1
Valid prediction for Augustus_model.g178.t1
Valid prediction for Augustus_model.g194.t1
Valid prediction for GeneMark_model.279_t
Valid prediction for Augustus_model.g185.t1
Valid prediction for GlimmerHMM_glimmerT_246-T1
Valid prediction for Augustus_model.g191.t1
Valid prediction for Augustus_model.g186.t1
Valid prediction for GeneMark_model.283_t
Valid prediction for GlimmerHMM_glimmerT_242-T1
Valid prediction for GeneMark_model.277_t
Valid prediction for GlimmerHMM_glimmerT_235-T1
Valid prediction for snap_scaffold_1-snap.307-T1
Valid prediction for GeneMark_model.270_t
Valid prediction for GlimmerHMM_glimmerT_252-T1
Valid prediction for GlimmerHMM_glimmerT_257-T1
Valid prediction for GeneMark_model.281_t
Valid prediction for GlimmerHMM_glimmerT_248-T1
Valid prediction for GlimmerHMM_glimmerT_239-T1
Valid prediction for HiQ_model.g179.t1
Couldn't classify 133482, 133496
Sorry, prediction pasa_asmbl_86.p1 fails validation.
(GGA)	 AC	133482-133496	GT	AGG
(GCA)	 AG	133638-133723	GT	AGG
(CCG)	 AG	133903-133978	GT	TGG
(CTG)	 AG	134266-134348	GT	AGG
(TGG)	 AG	135455-136166	GT	AGG
(GTA)	 AG	139139-139225	GT	AGG
(CAG)	 AG	139616-139720	CA	AGC
-recovered pasa_asmbl_86.p1, terminal, 139616, 139720
-recovered pasa_asmbl_86.p1, internal, 133638, 133723
-recovered pasa_asmbl_86.p1, internal, 133903, 133978
-recovered pasa_asmbl_86.p1, internal, 134266, 134348
-recovered pasa_asmbl_86.p1, internal, 135455, 136166
-recovered pasa_asmbl_86.p1, internal, 139139, 139225
Valid prediction for GlimmerHMM_glimmerT_231-T1
Valid prediction for snap_scaffold_1-snap.308-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.287_t
Valid prediction for GlimmerHMM_glimmerT_245-T1
Valid prediction for snap_scaffold_1-snap.323-T1
Valid prediction for snap_scaffold_1-snap.314-T1
Valid prediction for GlimmerHMM_glimmerT_237-T1
Valid prediction for snap_scaffold_1-snap.317-T1
Valid prediction for GlimmerHMM_glimmerT_247-T1
Valid prediction for snap_scaffold_1-snap.311-T1
Couldn't classify 153396, 153737
Sorry, prediction pasa_asmbl_83.p1 fails validation.
(CAT)	 CT	153396-153737	TG	ACT
Valid prediction for GlimmerHMM_glimmerT_253-T1
Valid prediction for GeneMark_model.289_t
Valid prediction for snap_scaffold_1-snap.328-T1
Valid prediction for Augustus_model.g183.t1
Valid prediction for snap_scaffold_1-snap.331-T1
Valid prediction for GlimmerHMM_glimmerT_262-T1
Valid prediction for GeneMark_model.275_t
Valid prediction for snap_scaffold_1-snap.316-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g174.t1
Valid prediction for GeneMark_model.285_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 193563, rend_intergenic: 190693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 254289
-exon list size: 467


building trellis

0.2    
0.4    
0.6    
0.9    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.6    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.8    
6.0    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.7    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.4    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
17.1    
17.3    
17.5    
17.7    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 193563, rend_intergenic: 190693  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