-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_152907-326214

-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_2-snap.36-T1
Valid prediction for snap_scaffold_2-snap.59-T1
Valid prediction for snap_scaffold_2-snap.72-T1
Valid prediction for GlimmerHMM_glimmerT_3018-T1
Valid prediction for snap_scaffold_2-snap.42-T1
Valid prediction for GlimmerHMM_glimmerT_3031-T1
Valid prediction for snap_scaffold_2-snap.61-T1
Valid prediction for snap_scaffold_2-snap.50-T1
Valid prediction for snap_scaffold_2-snap.39-T1
Valid prediction for snap_scaffold_2-snap.53-T1
Valid prediction for CodingQuarry_transcript_28416-T1
Valid prediction for CodingQuarry_transcript_28417-T1
Valid prediction for snap_scaffold_2-snap.57-T1
Valid prediction for snap_scaffold_2-snap.54-T1
Valid prediction for pasa_asmbl_24079.p1
Valid prediction for GlimmerHMM_glimmerT_3016-T1
Valid prediction for snap_scaffold_2-snap.49-T1
Valid prediction for snap_scaffold_2-snap.75-T1
Valid prediction for snap_scaffold_2-snap.70-T1
Valid prediction for GlimmerHMM_glimmerT_3029-T1
Valid prediction for GlimmerHMM_glimmerT_3036-T1
Valid prediction for GlimmerHMM_glimmerT_3034-T1
Valid prediction for snap_scaffold_2-snap.48-T1
Valid prediction for GlimmerHMM_glimmerT_3030-T1
Valid prediction for GlimmerHMM_glimmerT_3026-T1
Valid prediction for GlimmerHMM_glimmerT_3024-T1
Valid prediction for pasa_asmbl_24084.p1
Valid prediction for snap_scaffold_2-snap.55-T1
Valid prediction for GlimmerHMM_glimmerT_3027-T1
Valid prediction for Augustus_model.g2062.t1
Valid prediction for CodingQuarry_transcript_28419-T1
Valid prediction for snap_scaffold_2-snap.68-T1
Valid prediction for snap_scaffold_2-snap.62-T1
Valid prediction for snap_scaffold_2-snap.64-T1
Valid prediction for snap_scaffold_2-snap.46-T1
Valid prediction for HiQ_model.g2060.t1
Valid prediction for snap_scaffold_2-snap.51-T1
Valid prediction for snap_scaffold_2-snap.74-T1
Valid prediction for Augustus_model.g2067.t1
Valid prediction for snap_scaffold_2-snap.65-T1
Valid prediction for snap_scaffold_2-snap.37-T1
Valid prediction for snap_scaffold_2-snap.69-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_2-snap.44-T1
Valid prediction for Augustus_model.g2069.t1
Valid prediction for snap_scaffold_2-snap.58-T1
Valid prediction for CodingQuarry_transcript_28418-T1
Valid prediction for GlimmerHMM_glimmerT_3019-T1
Valid prediction for GlimmerHMM_glimmerT_3032-T1
Valid prediction for snap_scaffold_2-snap.56-T1
Valid prediction for GlimmerHMM_glimmerT_3021-T1
Valid prediction for snap_scaffold_2-snap.38-T1
Valid prediction for pasa_asmbl_22790.p1
Valid prediction for GlimmerHMM_glimmerT_3035-T1
Valid prediction for Augustus_model.g2063.t1
Couldn't classify 18122, 18430
Couldn't classify 18779, 18934
Sorry, prediction pasa_asmbl_22801.p1 fails validation.
(TCT)	 GC	18122-18430	GT	AGG
(GAG)	 AG	18779-18934	GC	GCG
-recovered pasa_asmbl_22801.p1, internal, 18779, 18934
Valid prediction for CodingQuarry_transcript_28420-T1
Valid prediction for snap_scaffold_2-snap.60-T1
Valid prediction for snap_scaffold_2-snap.45-T1
Valid prediction for Augustus_model.g2071.t1
Valid prediction for snap_scaffold_2-snap.41-T1
Valid prediction for snap_scaffold_2-snap.52-T1
Valid prediction for HiQ_model.g2061.t1
Valid prediction for Augustus_model.g2070.t1
Couldn't classify 39732, 39786
Couldn't classify 42925, 42975
Sorry, prediction pasa_asmbl_22797.p1 fails validation.
(TCC)	 AC	39732-39786	GT	AGG
(TGT)	 AG	40177-40280	GT	AGG
(GTG)	 AG	41270-41368	GT	AGG
(TAT)	 AG	42204-42275	GT	AGG
(GTG)	 AG	42925-42975	TC	CCT
-recovered pasa_asmbl_22797.p1, internal, 40177, 40280
-recovered pasa_asmbl_22797.p1, internal, 41270, 41368
-recovered pasa_asmbl_22797.p1, internal, 42204, 42275
Valid prediction for snap_scaffold_2-snap.71-T1
Valid prediction for snap_scaffold_2-snap.67-T1
Valid prediction for pasa_asmbl_22788.p1
Couldn't classify 21278, 21577
Sorry, prediction pasa_asmbl_22800.p1 fails validation.
(ATG)	 TT	21278-21577	GG	CGG
Valid prediction for GlimmerHMM_glimmerT_3033-T1
Valid prediction for snap_scaffold_2-snap.47-T1
Valid prediction for snap_scaffold_2-snap.66-T1
Valid prediction for GlimmerHMM_glimmerT_3025-T1
Valid prediction for GlimmerHMM_glimmerT_3017-T1
Valid prediction for Augustus_model.g2068.t1
Valid prediction for Augustus_model.g2065.t1
Valid prediction for snap_scaffold_2-snap.63-T1
Valid prediction for Augustus_model.g2066.t1
Valid prediction for GlimmerHMM_glimmerT_3020-T1
Valid prediction for snap_scaffold_2-snap.40-T1
Valid prediction for snap_scaffold_2-snap.43-T1
Valid prediction for GlimmerHMM_glimmerT_3023-T1
Valid prediction for GlimmerHMM_glimmerT_3028-T1
Valid prediction for GlimmerHMM_glimmerT_3022-T1
Valid prediction for HiQ_model.g2064.t1
Valid prediction for GlimmerHMM_glimmerT_3037-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17751, rend_intergenic: 10304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31809, rend_intergenic: 28905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61065, rend_intergenic: 42154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63190, rend_intergenic: 61501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84581, rend_intergenic: 63810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87919, rend_intergenic: 86559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90330, rend_intergenic: 89227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102336, rend_intergenic: 96849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125312, rend_intergenic: 117943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145024, rend_intergenic: 127991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158703, rend_intergenic: 147638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173308
-exon list size: 355


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.2    
2.5    
2.8    
3.1    
3.4    
3.6    
3.9    
4.2    
4.5    
4.8    
5.0    
5.3    
5.6    
5.9    
6.2    
6.4    
6.7    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.1    
10.4    
10.6    
10.9    
11.2    
11.5    
11.8    
12.0    
12.3    
12.6    
12.9    
13.2    
13.4    
13.7    
14.0    
14.3    
14.6    
14.8    
15.1    
15.4    
15.7    
16.0    
16.2    
16.5    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.3    
21.6    
21.8    
22.1    
22.4    
22.7    
23.0    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
30.0    
30.3    
30.5    
30.8    
31.1    
31.4    
31.7    
31.9    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.6    
35.9    
36.1    
36.4    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.4    
38.7    
38.9    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.2    
41.5    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.5    
44.8    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.2    
55.5    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.5    
58.8    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.1    
61.3    
61.6    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.6    
63.9    
64.1    
64.4    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.1    
68.3    
68.6    
68.9    
69.2    
69.5    
69.7    
70.0    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.0    
77.3    
77.6    
77.9    
78.2    
78.4    
78.7    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.5    
83.8    
84.0    
84.3    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.7    
88.0    
88.2    
88.5    
88.8    
89.1    
89.4    
89.6    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.3    
93.6    
93.8    
94.1    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.1    
96.4    
96.6    
96.9    
97.2    
97.5    
97.8    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 17751, rend_intergenic: 10304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31809, rend_intergenic: 28905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61065, rend_intergenic: 42154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63190, rend_intergenic: 61501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84581, rend_intergenic: 63810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87919, rend_intergenic: 86559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90330, rend_intergenic: 89227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102336, rend_intergenic: 96849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125312, rend_intergenic: 117943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145024, rend_intergenic: 127991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158703, rend_intergenic: 147638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support