-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_4114113-4322871

-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 CodingQuarry_transcript_19946-T1
Valid prediction for GlimmerHMM_glimmerT_38195-T1
Valid prediction for snap_scaffold_16-snap.819-T1
Valid prediction for snap_scaffold_16-snap.832-T1
Valid prediction for GlimmerHMM_glimmerT_38194-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g25496.t1
Valid prediction for CodingQuarry_transcript_19944-T1
Valid prediction for GlimmerHMM_glimmerT_38190-T1
Valid prediction for GlimmerHMM_glimmerT_38192-T1
Valid prediction for Augustus_model.g25489.t1
Valid prediction for GlimmerHMM_glimmerT_38182-T1
Valid prediction for HiQ_model.g25485.t1
Valid prediction for snap_scaffold_16-snap.802-T1
Valid prediction for snap_scaffold_16-snap.799-T1
Couldn't classify 39129, 39192
Couldn't classify 41922, 41998
Sorry, prediction pasa_asmbl_16181.p1 fails validation.
(CTA)	 TT	39129-39192	GT	GGG
(TTT)	 AG	40805-40864	GT	AGG
(CGG)	 AG	41070-41231	GT	AGG
(AGT)	 AG	41320-41403	GT	GGG
(CTG)	 AG	41922-41998	GA	GGG
-recovered pasa_asmbl_16181.p1, internal, 40805, 40864
-recovered pasa_asmbl_16181.p1, internal, 41070, 41231
-recovered pasa_asmbl_16181.p1, internal, 41320, 41403
Valid prediction for GlimmerHMM_glimmerT_38202-T1
Valid prediction for GlimmerHMM_glimmerT_38191-T1
Valid prediction for GlimmerHMM_glimmerT_38189-T1
Valid prediction for snap_scaffold_16-snap.811-T1
Couldn't classify 43374, 43510
Sorry, prediction CodingQuarry_transcript_19947-T1 fails validation.
(ATG)	 TC	39069-39192	GT	GGG
(TTT)	 AG	40805-40864	GT	AGG
(CGG)	 AG	41070-41231	GT	AGG
(AGT)	 AG	41320-41403	GT	GGG
(CTG)	 AG	41922-42148	GT	AGG
(TTG)	 AG	42534-42599	GT	AAG
(TAC)	 AG	42748-42864	GT	AGG
(ATT)	 AG	43051-43134	GT	AGG
(TTT)	 GT	43374-43510	GT	AGG
(AAC)	 AG	43688-43781	GT	GGG
(GTC)	 AG	43996-44124	GT	TGG
(ATG)	 AG	44396-44497	GT	AGG
(GCT)	 AG	44822-44899	GT	AGG
(CTC)	 AG	45037-45140	GT	GAG
(GTG)	 AG	45236-45294	GT	CCG
(GGT)	 AG	45420-45474	GT	CGG
(GTC)	 AG	45713-45780	GT	TGG
(GCC)	 AG	45906-46036	GT	ATG
(GTG)	 AG	46190-46255	GT	GGG
(GCC)	 AG	46643-46747	GT	ATG
(GTG)	 AG	46909-46985	GT	AGG
(GGT)	 AG	47091-47193	TC	AGT
-recovered CodingQuarry_transcript_19947-T1, initial, 39069, 39192
-recovered CodingQuarry_transcript_19947-T1, initial, 44396, 44497
-recovered CodingQuarry_transcript_19947-T1, terminal, 47091, 47193
-recovered CodingQuarry_transcript_19947-T1, internal, 40805, 40864
-recovered CodingQuarry_transcript_19947-T1, internal, 41070, 41231
-recovered CodingQuarry_transcript_19947-T1, internal, 41320, 41403
-recovered CodingQuarry_transcript_19947-T1, internal, 41922, 42148
-recovered CodingQuarry_transcript_19947-T1, internal, 42534, 42599
-recovered CodingQuarry_transcript_19947-T1, internal, 42748, 42864
-recovered CodingQuarry_transcript_19947-T1, internal, 43051, 43134
-recovered CodingQuarry_transcript_19947-T1, internal, 43688, 43781
-recovered CodingQuarry_transcript_19947-T1, internal, 43996, 44124
-recovered CodingQuarry_transcript_19947-T1, internal, 44396, 44497
-recovered CodingQuarry_transcript_19947-T1, internal, 44822, 44899
-recovered CodingQuarry_transcript_19947-T1, internal, 45037, 45140
-recovered CodingQuarry_transcript_19947-T1, internal, 45236, 45294
-recovered CodingQuarry_transcript_19947-T1, internal, 45420, 45474
-recovered CodingQuarry_transcript_19947-T1, internal, 45713, 45780
-recovered CodingQuarry_transcript_19947-T1, internal, 45906, 46036
-recovered CodingQuarry_transcript_19947-T1, internal, 46190, 46255
-recovered CodingQuarry_transcript_19947-T1, internal, 46643, 46747
-recovered CodingQuarry_transcript_19947-T1, internal, 46909, 46985
Valid prediction for Augustus_model.g25494.t1
Valid prediction for GlimmerHMM_glimmerT_38183-T1
Valid prediction for snap_scaffold_16-snap.808-T1
Valid prediction for Augustus_model.g25480.t1
Valid prediction for snap_scaffold_16-snap.814-T1
Valid prediction for Augustus_model.g25491.t1
Valid prediction for snap_scaffold_16-snap.828-T1
Valid prediction for GlimmerHMM_glimmerT_38187-T1
Valid prediction for GlimmerHMM_glimmerT_38188-T1
Valid prediction for snap_scaffold_16-snap.824-T1
Valid prediction for snap_scaffold_16-snap.836-T1
Valid prediction for snap_scaffold_16-snap.804-T1
Valid prediction for GlimmerHMM_glimmerT_38197-T1
Valid prediction for GlimmerHMM_glimmerT_38203-T1
Valid prediction for GlimmerHMM_glimmerT_38204-T1
Valid prediction for snap_scaffold_16-snap.797-T1
Valid prediction for snap_scaffold_16-snap.812-T1
Valid prediction for snap_scaffold_16-snap.835-T1
Valid prediction for GlimmerHMM_glimmerT_38181-T1
Valid prediction for Augustus_model.g25487.t1
Valid prediction for Augustus_model.g25492.t1
Valid prediction for GlimmerHMM_glimmerT_38201-T1
Valid prediction for HiQ_model.g25484.t1
Valid prediction for snap_scaffold_16-snap.805-T1
Valid prediction for snap_scaffold_16-snap.826-T1
Valid prediction for GlimmerHMM_glimmerT_38206-T1
Valid prediction for CodingQuarry_transcript_19945-T1
Valid prediction for snap_scaffold_16-snap.818-T1
Couldn't classify 35999, 36322
Sorry, prediction pasa_asmbl_16177.p4 fails validation.
(ATG)	 CC	35999-36322	TT	TCT
Valid prediction for Augustus_model.g25488.t1
Valid prediction for GlimmerHMM_glimmerT_38208-T1
Valid prediction for snap_scaffold_16-snap.816-T1
Valid prediction for GlimmerHMM_glimmerT_38209-T1
Couldn't classify 35999, 36322
Sorry, prediction pasa_asmbl_16178.p1 fails validation.
(ATG)	 CC	35999-36322	TT	TCT
Valid prediction for GlimmerHMM_glimmerT_38198-T1
Valid prediction for GlimmerHMM_glimmerT_38196-T1
Valid prediction for snap_scaffold_16-snap.825-T1
Valid prediction for Augustus_model.g25493.t1
Valid prediction for GlimmerHMM_glimmerT_38184-T1
Valid prediction for GlimmerHMM_glimmerT_38210-T1
Valid prediction for Augustus_model.g25486.t1
Valid prediction for snap_scaffold_16-snap.822-T1
Valid prediction for snap_scaffold_16-snap.820-T1
Valid prediction for Augustus_model.g25481.t1
Valid prediction for Augustus_model.g25497.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_16-snap.806-T1
Valid prediction for snap_scaffold_16-snap.830-T1
Valid prediction for Augustus_model.g25490.t1
Valid prediction for snap_scaffold_16-snap.800-T1
Valid prediction for snap_scaffold_16-snap.827-T1
Valid prediction for snap_scaffold_16-snap.821-T1
Valid prediction for GlimmerHMM_glimmerT_38205-T1
Valid prediction for GlimmerHMM_glimmerT_38193-T1
Valid prediction for snap_scaffold_16-snap.809-T1
Valid prediction for HiQ_model.g25483.t1
Valid prediction for GlimmerHMM_glimmerT_38199-T1
Valid prediction for pasa_asmbl_17052.p1
Valid prediction for CodingQuarry_transcript_19943-T1
Valid prediction for snap_scaffold_16-snap.823-T1
Valid prediction for snap_scaffold_16-snap.837-T1
Valid prediction for snap_scaffold_16-snap.829-T1
Valid prediction for snap_scaffold_16-snap.833-T1
Valid prediction for snap_scaffold_16-snap.801-T1
Valid prediction for snap_scaffold_16-snap.810-T1
Valid prediction for snap_scaffold_16-snap.831-T1
Valid prediction for GlimmerHMM_glimmerT_38186-T1
Valid prediction for GlimmerHMM_glimmerT_38200-T1
Valid prediction for snap_scaffold_16-snap.817-T1
Valid prediction for GlimmerHMM_glimmerT_38185-T1
Valid prediction for snap_scaffold_16-snap.796-T1
Valid prediction for snap_scaffold_16-snap.803-T1
Valid prediction for snap_scaffold_16-snap.807-T1
Valid prediction for snap_scaffold_16-snap.815-T1
Valid prediction for snap_scaffold_16-snap.813-T1
Valid prediction for Augustus_model.g25495.t1
Valid prediction for Augustus_model.g25482.t1
Valid prediction for snap_scaffold_16-snap.798-T1
Valid prediction for snap_scaffold_16-snap.834-T1
Valid prediction for GlimmerHMM_glimmerT_38207-T1
Valid prediction for snap_scaffold_16-snap.839-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6417, rend_intergenic: 1842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8810, rend_intergenic: 6538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9587, rend_intergenic: 9026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16014, rend_intergenic: 9693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17435, rend_intergenic: 16078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20317, rend_intergenic: 18754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29882, rend_intergenic: 20589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52664, rend_intergenic: 31687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58827, rend_intergenic: 54473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67958, rend_intergenic: 58827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73425, rend_intergenic: 70431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79619, rend_intergenic: 75782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133407, rend_intergenic: 132791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142137, rend_intergenic: 137957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171035, rend_intergenic: 156353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200223, rend_intergenic: 194043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208759
-exon list size: 424


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.9    
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2.3    
2.6    
2.8    
3.1    
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3.8    
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4.9    
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5.9    
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7.0    
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9.2    
9.4    
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10.1    
10.3    
10.6    
10.8    
11.0    
11.3    
11.5    
11.7    
12.0    
12.2    
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13.4    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.0    
15.3    
15.5    
15.7    
16.0    
16.2    
16.4    
16.7    
16.9    
17.1    
17.4    
17.6    
17.8    
18.1    
18.3    
18.5    
18.8    
19.0    
19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.1    
21.4    
21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
23.0    
23.2    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.8    
27.0    
27.2    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.7    
35.9    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.7    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.1    
44.4    
44.6    
44.8    
45.1    
45.3    
45.5    
45.8    
46.0    
46.2    
46.5    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.1    
48.4    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.6    
51.9    
52.1    
52.3    
52.6    
52.8    
53.1    
53.3    
53.5    
53.8    
54.0    
54.2    
54.5    
54.7    
54.9    
55.2    
55.4    
55.6    
55.9    
56.1    
56.3    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.3    
61.5    
61.7    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.1    
64.3    
64.6    
64.8    
65.0    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.8    
73.0    
73.2    
73.5    
73.7    
73.9    
74.2    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.8    
77.0    
77.2    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
85.0    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.7    
93.0    
93.2    
93.4    
93.7    
93.9    
94.1    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 6417, rend_intergenic: 1842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8810, rend_intergenic: 6538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9587, rend_intergenic: 9026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16014, rend_intergenic: 9693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17435, rend_intergenic: 16078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20317, rend_intergenic: 18754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29882, rend_intergenic: 20589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52664, rend_intergenic: 31687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58827, rend_intergenic: 54473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67958, rend_intergenic: 58827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73425, rend_intergenic: 70431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79619, rend_intergenic: 75782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133407, rend_intergenic: 132791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142137, rend_intergenic: 137957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171035, rend_intergenic: 156353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200223, rend_intergenic: 194043  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