-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_1848308-2060636

-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_25-snap.382-T1
Valid prediction for snap_scaffold_25-snap.367-T1
Valid prediction for GlimmerHMM_glimmerT_53659-T1
Valid prediction for GlimmerHMM_glimmerT_53670-T1
Valid prediction for snap_scaffold_25-snap.366-T1
Valid prediction for snap_scaffold_25-snap.360-T1
Valid prediction for snap_scaffold_25-snap.380-T1
Valid prediction for GlimmerHMM_glimmerT_53671-T1
Valid prediction for snap_scaffold_25-snap.363-T1
Valid prediction for GlimmerHMM_glimmerT_53678-T1
Valid prediction for GlimmerHMM_glimmerT_53668-T1
Valid prediction for snap_scaffold_25-snap.394-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.371-T1
Valid prediction for snap_scaffold_25-snap.378-T1
Valid prediction for snap_scaffold_25-snap.387-T1
Valid prediction for snap_scaffold_25-snap.398-T1
Valid prediction for GlimmerHMM_glimmerT_53666-T1
Valid prediction for GlimmerHMM_glimmerT_53656-T1
Valid prediction for snap_scaffold_25-snap.374-T1
Valid prediction for GlimmerHMM_glimmerT_53664-T1
Valid prediction for snap_scaffold_25-snap.372-T1
Valid prediction for snap_scaffold_25-snap.391-T1
Valid prediction for snap_scaffold_25-snap.369-T1
Valid prediction for snap_scaffold_25-snap.376-T1
Valid prediction for snap_scaffold_25-snap.401-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.395-T1
Valid prediction for GlimmerHMM_glimmerT_53675-T1
Valid prediction for snap_scaffold_25-snap.362-T1
Valid prediction for snap_scaffold_25-snap.357-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 GlimmerHMM_glimmerT_53657-T1
Valid prediction for GlimmerHMM_glimmerT_53658-T1
Valid prediction for snap_scaffold_25-snap.386-T1
Valid prediction for snap_scaffold_25-snap.381-T1
Valid prediction for GlimmerHMM_glimmerT_53676-T1
Valid prediction for snap_scaffold_25-snap.390-T1
Valid prediction for snap_scaffold_25-snap.383-T1
Valid prediction for snap_scaffold_25-snap.388-T1
Valid prediction for snap_scaffold_25-snap.375-T1
Valid prediction for GlimmerHMM_glimmerT_53672-T1
Valid prediction for snap_scaffold_25-snap.368-T1
Valid prediction for snap_scaffold_25-snap.393-T1
Valid prediction for snap_scaffold_25-snap.377-T1
Valid prediction for GlimmerHMM_glimmerT_53667-T1
Valid prediction for GlimmerHMM_glimmerT_53679-T1
Valid prediction for snap_scaffold_25-snap.385-T1
Valid prediction for Augustus_model.g35654.t1
Valid prediction for snap_scaffold_25-snap.359-T1
Valid prediction for GlimmerHMM_glimmerT_53681-T1
Valid prediction for GlimmerHMM_glimmerT_53662-T1
Valid prediction for Augustus_model.g35657.t1
Valid prediction for snap_scaffold_25-snap.397-T1
Couldn't classify 200580, 200725
Sorry, prediction pasa_asmbl_34045.p1 fails validation.
(TGG)	 AC	200580-200725	GT	AAG
(TGT)	 AG	201011-201126	GT	CGG
(GTT)	 AG	201430-201565	GC	AGG
(GTA)	 AG	201778-201961	GT	AGG
(GGC)	 AG	202487-202621	GT	AGG
(GTG)	 AG	204301-204390	TT	GAT
-recovered pasa_asmbl_34045.p1, terminal, 204301, 204390
-recovered pasa_asmbl_34045.p1, internal, 201011, 201126
-recovered pasa_asmbl_34045.p1, internal, 201430, 201565
-recovered pasa_asmbl_34045.p1, internal, 201778, 201961
-recovered pasa_asmbl_34045.p1, internal, 202487, 202621
Valid prediction for GlimmerHMM_glimmerT_53661-T1
Valid prediction for pasa_asmbl_34050.p2
Valid prediction for GlimmerHMM_glimmerT_53680-T1
Valid prediction for GlimmerHMM_glimmerT_53665-T1
Valid prediction for snap_scaffold_25-snap.364-T1
Valid prediction for snap_scaffold_25-snap.370-T1
Couldn't classify 199938, 200128
Sorry, prediction pasa_asmbl_34562.p1 fails validation.
(ATG)	 AA	196007-196252	GT	GGG
(ATC)	 AG	197815-197977	GT	AGG
(GTC)	 AG	199383-199526	GT	AGG
(TGG)	 AG	199656-199781	GT	AGG
(TGG)	 AG	199938-200128	GT	GGG
-recovered pasa_asmbl_34562.p1, initial, 196007, 196252
-recovered pasa_asmbl_34562.p1, internal, 197815, 197977
-recovered pasa_asmbl_34562.p1, internal, 199383, 199526
-recovered pasa_asmbl_34562.p1, internal, 199656, 199781
-recovered pasa_asmbl_34562.p1, internal, 199938, 200128
Valid prediction for snap_scaffold_25-snap.373-T1
Valid prediction for snap_scaffold_25-snap.392-T1
Valid prediction for Augustus_model.g35653.t1
Couldn't classify 187705, 187798
Couldn't classify 190534, 190689
Sorry, prediction pasa_asmbl_34048.p1 fails validation.
(GGG)	 AA	187705-187798	GT	TGG
(ACA)	 AG	188199-188311	GT	AGG
(AAG)	 AG	188842-189002	GT	AGG
(GGC)	 AG	189237-189370	GT	AGG
(AGA)	 AG	190106-190254	GT	AGG
(GCC)	 AG	190534-190689	CT	GCC
-recovered pasa_asmbl_34048.p1, internal, 188199, 188311
-recovered pasa_asmbl_34048.p1, internal, 188842, 189002
-recovered pasa_asmbl_34048.p1, internal, 189237, 189370
-recovered pasa_asmbl_34048.p1, internal, 190106, 190254
Valid prediction for snap_scaffold_25-snap.399-T1
Valid prediction for snap_scaffold_25-snap.396-T1
Valid prediction for HiQ_model.g35652.t1
Valid prediction for GlimmerHMM_glimmerT_53674-T1
Valid prediction for snap_scaffold_25-snap.361-T1
Valid prediction for snap_scaffold_25-snap.365-T1
Valid prediction for snap_scaffold_25-snap.358-T1
Valid prediction for GlimmerHMM_glimmerT_53663-T1
Valid prediction for snap_scaffold_25-snap.379-T1
Valid prediction for GlimmerHMM_glimmerT_53677-T1
Valid prediction for GlimmerHMM_glimmerT_53660-T1
Valid prediction for Augustus_model.g35656.t1
Valid prediction for GlimmerHMM_glimmerT_53669-T1
Valid prediction for snap_scaffold_25-snap.389-T1
Valid prediction for Augustus_model.g35655.t1
Valid prediction for GlimmerHMM_glimmerT_53673-T1
Valid prediction for snap_scaffold_25-snap.384-T1
Valid prediction for snap_scaffold_25-snap.400-T1
Valid prediction for CodingQuarry_transcript_38646-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9930, rend_intergenic: 5091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14138, rend_intergenic: 12140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22255, rend_intergenic: 18364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30486, rend_intergenic: 22937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42341, rend_intergenic: 41932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45595, rend_intergenic: 42940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48717, rend_intergenic: 47354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72112, rend_intergenic: 57489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92696, rend_intergenic: 91450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92865, rend_intergenic: 92839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95678, rend_intergenic: 92887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98108, rend_intergenic: 97468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146539, rend_intergenic: 98921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169451, rend_intergenic: 149639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173754, rend_intergenic: 173496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178032, rend_intergenic: 177278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187148, rend_intergenic: 187025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198480, rend_intergenic: 190363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212329
-exon list size: 285


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.8    
3.1    
3.5    
3.8    
4.2    
4.5    
4.9    
5.2    
5.6    
5.9    
6.3    
6.6    
7.0    
7.3    
7.7    
8.0    
8.4    
8.7    
9.1    
9.4    
9.8    
10.1    
10.5    
10.8    
11.1    
11.5    
11.8    
12.2    
12.5    
12.9    
13.2    
13.6    
13.9    
14.3    
14.6    
15.0    
15.3    
15.7    
16.0    
16.4    
16.7    
17.1    
17.4    
17.8    
18.1    
18.5    
18.8    
19.2    
19.5    
19.9    
20.2    
20.6    
20.9    
21.3    
21.6    
22.0    
22.3    
22.6    
23.0    
23.3    
23.7    
24.0    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.5    
26.8    
27.2    
27.5    
27.9    
28.2    
28.6    
28.9    
29.3    
29.6    
30.0    
30.3    
30.7    
31.0    
31.4    
31.7    
32.1    
32.4    
32.8    
33.1    
33.4    
33.8    
34.1    
34.5    
34.8    
35.2    
35.5    
35.9    
36.2    
36.6    
36.9    
37.3    
37.6    
38.0    
38.3    
38.7    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.1    
41.5    
41.8    
42.2    
42.5    
42.9    
43.2    
43.6    
43.9    
44.3    
44.6    
44.9    
45.3    
45.6    
46.0    
46.3    
46.7    
47.0    
47.4    
47.7    
48.1    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
51.9    
52.3    
52.6    
53.0    
53.3    
53.7    
54.0    
54.4    
54.7    
55.1    
55.4    
55.7    
56.1    
56.4    
56.8    
57.1    
57.5    
57.8    
58.2    
58.5    
58.9    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.3    
61.7    
62.0    
62.4    
62.7    
63.1    
63.4    
63.8    
64.1    
64.5    
64.8    
65.2    
65.5    
65.9    
66.2    
66.6    
66.9    
67.2    
67.6    
67.9    
68.3    
68.6    
69.0    
69.3    
69.7    
70.0    
70.4    
70.7    
71.1    
71.4    
71.8    
72.1    
72.5    
72.8    
73.2    
73.5    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
76.0    
76.3    
76.7    
77.0    
77.4    
77.7    
78.0    
78.4    
78.7    
79.1    
79.4    
79.8    
80.1    
80.5    
80.8    
81.2    
81.5    
81.9    
82.2    
82.6    
82.9    
83.3    
83.6    
84.0    
84.3    
84.7    
85.0    
85.4    
85.7    
86.1    
86.4    
86.8    
87.1    
87.5    
87.8    
88.2    
88.5    
88.9    
89.2    
89.5    
89.9    
90.2    
90.6    
90.9    
91.3    
91.6    
92.0    
92.3    
92.7    
93.0    
93.4    
93.7    
94.1    
94.4    
94.8    
95.1    
95.5    
95.8    
96.2    
96.5    
96.9    
97.2    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 9930, rend_intergenic: 5091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14138, rend_intergenic: 12140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22255, rend_intergenic: 18364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30486, rend_intergenic: 22937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42341, rend_intergenic: 41932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45595, rend_intergenic: 42940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48717, rend_intergenic: 47354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72112, rend_intergenic: 57489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92696, rend_intergenic: 91450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92865, rend_intergenic: 92839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95678, rend_intergenic: 92887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98108, rend_intergenic: 97468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146539, rend_intergenic: 98921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169451, rend_intergenic: 149639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173754, rend_intergenic: 173496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178032, rend_intergenic: 177278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187148, rend_intergenic: 187025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198480, rend_intergenic: 190363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support