-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_234735-429781

-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_28-snap.60-T1
Valid prediction for snap_scaffold_28-snap.85-T1
Valid prediction for snap_scaffold_28-snap.75-T1
Valid prediction for pasa_asmbl_37273.p1
Valid prediction for GlimmerHMM_glimmerT_57962-T1
Valid prediction for Augustus_model.g38375.t1
Couldn't classify 59064, 59102
Sorry, prediction pasa_asmbl_37267.p1 fails validation.
(GAG)	 AG	59064-59102	GT	AGG
(GCC)	 AG	59498-59790	GT	AGG
(ATG)	 AG	59901-60072	GT	AGG
(GAG)	 AG	60158-60343	GT	AGG
(ATT)	 AG	60532-60665	GT	AAG
(GTG)	 AG	60755-60803	GT	AGG
(GCA)	 AG	60884-61003	GT	TGG
(GTC)	 AG	61124-61222	GT	AGG
(TTG)	 AG	61321-61378	GT	GAG
(CAG)	 AG	61535-61771	GT	AGG
(GTG)	 AG	61859-61899	AA	AAA
-recovered pasa_asmbl_37267.p1, initial, 59901, 60072
-recovered pasa_asmbl_37267.p1, terminal, 61859, 61899
-recovered pasa_asmbl_37267.p1, internal, 59064, 59102
-recovered pasa_asmbl_37267.p1, internal, 59498, 59790
-recovered pasa_asmbl_37267.p1, internal, 59901, 60072
-recovered pasa_asmbl_37267.p1, internal, 60158, 60343
-recovered pasa_asmbl_37267.p1, internal, 60532, 60665
-recovered pasa_asmbl_37267.p1, internal, 60755, 60803
-recovered pasa_asmbl_37267.p1, internal, 60884, 61003
-recovered pasa_asmbl_37267.p1, internal, 61124, 61222
-recovered pasa_asmbl_37267.p1, internal, 61321, 61378
-recovered pasa_asmbl_37267.p1, internal, 61535, 61771
Valid prediction for GlimmerHMM_glimmerT_57985-T1
Valid prediction for Augustus_model.g38357.t1
Valid prediction for GlimmerHMM_glimmerT_57977-T1
Valid prediction for snap_scaffold_28-snap.55-T1
Valid prediction for GlimmerHMM_glimmerT_57976-T1
Valid prediction for GlimmerHMM_glimmerT_57958-T1
Valid prediction for GlimmerHMM_glimmerT_57968-T1
Couldn't classify 5848, 5874
Sorry, prediction pasa_asmbl_37262.p1 fails validation.
(GCA)	 TT	5848-5874	GT	AGG
(AAC)	 AG	5974-6069	GT	AGG
(GGT)	 AG	6159-6308	GT	ACG
(GGT)	 AG	6416-6521	GT	GGG
(GTG)	 AG	6718-6851	GT	AGG
(AAC)	 AG	7029-7145	GT	AAG
-recovered pasa_asmbl_37262.p1, terminal, 7029, 7145
-recovered pasa_asmbl_37262.p1, internal, 5974, 6069
-recovered pasa_asmbl_37262.p1, internal, 6159, 6308
-recovered pasa_asmbl_37262.p1, internal, 6416, 6521
-recovered pasa_asmbl_37262.p1, internal, 6718, 6851
-recovered pasa_asmbl_37262.p1, internal, 7029, 7145
Valid prediction for HiQ_model.g38363.t1
Valid prediction for GlimmerHMM_glimmerT_57966-T1
Valid prediction for snap_scaffold_28-snap.69-T1
Valid prediction for HiQ_model.g38378.t1
Valid prediction for GlimmerHMM_glimmerT_57970-T1
Valid prediction for GlimmerHMM_glimmerT_57963-T1
Valid prediction for snap_scaffold_28-snap.53-T1
Valid prediction for snap_scaffold_28-snap.81-T1
Valid prediction for Augustus_model.g38376.t1
Valid prediction for GlimmerHMM_glimmerT_57965-T1
Valid prediction for snap_scaffold_28-snap.77-T1
Valid prediction for snap_scaffold_28-snap.84-T1
Valid prediction for snap_scaffold_28-snap.72-T1
Valid prediction for GlimmerHMM_glimmerT_57967-T1
Valid prediction for snap_scaffold_28-snap.44-T1
Valid prediction for Augustus_model.g38379.t1
Valid prediction for Augustus_model.g38361.t1
Valid prediction for Augustus_model.g38365.t1
Valid prediction for snap_scaffold_28-snap.65-T1
Valid prediction for CodingQuarry_transcript_43510-T1
Valid prediction for snap_scaffold_28-snap.52-T1
Valid prediction for snap_scaffold_28-snap.58-T1
Valid prediction for CodingQuarry_transcript_43508-T1
Valid prediction for Augustus_model.g38358.t1
Valid prediction for Augustus_model.g38371.t1
Valid prediction for CodingQuarry_transcript_43509-T1
Valid prediction for Augustus_model.g38359.t1
Valid prediction for snap_scaffold_28-snap.87-T1
Valid prediction for snap_scaffold_28-snap.62-T1
Valid prediction for snap_scaffold_28-snap.64-T1
Valid prediction for snap_scaffold_28-snap.88-T1
Valid prediction for Augustus_model.g38360.t1
Valid prediction for GlimmerHMM_glimmerT_57986-T1
Valid prediction for snap_scaffold_28-snap.76-T1
Valid prediction for snap_scaffold_28-snap.78-T1
Valid prediction for GlimmerHMM_glimmerT_57978-T1
Valid prediction for snap_scaffold_28-snap.50-T1
Valid prediction for GlimmerHMM_glimmerT_57984-T1
Valid prediction for snap_scaffold_28-snap.63-T1
Valid prediction for CodingQuarry_transcript_43507-T1
Valid prediction for snap_scaffold_28-snap.90-T1
Valid prediction for GlimmerHMM_glimmerT_57961-T1
Valid prediction for snap_scaffold_28-snap.70-T1
Valid prediction for HiQ_model.g38364.t1
Valid prediction for Augustus_model.g38370.t1
Valid prediction for Augustus_model.g38362.t1
Valid prediction for GlimmerHMM_glimmerT_57964-T1
Valid prediction for snap_scaffold_28-snap.89-T1
Valid prediction for Augustus_model.g38373.t1
Valid prediction for snap_scaffold_28-snap.61-T1
Valid prediction for GlimmerHMM_glimmerT_57957-T1
Valid prediction for GlimmerHMM_glimmerT_57981-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.g38368.t1
Valid prediction for snap_scaffold_28-snap.57-T1
Valid prediction for snap_scaffold_28-snap.45-T1
Valid prediction for Augustus_model.g38367.t1
Valid prediction for snap_scaffold_28-snap.54-T1
Valid prediction for snap_scaffold_28-snap.56-T1
Valid prediction for snap_scaffold_28-snap.48-T1
Valid prediction for GlimmerHMM_glimmerT_57974-T1
Valid prediction for snap_scaffold_28-snap.79-T1
Valid prediction for GlimmerHMM_glimmerT_57983-T1
Valid prediction for GlimmerHMM_glimmerT_57980-T1
Valid prediction for Augustus_model.g38366.t1
Valid prediction for GlimmerHMM_glimmerT_57969-T1
Valid prediction for snap_scaffold_28-snap.68-T1
Valid prediction for Augustus_model.g38377.t1
Valid prediction for snap_scaffold_28-snap.71-T1
Valid prediction for snap_scaffold_28-snap.51-T1
Valid prediction for GlimmerHMM_glimmerT_57973-T1
Valid prediction for Augustus_model.g38369.t1
Valid prediction for GlimmerHMM_glimmerT_57975-T1
Valid prediction for snap_scaffold_28-snap.80-T1
Valid prediction for GlimmerHMM_glimmerT_57979-T1
Valid prediction for GlimmerHMM_glimmerT_57960-T1
Valid prediction for snap_scaffold_28-snap.83-T1
Valid prediction for GlimmerHMM_glimmerT_57982-T1
Valid prediction for snap_scaffold_28-snap.82-T1
Valid prediction for GlimmerHMM_glimmerT_57971-T1
Valid prediction for snap_scaffold_28-snap.73-T1
Valid prediction for snap_scaffold_28-snap.86-T1
Valid prediction for snap_scaffold_28-snap.47-T1
Valid prediction for snap_scaffold_28-snap.67-T1
Valid prediction for GlimmerHMM_glimmerT_57959-T1
Valid prediction for snap_scaffold_28-snap.49-T1
Valid prediction for Augustus_model.g38372.t1
Valid prediction for snap_scaffold_28-snap.66-T1
Valid prediction for GlimmerHMM_glimmerT_57972-T1
Valid prediction for snap_scaffold_28-snap.74-T1
Valid prediction for snap_scaffold_28-snap.46-T1
Valid prediction for Augustus_model.g38374.t1
Valid prediction for snap_scaffold_28-snap.59-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 43394, rend_intergenic: 39354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52735, rend_intergenic: 50369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53285, rend_intergenic: 53078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56040, rend_intergenic: 53956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99348, rend_intergenic: 97156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107517, rend_intergenic: 103854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160171, rend_intergenic: 160014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195047
-exon list size: 366


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.3    
3.5    
3.8    
4.1    
4.3    
4.6    
4.9    
5.2    
5.4    
5.7    
6.0    
6.2    
6.5    
6.8    
7.1    
7.3    
7.6    
7.9    
8.2    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.1    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.6    
13.9    
14.1    
14.4    
14.7    
14.9    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.8    
17.1    
17.4    
17.7    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.7    
20.9    
21.2    
21.5    
21.7    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.1    
35.3    
35.6    
35.9    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.1    
64.4    
64.7    
64.9    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.4    
70.7    
70.9    
71.2    
71.5    
71.7    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.5    
78.8    
79.1    
79.3    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.3    
82.6    
82.9    
83.2    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.7    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 43394, rend_intergenic: 39354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52735, rend_intergenic: 50369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53285, rend_intergenic: 53078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56040, rend_intergenic: 53956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99348, rend_intergenic: 97156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107517, rend_intergenic: 103854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160171, rend_intergenic: 160014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support