-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_1889581-2191471

-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_4-snap.461-T1
Valid prediction for GlimmerHMM_glimmerT_8867-T1
Valid prediction for snap_scaffold_4-snap.451-T1
Valid prediction for snap_scaffold_4-snap.480-T1
Valid prediction for snap_scaffold_4-snap.491-T1
Valid prediction for GlimmerHMM_glimmerT_8879-T1
Valid prediction for snap_scaffold_4-snap.484-T1
Valid prediction for GlimmerHMM_glimmerT_8877-T1
Valid prediction for CodingQuarry_transcript_48887-T1
Valid prediction for GlimmerHMM_glimmerT_8876-T1
Valid prediction for snap_scaffold_4-snap.478-T1
Valid prediction for snap_scaffold_4-snap.456-T1
Valid prediction for GlimmerHMM_glimmerT_8886-T1
Valid prediction for snap_scaffold_4-snap.489-T1
Valid prediction for snap_scaffold_4-snap.482-T1
Valid prediction for CodingQuarry_transcript_48889-T1
Valid prediction for snap_scaffold_4-snap.463-T1
Valid prediction for snap_scaffold_4-snap.449-T1
Valid prediction for GlimmerHMM_glimmerT_8884-T1
Couldn't classify 44122, 44538
Sorry, prediction pasa_asmbl_41144.p1 fails validation.
(CCT)	 GA	44122-44538	CC	AAC
Couldn't classify 25694, 25908
Couldn't classify 27173, 27359
Sorry, prediction pasa_asmbl_41141.p1 fails validation.
(GAT)	 CA	25694-25908	GT	AGG
(GAG)	 AG	27173-27359	AA	GAA
Valid prediction for GlimmerHMM_glimmerT_8852-T1
Valid prediction for GlimmerHMM_glimmerT_8857-T1
Valid prediction for CodingQuarry_transcript_48891-T1
Valid prediction for snap_scaffold_4-snap.454-T1
Valid prediction for GlimmerHMM_glimmerT_8861-T1
Couldn't classify 542, 664
Couldn't classify 1403, 1543
Sorry, prediction pasa_asmbl_41136.p1 fails validation.
(GTG)	 AC	542-664	GT	AGG
(ATC)	 AG	998-1105	GT	AGG
(GTC)	 AG	1403-1543	CC	TGC
-recovered pasa_asmbl_41136.p1, internal, 998, 1105
Valid prediction for Augustus_model.g5711.t1
Valid prediction for GlimmerHMM_glimmerT_8859-T1
Valid prediction for Augustus_model.g5710.t1
Valid prediction for Augustus_model.g5707.t1
Valid prediction for HiQ_model.g5706.t1
Valid prediction for snap_scaffold_4-snap.472-T1
Valid prediction for snap_scaffold_4-snap.485-T1
Valid prediction for snap_scaffold_4-snap.468-T1
Valid prediction for snap_scaffold_4-snap.462-T1
Valid prediction for snap_scaffold_4-snap.446-T1
Valid prediction for Augustus_model.g5708.t1
Valid prediction for GlimmerHMM_glimmerT_8862-T1
Valid prediction for GlimmerHMM_glimmerT_8869-T1
Valid prediction for snap_scaffold_4-snap.458-T1
Valid prediction for snap_scaffold_4-snap.448-T1
Valid prediction for snap_scaffold_4-snap.466-T1
Valid prediction for GlimmerHMM_glimmerT_8875-T1
Valid prediction for HiQ_model.g5712.t1
Couldn't classify 80026, 80322
Sorry, prediction pasa_asmbl_41147.p1 fails validation.
(AAT)	 CC	80026-80322	GT	AGG
(GAT)	 AG	80572-80723	GT	ACG
(ACA)	 AG	82041-82173	GT	AGG
(GTC)	 AG	83001-83207	AG	GAA
-recovered pasa_asmbl_41147.p1, terminal, 83001, 83207
-recovered pasa_asmbl_41147.p1, internal, 80572, 80723
-recovered pasa_asmbl_41147.p1, internal, 82041, 82173
Valid prediction for GlimmerHMM_glimmerT_8855-T1
Valid prediction for snap_scaffold_4-snap.469-T1
Valid prediction for GlimmerHMM_glimmerT_8864-T1
Valid prediction for CodingQuarry_transcript_48886-T1
Valid prediction for snap_scaffold_4-snap.465-T1
Valid prediction for pasa_asmbl_41153.p1
Valid prediction for snap_scaffold_4-snap.445-T1
Valid prediction for GlimmerHMM_glimmerT_8871-T1
Valid prediction for Augustus_model.g5705.t1
Valid prediction for snap_scaffold_4-snap.470-T1
Valid prediction for snap_scaffold_4-snap.481-T1
Valid prediction for snap_scaffold_4-snap.457-T1
Valid prediction for GlimmerHMM_glimmerT_8866-T1
Valid prediction for snap_scaffold_4-snap.473-T1
Valid prediction for GlimmerHMM_glimmerT_8853-T1
Valid prediction for GlimmerHMM_glimmerT_8860-T1
Valid prediction for snap_scaffold_4-snap.483-T1
Valid prediction for GlimmerHMM_glimmerT_8863-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.g5715.t1
Valid prediction for GlimmerHMM_glimmerT_8888-T1
Valid prediction for GlimmerHMM_glimmerT_8887-T1
Valid prediction for GlimmerHMM_glimmerT_8874-T1
Valid prediction for snap_scaffold_4-snap.474-T1
Valid prediction for snap_scaffold_4-snap.487-T1
Valid prediction for snap_scaffold_4-snap.453-T1
Valid prediction for GlimmerHMM_glimmerT_8868-T1
Valid prediction for snap_scaffold_4-snap.467-T1
Valid prediction for Augustus_model.g5720.t1
Valid prediction for snap_scaffold_4-snap.471-T1
Valid prediction for GlimmerHMM_glimmerT_8858-T1
Valid prediction for snap_scaffold_4-snap.488-T1
Valid prediction for GlimmerHMM_glimmerT_8885-T1
Valid prediction for snap_scaffold_4-snap.459-T1
Valid prediction for GlimmerHMM_glimmerT_8878-T1
Valid prediction for GlimmerHMM_glimmerT_8872-T1
Valid prediction for snap_scaffold_4-snap.477-T1
Valid prediction for Augustus_model.g5717.t1
Valid prediction for snap_scaffold_4-snap.450-T1
Valid prediction for snap_scaffold_4-snap.447-T1
Valid prediction for snap_scaffold_4-snap.479-T1
Valid prediction for GlimmerHMM_glimmerT_8882-T1
Valid prediction for GlimmerHMM_glimmerT_8848-T1
Valid prediction for GlimmerHMM_glimmerT_8854-T1
Valid prediction for Augustus_model.g5713.t1
Valid prediction for GlimmerHMM_glimmerT_8880-T1
Valid prediction for Augustus_model.g5716.t1
Valid prediction for snap_scaffold_4-snap.476-T1
Valid prediction for snap_scaffold_4-snap.475-T1
Valid prediction for GlimmerHMM_glimmerT_8850-T1
Valid prediction for snap_scaffold_4-snap.455-T1
Valid prediction for snap_scaffold_4-snap.452-T1
Valid prediction for GlimmerHMM_glimmerT_8873-T1
Valid prediction for GlimmerHMM_glimmerT_8851-T1
Valid prediction for snap_scaffold_4-snap.464-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8870-T1
Valid prediction for GlimmerHMM_glimmerT_8881-T1
Valid prediction for GlimmerHMM_glimmerT_8849-T1
Valid prediction for snap_scaffold_4-snap.460-T1
Valid prediction for GlimmerHMM_glimmerT_8856-T1
Valid prediction for Augustus_model.g5718.t1
Valid prediction for snap_scaffold_4-snap.486-T1
Valid prediction for snap_scaffold_4-snap.490-T1
Valid prediction for GlimmerHMM_glimmerT_8865-T1
Valid prediction for GlimmerHMM_glimmerT_8883-T1
Valid prediction for Augustus_model.g5719.t1
Valid prediction for Augustus_model.g5714.t1
Valid prediction for Augustus_model.g5709.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42620, rend_intergenic: 35824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47621, rend_intergenic: 44500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53104, rend_intergenic: 49214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56240, rend_intergenic: 53216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78718, rend_intergenic: 71076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112350, rend_intergenic: 94162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128880, rend_intergenic: 112438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146193, rend_intergenic: 137390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153568, rend_intergenic: 146341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179896, rend_intergenic: 154140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227094, rend_intergenic: 186548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256905, rend_intergenic: 233699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 278185, rend_intergenic: 258876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 290074, rend_intergenic: 278374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 296531, rend_intergenic: 290297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 299447, rend_intergenic: 296703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 301891
-exon list size: 448


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.6    
1.8    
2.0    
2.2    
2.4    
2.7    
2.9    
3.1    
3.3    
3.6    
3.8    
4.0    
4.2    
4.4    
4.7    
4.9    
5.1    
5.3    
5.6    
5.8    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.3    
7.6    
7.8    
8.0    
8.2    
8.4    
8.7    
8.9    
9.1    
9.3    
9.6    
9.8    
10.0    
10.2    
10.4    
10.7    
10.9    
11.1    
11.3    
11.6    
11.8    
12.0    
12.2    
12.4    
12.7    
12.9    
13.1    
13.3    
13.6    
13.8    
14.0    
14.2    
14.4    
14.7    
14.9    
15.1    
15.3    
15.6    
15.8    
16.0    
16.2    
16.4    
16.7    
16.9    
17.1    
17.3    
17.6    
17.8    
18.0    
18.2    
18.4    
18.7    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.2    
20.4    
20.7    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.2    
22.4    
22.7    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.3    
27.6    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.2    
30.4    
30.7    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.2    
32.4    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.4    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
45.6    
45.8    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.2    
48.4    
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    
51.6    
51.8    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.2    
54.4    
54.7    
54.9    
55.1    
55.3    
55.6    
55.8    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.3    
57.6    
57.8    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.3    
61.6    
61.8    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.3    
63.6    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.3    
65.6    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.3    
67.6    
67.8    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.3    
69.6    
69.8    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.2    
72.4    
72.7    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.6    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.2    
84.4    
84.7    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.7    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 42620, rend_intergenic: 35824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47621, rend_intergenic: 44500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53104, rend_intergenic: 49214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56240, rend_intergenic: 53216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78718, rend_intergenic: 71076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112350, rend_intergenic: 94162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128880, rend_intergenic: 112438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146193, rend_intergenic: 137390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153568, rend_intergenic: 146341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179896, rend_intergenic: 154140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227094, rend_intergenic: 186548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256905, rend_intergenic: 233699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 278185, rend_intergenic: 258876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 290074, rend_intergenic: 278374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 296531, rend_intergenic: 290297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 299447, rend_intergenic: 296703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 280958 - 301891
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-found 3 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support