-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_6182247-6346182

-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.1043-T1
Valid prediction for GlimmerHMM_glimmerT_856-T1
Valid prediction for Augustus_model.g621.t1
Valid prediction for snap_scaffold_1-snap.1058-T1
Valid prediction for GeneMark_model.1049_t
Valid prediction for GeneMark_model.1046_t
Valid prediction for snap_scaffold_1-snap.1033-T1
Valid prediction for HiQ_model.g635.t1
Valid prediction for GlimmerHMM_glimmerT_836-T1
Valid prediction for GlimmerHMM_glimmerT_842-T1
Valid prediction for snap_scaffold_1-snap.1060-T1
Valid prediction for snap_scaffold_1-snap.1031-T1
Valid prediction for GeneMark_model.1033_t
Valid prediction for snap_scaffold_1-snap.1044-T1
Valid prediction for snap_scaffold_1-snap.1062-T1
Valid prediction for GeneMark_model.1023_t
Valid prediction for GeneMark_model.1031_t
Valid prediction for CodingQuarry_transcript_2649-T1
Couldn't classify 148816, 148884
Sorry, prediction pasa_asmbl_1821.p1 fails validation.
(ATG)	 CG	143041-143128	GT	CGG
(TCA)	 AG	143590-143660	GT	AGG
(GTC)	 AG	144223-144310	GT	CTG
(ACC)	 AG	144416-144535	GT	CGG
(AGA)	 AG	144694-144787	GT	AAG
(GTG)	 AG	145003-145168	GT	AGG
(GTG)	 AG	145265-145322	GT	TGG
(TTC)	 AG	146714-146745	GT	ATG
(ATC)	 AG	146858-146954	GT	AGG
(CAT)	 AG	148659-148723	GT	AGG
(GTG)	 AG	148816-148884	GG	AGG
-recovered pasa_asmbl_1821.p1, initial, 143041, 143128
-recovered pasa_asmbl_1821.p1, internal, 143590, 143660
-recovered pasa_asmbl_1821.p1, internal, 144223, 144310
-recovered pasa_asmbl_1821.p1, internal, 144416, 144535
-recovered pasa_asmbl_1821.p1, internal, 144694, 144787
-recovered pasa_asmbl_1821.p1, internal, 145003, 145168
-recovered pasa_asmbl_1821.p1, internal, 145265, 145322
-recovered pasa_asmbl_1821.p1, internal, 146714, 146745
-recovered pasa_asmbl_1821.p1, internal, 146858, 146954
-recovered pasa_asmbl_1821.p1, internal, 148659, 148723
Valid prediction for pasa_asmbl_1824.p1
Valid prediction for pasa_asmbl_1818.p1
Valid prediction for snap_scaffold_1-snap.1030-T1
Valid prediction for Augustus_model.g629.t1
Valid prediction for GlimmerHMM_glimmerT_864-T1
Valid prediction for snap_scaffold_1-snap.1053-T1
Valid prediction for GlimmerHMM_glimmerT_838-T1
Valid prediction for GeneMark_model.1039_t
Valid prediction for snap_scaffold_1-snap.1054-T1
Valid prediction for GlimmerHMM_glimmerT_823-T1
Valid prediction for GlimmerHMM_glimmerT_846-T1
Valid prediction for GeneMark_model.1020_t
Valid prediction for GeneMark_model.1043_t
Valid prediction for GeneMark_model.1036_t
Valid prediction for GeneMark_model.1040_t
Valid prediction for snap_scaffold_1-snap.1048-T1
Valid prediction for HiQ_model.g638.t1
Valid prediction for GlimmerHMM_glimmerT_828-T1
Valid prediction for GeneMark_model.1025_t
Valid prediction for GlimmerHMM_glimmerT_826-T1
Valid prediction for GlimmerHMM_glimmerT_851-T1
Valid prediction for GeneMark_model.1015_t
Valid prediction for GlimmerHMM_glimmerT_860-T1
Valid prediction for HiQ_model.g637.t1
Valid prediction for CodingQuarry_transcript_2646-T1
Valid prediction for HiQ_model.g641.t1
Valid prediction for HiQ_model.g632.t1
Valid prediction for GeneMark_model.1035_t
Valid prediction for Augustus_model.g626.t1
Valid prediction for snap_scaffold_1-snap.1065-T1
Valid prediction for GlimmerHMM_glimmerT_824-T1
Valid prediction for pasa_asmbl_1817.p1
Valid prediction for snap_scaffold_1-snap.1049-T1
Valid prediction for snap_scaffold_1-snap.1038-T1
Valid prediction for GlimmerHMM_glimmerT_862-T1
Valid prediction for snap_scaffold_1-snap.1036-T1
Valid prediction for CodingQuarry_transcript_2651-T1
Valid prediction for GlimmerHMM_glimmerT_840-T1
Valid prediction for pasa_asmbl_1815.p1
Valid prediction for snap_scaffold_1-snap.1051-T1
Valid prediction for GeneMark_model.1048_t
Valid prediction for GeneMark_model.1053_t
Valid prediction for GlimmerHMM_glimmerT_841-T1
Valid prediction for GlimmerHMM_glimmerT_861-T1
Valid prediction for GeneMark_model.1026_t
Valid prediction for snap_scaffold_1-snap.1064-T1
Valid prediction for snap_scaffold_1-snap.1046-T1
Valid prediction for Augustus_model.g625.t1
Valid prediction for GeneMark_model.1018_t
Valid prediction for GlimmerHMM_glimmerT_848-T1
Valid prediction for GlimmerHMM_glimmerT_857-T1
Valid prediction for snap_scaffold_1-snap.1035-T1
Valid prediction for GeneMark_model.1022_t
Valid prediction for snap_scaffold_1-snap.1039-T1
Valid prediction for snap_scaffold_1-snap.1037-T1
Valid prediction for Augustus_model.g640.t1
Valid prediction for GlimmerHMM_glimmerT_854-T1
Valid prediction for GeneMark_model.1014_t
Couldn't classify 5016, 5075
Couldn't classify 7983, 8075
Sorry, prediction pasa_asmbl_1812.p1 fails validation.
(CTC)	 GC	5016-5075	GT	ACG
(ACC)	 AG	6401-6599	GT	CGG
(ACC)	 AG	6683-6774	GT	AGG
(GAC)	 AG	7983-8075	GT	AGG
-recovered pasa_asmbl_1812.p1, internal, 6401, 6599
-recovered pasa_asmbl_1812.p1, internal, 6683, 6774
-recovered pasa_asmbl_1812.p1, internal, 7983, 8075
Valid prediction for GlimmerHMM_glimmerT_833-T1
Valid prediction for snap_scaffold_1-snap.1061-T1
Valid prediction for GeneMark_model.1024_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 GlimmerHMM_glimmerT_843-T1
Valid prediction for HiQ_model.g639.t1
Valid prediction for CodingQuarry_transcript_2636-T1
Valid prediction for pasa_asmbl_335.p1
Valid prediction for snap_scaffold_1-snap.1057-T1
Valid prediction for GlimmerHMM_glimmerT_863-T1
Couldn't classify 40772, 40797
Couldn't classify 41803, 41969
Sorry, prediction pasa_asmbl_363.p1 fails validation.
(GCG)	 AA	40772-40797	GT	AGG
(AAA)	 AG	41143-41242	GT	TGG
(GAC)	 AG	41434-41596	GT	AGG
(AGG)	 AG	41803-41969	GT	TGG
-recovered pasa_asmbl_363.p1, internal, 41143, 41242
-recovered pasa_asmbl_363.p1, internal, 41434, 41596
-recovered pasa_asmbl_363.p1, internal, 41803, 41969
Valid prediction for GlimmerHMM_glimmerT_834-T1
Valid prediction for Augustus_model.g630.t1
Valid prediction for pasa_asmbl_346.p1
Valid prediction for Augustus_model.g627.t1
Valid prediction for GeneMark_model.1047_t
Valid prediction for CodingQuarry_transcript_2644-T1
Valid prediction for GeneMark_model.1037_t
Valid prediction for CodingQuarry_transcript_2642-T1
Valid prediction for snap_scaffold_1-snap.1056-T1
Valid prediction for snap_scaffold_1-snap.1032-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_859-T1
Valid prediction for GeneMark_model.1045_t
Valid prediction for snap_scaffold_1-snap.1034-T1
Valid prediction for HiQ_model.g628.t1
Valid prediction for Augustus_model.g624.t1
Valid prediction for GlimmerHMM_glimmerT_831-T1
Valid prediction for GeneMark_model.1029_t
Valid prediction for snap_scaffold_1-snap.1047-T1
Valid prediction for GlimmerHMM_glimmerT_844-T1
Valid prediction for Augustus_model.g620.t1
Valid prediction for Augustus_model.g622.t1
Couldn't classify 62197, 62349
Sorry, prediction pasa_asmbl_347.p1 fails validation.
(ATG)	 CA	60032-60048	GC	AGG
(AAT)	 AG	60355-60526	GT	CGG
(AGG)	 AG	60641-60799	GT	ACG
(ATC)	 AG	61033-61102	GT	AGG
(GTA)	 AG	61522-61595	GT	AGG
(AGT)	 AG	62197-62349	TG	GGT
-recovered pasa_asmbl_347.p1, initial, 60032, 60048
-recovered pasa_asmbl_347.p1, internal, 60355, 60526
-recovered pasa_asmbl_347.p1, internal, 60641, 60799
-recovered pasa_asmbl_347.p1, internal, 61033, 61102
-recovered pasa_asmbl_347.p1, internal, 61522, 61595
Valid prediction for GeneMark_model.1027_t
Valid prediction for HiQ_model.g633.t1
Valid prediction for CodingQuarry_transcript_2640-T1
Valid prediction for snap_scaffold_1-snap.1052-T1
Valid prediction for GeneMark_model.1028_t
Valid prediction for pasa_asmbl_328.p1
Valid prediction for CodingQuarry_transcript_2648-T1
Valid prediction for GlimmerHMM_glimmerT_837-T1
Valid prediction for GeneMark_model.1044_t
Couldn't classify 123629, 123789
Couldn't classify 127949, 128101
Sorry, prediction pasa_asmbl_331.p1 fails validation.
(GAT)	 AG	123629-123789	GT	TAG
(CTA)	 AG	125975-126103	GT	AAG
(GAT)	 AG	127499-127628	GT	TGG
(AAC)	 AG	127949-128101	GG	CAG
-recovered pasa_asmbl_331.p1, internal, 123629, 123789
-recovered pasa_asmbl_331.p1, internal, 125975, 126103
-recovered pasa_asmbl_331.p1, internal, 127499, 127628
Valid prediction for GeneMark_model.1019_t
Valid prediction for snap_scaffold_1-snap.1045-T1
Valid prediction for GlimmerHMM_glimmerT_835-T1
Valid prediction for GeneMark_model.1021_t
Valid prediction for CodingQuarry_transcript_2647-T1
Valid prediction for GeneMark_model.1038_t
Valid prediction for GlimmerHMM_glimmerT_853-T1
Valid prediction for GeneMark_model.1016_t
Valid prediction for GlimmerHMM_glimmerT_850-T1
Couldn't classify 43289, 43398
Sorry, prediction pasa_asmbl_362.p1 fails validation.
(CCG)	 CC	43289-43398	GT	AAG
(GGA)	 AG	43504-43843	GA	AGG
-recovered pasa_asmbl_362.p1, terminal, 43504, 43843
Valid prediction for CodingQuarry_transcript_2643-T1
Valid prediction for GlimmerHMM_glimmerT_827-T1
Valid prediction for CodingQuarry_transcript_2641-T1
Valid prediction for GeneMark_model.1041_t
Valid prediction for GeneMark_model.1030_t
Valid prediction for GlimmerHMM_glimmerT_849-T1
Valid prediction for HiQ_model.g636.t1
Valid prediction for GlimmerHMM_glimmerT_855-T1
Valid prediction for CodingQuarry_transcript_2650-T1
Valid prediction for snap_scaffold_1-snap.1041-T1
Valid prediction for CodingQuarry_transcript_2645-T1
Valid prediction for snap_scaffold_1-snap.1063-T1
Valid prediction for CodingQuarry_transcript_2639-T1
Valid prediction for Augustus_model.g623.t1
Valid prediction for GlimmerHMM_glimmerT_829-T1
Valid prediction for Augustus_model.g634.t1
Valid prediction for GeneMark_model.1050_t
Valid prediction for GlimmerHMM_glimmerT_839-T1
Valid prediction for pasa_asmbl_354.p1
Valid prediction for snap_scaffold_1-snap.1040-T1
Valid prediction for GlimmerHMM_glimmerT_825-T1
Valid prediction for GlimmerHMM_glimmerT_830-T1
Valid prediction for GlimmerHMM_glimmerT_847-T1
Valid prediction for GeneMark_model.1051_t
Valid prediction for pasa_asmbl_364.p1
Valid prediction for GlimmerHMM_glimmerT_852-T1
Valid prediction for snap_scaffold_1-snap.1050-T1
Valid prediction for GeneMark_model.1034_t
Valid prediction for GeneMark_model.1042_t
Valid prediction for snap_scaffold_1-snap.1055-T1
Valid prediction for CodingQuarry_transcript_2638-T1
Valid prediction for snap_scaffold_1-snap.1059-T1
Valid prediction for HiQ_model.g631.t1
Valid prediction for GeneMark_model.1052_t
Valid prediction for GlimmerHMM_glimmerT_832-T1
Valid prediction for GlimmerHMM_glimmerT_858-T1
Valid prediction for GeneMark_model.1032_t
Valid prediction for snap_scaffold_1-snap.1042-T1
Valid prediction for GlimmerHMM_glimmerT_845-T1
Valid prediction for GeneMark_model.1017_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12170, rend_intergenic: 6451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16510, rend_intergenic: 14774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50245, rend_intergenic: 39725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61221, rend_intergenic: 53953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80933, rend_intergenic: 73280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101022, rend_intergenic: 95837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163936
-exon list size: 597


building trellis

0.2    
0.3    
0.5    
0.7    
0.8    
1.0    
1.2    
1.3    
1.5    
1.7    
1.8    
2.0    
2.2    
2.3    
2.5    
2.7    
2.8    
3.0    
3.2    
3.3    
3.5    
3.7    
3.8    
4.0    
4.2    
4.3    
4.5    
4.7    
4.8    
5.0    
5.2    
5.3    
5.5    
5.7    
5.8    
6.0    
6.2    
6.3    
6.5    
6.7    
6.8    
7.0    
7.2    
7.3    
7.5    
7.7    
7.8    
8.0    
8.2    
8.3    
8.5    
8.7    
8.8    
9.0    
9.2    
9.3    
9.5    
9.7    
9.8    
10.0    
10.2    
10.4    
10.5    
10.7    
10.9    
11.0    
11.2    
11.4    
11.5    
11.7    
11.9    
12.0    
12.2    
12.4    
12.5    
12.7    
12.9    
13.0    
13.2    
13.4    
13.5    
13.7    
13.9    
14.0    
14.2    
14.4    
14.5    
14.7    
14.9    
15.0    
15.2    
15.4    
15.5    
15.7    
15.9    
16.0    
16.2    
16.4    
16.5    
16.7    
16.9    
17.0    
17.2    
17.4    
17.5    
17.7    
17.9    
18.0    
18.2    
18.4    
18.5    
18.7    
18.9    
19.0    
19.2    
19.4    
19.5    
19.7    
19.9    
20.0    
20.2    
20.4    
20.5    
20.7    
20.9    
21.0    
21.2    
21.4    
21.5    
21.7    
21.9    
22.0    
22.2    
22.4    
22.5    
22.7    
22.9    
23.0    
23.2    
23.4    
23.5    
23.7    
23.9    
24.0    
24.2    
24.4    
24.5    
24.7    
24.9    
25.0    
25.2    
25.4    
25.5    
25.7    
25.9    
26.0    
26.2    
26.4    
26.5    
26.7    
26.9    
27.0    
27.2    
27.4    
27.5    
27.7    
27.9    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.0    
29.2    
29.4    
29.5    
29.7    
29.9    
30.1    
30.2    
30.4    
30.6    
30.7    
30.9    
31.1    
31.2    
31.4    
31.6    
31.7    
31.9    
32.1    
32.2    
32.4    
32.6    
32.7    
32.9    
33.1    
33.2    
33.4    
33.6    
33.7    
33.9    
34.1    
34.2    
34.4    
34.6    
34.7    
34.9    
35.1    
35.2    
35.4    
35.6    
35.7    
35.9    
36.1    
36.2    
36.4    
36.6    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.7    
37.9    
38.1    
38.2    
38.4    
38.6    
38.7    
38.9    
39.1    
39.2    
39.4    
39.6    
39.7    
39.9    
40.1    
40.2    
40.4    
40.6    
40.7    
40.9    
41.1    
41.2    
41.4    
41.6    
41.7    
41.9    
42.1    
42.2    
42.4    
42.6    
42.7    
42.9    
43.1    
43.2    
43.4    
43.6    
43.7    
43.9    
44.1    
44.2    
44.4    
44.6    
44.7    
44.9    
45.1    
45.2    
45.4    
45.6    
45.7    
45.9    
46.1    
46.2    
46.4    
46.6    
46.7    
46.9    
47.1    
47.2    
47.4    
47.6    
47.7    
47.9    
48.1    
48.2    
48.4    
48.6    
48.7    
48.9    
49.1    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
50.9    
51.1    
51.3    
51.4    
51.6    
51.8    
51.9    
52.1    
52.3    
52.4    
52.6    
52.8    
52.9    
53.1    
53.3    
53.4    
53.6    
53.8    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
56.4    
56.6    
56.8    
56.9    
57.1    
57.3    
57.4    
57.6    
57.8    
57.9    
58.1    
58.3    
58.4    
58.6    
58.8    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
59.9    
60.1    
60.3    
60.4    
60.6    
60.8    
60.9    
61.1    
61.3    
61.4    
61.6    
61.8    
61.9    
62.1    
62.3    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.4    
63.6    
63.8    
63.9    
64.1    
64.3    
64.4    
64.6    
64.8    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
65.9    
66.1    
66.3    
66.4    
66.6    
66.8    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
67.9    
68.1    
68.3    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.1    
79.3    
79.5    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 12170, rend_intergenic: 6451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16510, rend_intergenic: 14774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50245, rend_intergenic: 39725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61221, rend_intergenic: 53953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80933, rend_intergenic: 73280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101022, rend_intergenic: 95837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support