-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_5720529-5931955

-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 HiQ_model.g28255.t1
Valid prediction for pasa_asmbl_20603.p1
Valid prediction for GlimmerHMM_glimmerT_42403-T1
Valid prediction for pasa_asmbl_20595.p1
Valid prediction for GlimmerHMM_glimmerT_42412-T1
Valid prediction for Augustus_model.g28245.t1
Valid prediction for GlimmerHMM_glimmerT_42389-T1
Valid prediction for Augustus_model.g28246.t1
Valid prediction for snap_scaffold_18-snap.1234-T1
Valid prediction for snap_scaffold_18-snap.1208-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_42409-T1
Valid prediction for snap_scaffold_18-snap.1236-T1
Couldn't classify 200374, 200451
Sorry, prediction pasa_asmbl_20624.p1 fails validation.
(AGA)	 GG	200374-200451	GT	GGG
(ATG)	 AG	200715-200783	GT	CGG
(ACT)	 AG	200950-201029	GT	AGG
(TGC)	 AG	201113-201234	GT	GGG
(ACG)	 AG	201454-201593	GT	AGG
(GCT)	 AG	201693-201794	GT	AGG
(GCC)	 AG	202013-202076	GT	AGG
(GGA)	 AG	202159-202260	GT	ATG
(ACA)	 AG	202357-202401	GT	AGG
(ACT)	 AG	202496-202566	GT	CGG
(GGT)	 AG	202652-202766	GT	GGG
(GCC)	 AG	202876-202968	GT	AGG
(AGC)	 AG	203081-203130	GT	TGG
(GAG)	 AG	203246-203347	GT	AGG
(GAG)	 AG	203546-203695	GT	TGG
(GCT)	 AG	203793-203933	GC	GAG
-recovered pasa_asmbl_20624.p1, initial, 200715, 200783
-recovered pasa_asmbl_20624.p1, terminal, 203793, 203933
-recovered pasa_asmbl_20624.p1, internal, 200715, 200783
-recovered pasa_asmbl_20624.p1, internal, 200950, 201029
-recovered pasa_asmbl_20624.p1, internal, 201113, 201234
-recovered pasa_asmbl_20624.p1, internal, 201454, 201593
-recovered pasa_asmbl_20624.p1, internal, 201693, 201794
-recovered pasa_asmbl_20624.p1, internal, 202013, 202076
-recovered pasa_asmbl_20624.p1, internal, 202159, 202260
-recovered pasa_asmbl_20624.p1, internal, 202357, 202401
-recovered pasa_asmbl_20624.p1, internal, 202496, 202566
-recovered pasa_asmbl_20624.p1, internal, 202652, 202766
-recovered pasa_asmbl_20624.p1, internal, 202876, 202968
-recovered pasa_asmbl_20624.p1, internal, 203081, 203130
-recovered pasa_asmbl_20624.p1, internal, 203246, 203347
-recovered pasa_asmbl_20624.p1, internal, 203546, 203695
-recovered pasa_asmbl_20624.p1, internal, 203793, 203933
Valid prediction for Augustus_model.g28261.t1
Valid prediction for GlimmerHMM_glimmerT_42397-T1
Valid prediction for GlimmerHMM_glimmerT_42392-T1
Valid prediction for snap_scaffold_18-snap.1216-T1
Valid prediction for snap_scaffold_18-snap.1214-T1
Valid prediction for snap_scaffold_18-snap.1224-T1
Valid prediction for snap_scaffold_18-snap.1240-T1
Valid prediction for snap_scaffold_18-snap.1211-T1
Valid prediction for CodingQuarry_transcript_23771-T1
Valid prediction for Augustus_model.g28254.t1
Valid prediction for Augustus_model.g28259.t1
Valid prediction for snap_scaffold_18-snap.1218-T1
Valid prediction for snap_scaffold_18-snap.1213-T1
Valid prediction for GlimmerHMM_glimmerT_42408-T1
Valid prediction for GlimmerHMM_glimmerT_42395-T1
Valid prediction for snap_scaffold_18-snap.1226-T1
Valid prediction for Augustus_model.g28252.t1
Valid prediction for Augustus_model.g28256.t1
Valid prediction for Augustus_model.g28247.t1
Valid prediction for GlimmerHMM_glimmerT_42391-T1
Valid prediction for Augustus_model.g28248.t1
Valid prediction for GlimmerHMM_glimmerT_42416-T1
Valid prediction for GlimmerHMM_glimmerT_42394-T1
Valid prediction for HiQ_model.g28244.t1
Valid prediction for GlimmerHMM_glimmerT_42400-T1
Valid prediction for Augustus_model.g28250.t1
Valid prediction for snap_scaffold_18-snap.1233-T1
Valid prediction for HiQ_model.g28251.t1
Valid prediction for Augustus_model.g28263.t1
Valid prediction for snap_scaffold_18-snap.1210-T1
Valid prediction for GlimmerHMM_glimmerT_42419-T1
Valid prediction for pasa_asmbl_20606.p1
Valid prediction for snap_scaffold_18-snap.1207-T1
Couldn't classify 51095, 51143
Couldn't classify 52202, 52206
Sorry, prediction pasa_asmbl_20600.p1 fails validation.
(TCG)	 CC	51095-51143	GT	CAG
(GTA)	 AG	51233-51358	GT	AGG
(AGC)	 AG	51575-51811	GT	AGG
(TTC)	 AG	51981-52091	GT	TTG
(ACC)	 AG	52202-52206	AC	CCA
-recovered pasa_asmbl_20600.p1, internal, 51233, 51358
-recovered pasa_asmbl_20600.p1, internal, 51575, 51811
-recovered pasa_asmbl_20600.p1, internal, 51981, 52091
Valid prediction for GlimmerHMM_glimmerT_42390-T1
Valid prediction for CodingQuarry_transcript_23772-T1
Valid prediction for GlimmerHMM_glimmerT_42396-T1
Couldn't classify 120476, 120546
Couldn't classify 125632, 125691
Sorry, prediction pasa_asmbl_20612.p1 fails validation.
(CCC)	 GC	120476-120546	GT	AAG
(TGG)	 AG	121657-121724	GT	CGG
(AGC)	 AG	124336-124403	GT	AGG
(CAC)	 AG	124571-124732	GT	AGG
(AAT)	 AG	125335-125484	GT	AGG
(GCG)	 AG	125632-125691	AA	TCA
-recovered pasa_asmbl_20612.p1, internal, 121657, 121724
-recovered pasa_asmbl_20612.p1, internal, 124336, 124403
-recovered pasa_asmbl_20612.p1, internal, 124571, 124732
-recovered pasa_asmbl_20612.p1, internal, 125335, 125484
Valid prediction for snap_scaffold_18-snap.1209-T1
Valid prediction for GlimmerHMM_glimmerT_42415-T1
Valid prediction for GlimmerHMM_glimmerT_42407-T1
Couldn't classify 75468, 75848
Sorry, prediction pasa_asmbl_20607.p1 fails validation.
(TTT)	 CG	75468-75848	GG	GAG
Valid prediction for snap_scaffold_18-snap.1221-T1
Valid prediction for snap_scaffold_18-snap.1220-T1
Valid prediction for CodingQuarry_transcript_23776-T1
Valid prediction for snap_scaffold_18-snap.1206-T1
Valid prediction for GlimmerHMM_glimmerT_42418-T1
Valid prediction for GlimmerHMM_glimmerT_42402-T1
Valid prediction for pasa_asmbl_20598.p1
Valid prediction for snap_scaffold_18-snap.1225-T1
Valid prediction for GlimmerHMM_glimmerT_42404-T1
Valid prediction for snap_scaffold_18-snap.1217-T1
Valid prediction for snap_scaffold_18-snap.1222-T1
Valid prediction for CodingQuarry_transcript_23774-T1
Valid prediction for Augustus_model.g28249.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 Augustus_model.g28260.t1
Valid prediction for GlimmerHMM_glimmerT_42410-T1
Valid prediction for snap_scaffold_18-snap.1238-T1
Couldn't classify 58635, 58682
Couldn't classify 62047, 62184
Sorry, prediction pasa_asmbl_19873.p2 fails validation.
(GTG)	 AG	58635-58682	GT	ACG
(GTT)	 AG	60116-60236	GT	AGG
(AGC)	 AG	61070-61203	GT	AGG
(GCA)	 AG	62047-62184	GG	TGG
add_exon() Sorry, pasa_asmbl_19873.p2 60116-60236-terminal-3 is invalid.
-recovered pasa_asmbl_19873.p2, terminal, 60116, 60236
-recovered pasa_asmbl_19873.p2, internal, 58635, 58682
-recovered pasa_asmbl_19873.p2, internal, 60116, 60236
-recovered pasa_asmbl_19873.p2, internal, 61070, 61203
Valid prediction for pasa_asmbl_19871.p1
Valid prediction for CodingQuarry_transcript_23775-T1
Couldn't classify 18989, 19363
Sorry, prediction pasa_asmbl_19883.p1 fails validation.
(TTC)	 CA	18989-19363	TA	AAT
Valid prediction for Augustus_model.g28262.t1
Valid prediction for GlimmerHMM_glimmerT_42421-T1
Valid prediction for HiQ_model.g28253.t1
Valid prediction for Augustus_model.g28258.t1
Valid prediction for GlimmerHMM_glimmerT_42406-T1
Valid prediction for GlimmerHMM_glimmerT_42393-T1
Valid prediction for snap_scaffold_18-snap.1229-T1
Valid prediction for GlimmerHMM_glimmerT_42417-T1
Valid prediction for snap_scaffold_18-snap.1223-T1
Valid prediction for pasa_asmbl_19884.p1
Valid prediction for GlimmerHMM_glimmerT_42401-T1
Valid prediction for snap_scaffold_18-snap.1241-T1
Valid prediction for GlimmerHMM_glimmerT_42399-T1
Valid prediction for GlimmerHMM_glimmerT_42411-T1
Valid prediction for snap_scaffold_18-snap.1219-T1
Valid prediction for snap_scaffold_18-snap.1237-T1
Valid prediction for snap_scaffold_18-snap.1212-T1
Valid prediction for snap_scaffold_18-snap.1215-T1
Valid prediction for snap_scaffold_18-snap.1231-T1
Valid prediction for snap_scaffold_18-snap.1230-T1
Valid prediction for GlimmerHMM_glimmerT_42413-T1
Valid prediction for snap_scaffold_18-snap.1227-T1
Valid prediction for GlimmerHMM_glimmerT_42405-T1
Valid prediction for GlimmerHMM_glimmerT_42414-T1
Valid prediction for snap_scaffold_18-snap.1239-T1
Valid prediction for snap_scaffold_18-snap.1242-T1
Valid prediction for CodingQuarry_transcript_23780-T1
Valid prediction for GlimmerHMM_glimmerT_42398-T1
Valid prediction for Augustus_model.g28257.t1
Valid prediction for snap_scaffold_18-snap.1232-T1
Valid prediction for CodingQuarry_transcript_23778-T1
Valid prediction for CodingQuarry_transcript_23777-T1
Valid prediction for GlimmerHMM_glimmerT_42420-T1
Valid prediction for snap_scaffold_18-snap.1235-T1
Valid prediction for snap_scaffold_18-snap.1228-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34368, rend_intergenic: 32058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35502, rend_intergenic: 35282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49341, rend_intergenic: 38670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172651, rend_intergenic: 168859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211427
-exon list size: 408


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.4    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.1    
4.4    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
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8.0    
8.3    
8.5    
8.8    
9.0    
9.3    
9.5    
9.8    
10.0    
10.2    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.7    
22.0    
22.2    
22.4    
22.7    
22.9    
23.2    
23.4    
23.7    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.0    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.3    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.5    
69.8    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.7    
72.0    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 34368, rend_intergenic: 32058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35502, rend_intergenic: 35282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49341, rend_intergenic: 38670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172651, rend_intergenic: 168859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support