-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_3283462-3496739

-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_19-snap.707-T1
Valid prediction for GlimmerHMM_glimmerT_43847-T1
Valid prediction for Augustus_model.g29096.t1
Valid prediction for Augustus_model.g29094.t1
Valid prediction for GlimmerHMM_glimmerT_43834-T1
Valid prediction for snap_scaffold_19-snap.698-T1
Valid prediction for snap_scaffold_19-snap.711-T1
Valid prediction for GlimmerHMM_glimmerT_43842-T1
Valid prediction for CodingQuarry_transcript_25625-T1
Valid prediction for GlimmerHMM_glimmerT_43856-T1
Valid prediction for snap_scaffold_19-snap.699-T1
Valid prediction for snap_scaffold_19-snap.725-T1
Valid prediction for GlimmerHMM_glimmerT_43857-T1
Valid prediction for snap_scaffold_19-snap.690-T1
Valid prediction for GlimmerHMM_glimmerT_43838-T1
Valid prediction for snap_scaffold_19-snap.696-T1
Valid prediction for Augustus_model.g29098.t1
Valid prediction for GlimmerHMM_glimmerT_43843-T1
Valid prediction for snap_scaffold_19-snap.700-T1
Valid prediction for snap_scaffold_19-snap.694-T1
Valid prediction for pasa_asmbl_21318.p1
Valid prediction for Augustus_model.g29099.t1
Valid prediction for GlimmerHMM_glimmerT_43845-T1
Valid prediction for snap_scaffold_19-snap.703-T1
Valid prediction for snap_scaffold_19-snap.713-T1
Valid prediction for snap_scaffold_19-snap.717-T1
Valid prediction for GlimmerHMM_glimmerT_43846-T1
Valid prediction for snap_scaffold_19-snap.721-T1
Valid prediction for GlimmerHMM_glimmerT_43836-T1
Valid prediction for snap_scaffold_19-snap.702-T1
Valid prediction for snap_scaffold_19-snap.714-T1
Valid prediction for snap_scaffold_19-snap.724-T1
Valid prediction for Augustus_model.g29097.t1
Valid prediction for snap_scaffold_19-snap.710-T1
Valid prediction for HiQ_model.g29104.t1
Valid prediction for snap_scaffold_19-snap.704-T1
Valid prediction for GlimmerHMM_glimmerT_43853-T1
Valid prediction for GlimmerHMM_glimmerT_43833-T1
Valid prediction for snap_scaffold_19-snap.688-T1
Valid prediction for GlimmerHMM_glimmerT_43861-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 pasa_asmbl_22695.p1
Valid prediction for snap_scaffold_19-snap.726-T1
Valid prediction for HiQ_model.g29103.t1
Valid prediction for snap_scaffold_19-snap.718-T1
Valid prediction for GlimmerHMM_glimmerT_43841-T1
Couldn't classify 186432, 186655
Sorry, prediction pasa_asmbl_22101.p1 fails validation.
(ATG)	 CC	182161-182353	GT	AGG
(GTT)	 AG	183217-183376	GT	GAG
(GCG)	 AG	184976-185166	GT	AGG
(TGG)	 AG	185615-185711	GT	AGG
(GTA)	 AG	185854-185990	GT	GGG
(GTG)	 AG	186432-186655	AA	CCA
-recovered pasa_asmbl_22101.p1, initial, 182161, 182353
-recovered pasa_asmbl_22101.p1, internal, 183217, 183376
-recovered pasa_asmbl_22101.p1, internal, 184976, 185166
-recovered pasa_asmbl_22101.p1, internal, 185615, 185711
-recovered pasa_asmbl_22101.p1, internal, 185854, 185990
Valid prediction for Augustus_model.g29091.t1
Valid prediction for GlimmerHMM_glimmerT_43837-T1
Valid prediction for Augustus_model.g29100.t1
Valid prediction for GlimmerHMM_glimmerT_43844-T1
Valid prediction for snap_scaffold_19-snap.709-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g29089.t1
Valid prediction for snap_scaffold_19-snap.715-T1
Valid prediction for GlimmerHMM_glimmerT_43839-T1
Valid prediction for CodingQuarry_transcript_25623-T1
Couldn't classify 195919, 196090
Sorry, prediction pasa_asmbl_22097.p1 fails validation.
(GTG)	 AC	195919-196090	GT	GGG
(GAG)	 AG	196458-196539	GT	TTG
(TTG)	 AG	196853-197011	GT	AGG
(CAC)	 AG	197118-197277	GT	AGG
(GGC)	 AG	197655-197894	GT	GAG
-recovered pasa_asmbl_22097.p1, terminal, 197655, 197894
-recovered pasa_asmbl_22097.p1, internal, 196458, 196539
-recovered pasa_asmbl_22097.p1, internal, 196853, 197011
-recovered pasa_asmbl_22097.p1, internal, 197118, 197277
-recovered pasa_asmbl_22097.p1, internal, 197655, 197894
Valid prediction for GlimmerHMM_glimmerT_43840-T1
Valid prediction for GlimmerHMM_glimmerT_43852-T1
Valid prediction for snap_scaffold_19-snap.723-T1
Valid prediction for GlimmerHMM_glimmerT_43854-T1
Valid prediction for snap_scaffold_19-snap.720-T1
Valid prediction for snap_scaffold_19-snap.695-T1
Valid prediction for snap_scaffold_19-snap.722-T1
Valid prediction for Augustus_model.g29092.t1
Valid prediction for snap_scaffold_19-snap.719-T1
Couldn't classify 194448, 194559
Couldn't classify 195236, 195391
Sorry, prediction pasa_asmbl_22706.p1 fails validation.
(TTA)	 GA	194448-194559	GT	AGG
(GAG)	 AG	194771-194949	GT	TCG
(GCC)	 AG	195236-195391	GC	TGG
-recovered pasa_asmbl_22706.p1, internal, 194771, 194949
-recovered pasa_asmbl_22706.p1, internal, 195236, 195391
Valid prediction for snap_scaffold_19-snap.708-T1
Valid prediction for GlimmerHMM_glimmerT_43858-T1
Valid prediction for snap_scaffold_19-snap.689-T1
Valid prediction for snap_scaffold_19-snap.705-T1
Valid prediction for snap_scaffold_19-snap.692-T1
Valid prediction for snap_scaffold_19-snap.716-T1
Valid prediction for CodingQuarry_transcript_25624-T1
Valid prediction for GlimmerHMM_glimmerT_43850-T1
Valid prediction for Augustus_model.g29093.t1
Valid prediction for snap_scaffold_19-snap.701-T1
Valid prediction for GlimmerHMM_glimmerT_43848-T1
Valid prediction for Augustus_model.g29102.t1
Valid prediction for Augustus_model.g29101.t1
Valid prediction for Augustus_model.g29095.t1
Valid prediction for snap_scaffold_19-snap.691-T1
Valid prediction for snap_scaffold_19-snap.712-T1
Valid prediction for GlimmerHMM_glimmerT_43860-T1
Valid prediction for snap_scaffold_19-snap.693-T1
Couldn't classify 186722, 187114
Sorry, prediction pasa_asmbl_22099.p1 fails validation.
(CGC)	 AC	186722-187114	GC	GAG
Valid prediction for pasa_asmbl_22108.p1
Valid prediction for snap_scaffold_19-snap.697-T1
Valid prediction for GlimmerHMM_glimmerT_43855-T1
Valid prediction for GlimmerHMM_glimmerT_43849-T1
Valid prediction for GlimmerHMM_glimmerT_43835-T1
Valid prediction for GlimmerHMM_glimmerT_43859-T1
Valid prediction for GlimmerHMM_glimmerT_43851-T1
Valid prediction for snap_scaffold_19-snap.706-T1
Valid prediction for HiQ_model.g29090.t1
Couldn't classify 71698, 71808
Couldn't classify 73566, 73747
Sorry, prediction pasa_asmbl_22105.p1 fails validation.
(TTA)	 AG	71698-71808	GT	TGG
(GAT)	 AG	73207-73294	GT	GGG
(ACT)	 AG	73566-73747	AG	ACA
-recovered pasa_asmbl_22105.p1, internal, 71698, 71808
-recovered pasa_asmbl_22105.p1, internal, 73207, 73294

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31118, rend_intergenic: 28599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35490, rend_intergenic: 34084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35710, rend_intergenic: 35548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42261, rend_intergenic: 35735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69255, rend_intergenic: 48345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88962, rend_intergenic: 69488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94104, rend_intergenic: 90094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113001, rend_intergenic: 94276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118605, rend_intergenic: 113063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129366, rend_intergenic: 127547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150429, rend_intergenic: 129953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160441, rend_intergenic: 150611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170205, rend_intergenic: 166937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187073, rend_intergenic: 170449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200491, rend_intergenic: 190863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206019, rend_intergenic: 203630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211056, rend_intergenic: 207784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213278
-exon list size: 338


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 31118, rend_intergenic: 28599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35490, rend_intergenic: 34084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35710, rend_intergenic: 35548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42261, rend_intergenic: 35735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69255, rend_intergenic: 48345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88962, rend_intergenic: 69488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94104, rend_intergenic: 90094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113001, rend_intergenic: 94276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118605, rend_intergenic: 113063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129366, rend_intergenic: 127547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150429, rend_intergenic: 129953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160441, rend_intergenic: 150611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170205, rend_intergenic: 166937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187073, rend_intergenic: 170449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200491, rend_intergenic: 190863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206019, rend_intergenic: 203630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211056, rend_intergenic: 207784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support