-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_2816737-2995102

-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_20-snap.624-T1
Valid prediction for GlimmerHMM_glimmerT_45648-T1
Valid prediction for snap_scaffold_20-snap.598-T1
Valid prediction for GlimmerHMM_glimmerT_45668-T1
Valid prediction for Augustus_model.g30343.t1
Valid prediction for snap_scaffold_20-snap.604-T1
Couldn't classify 62224, 62637
Sorry, prediction pasa_asmbl_26510.p1 fails validation.
(AGC)	 CC	62224-62637	GA	AAG
Valid prediction for GlimmerHMM_glimmerT_45661-T1
Valid prediction for GlimmerHMM_glimmerT_45660-T1
Valid prediction for snap_scaffold_20-snap.632-T1
Valid prediction for GlimmerHMM_glimmerT_45656-T1
Valid prediction for Augustus_model.g30336.t1
Valid prediction for Augustus_model.g30334.t1
Valid prediction for snap_scaffold_20-snap.619-T1
Couldn't classify 60635, 60682
Couldn't classify 61699, 61977
Sorry, prediction pasa_asmbl_27158.p1 fails validation.
(TCC)	 CC	60635-60682	GT	AGG
(TCA)	 AG	61699-61977	GG	TCG
Valid prediction for GlimmerHMM_glimmerT_45649-T1
Couldn't classify 86742, 86886
Couldn't classify 88956, 89497
Sorry, prediction pasa_asmbl_26511.p1 fails validation.
(CCT)	 TC	86742-86886	GT	AGG
(GCG)	 AG	88956-89497	CA	ACC
Valid prediction for snap_scaffold_20-snap.609-T1
Valid prediction for snap_scaffold_20-snap.628-T1
Valid prediction for snap_scaffold_20-snap.623-T1
Valid prediction for snap_scaffold_20-snap.600-T1
Valid prediction for snap_scaffold_20-snap.601-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.625-T1
Valid prediction for GlimmerHMM_glimmerT_45673-T1
Valid prediction for snap_scaffold_20-snap.608-T1
Valid prediction for snap_scaffold_20-snap.620-T1
Valid prediction for Augustus_model.g30327.t1
Valid prediction for GlimmerHMM_glimmerT_45658-T1
Valid prediction for Augustus_model.g30328.t1
Valid prediction for snap_scaffold_20-snap.634-T1
Valid prediction for Augustus_model.g30326.t1
Valid prediction for snap_scaffold_20-snap.630-T1
Valid prediction for Augustus_model.g30335.t1
Valid prediction for GlimmerHMM_glimmerT_45650-T1
Valid prediction for GlimmerHMM_glimmerT_45669-T1
Valid prediction for snap_scaffold_20-snap.611-T1
Valid prediction for snap_scaffold_20-snap.626-T1
Valid prediction for snap_scaffold_20-snap.616-T1
Valid prediction for Augustus_model.g30325.t1
Valid prediction for CodingQuarry_transcript_30465-T1
Couldn't classify 47429, 47830
Sorry, prediction pasa_asmbl_26509.p1 fails validation.
(GAC)	 TA	47429-47830	GA	ACG
Valid prediction for GlimmerHMM_glimmerT_45651-T1
Valid prediction for GlimmerHMM_glimmerT_45672-T1
Valid prediction for Augustus_model.g30333.t1
Valid prediction for snap_scaffold_20-snap.633-T1
Valid prediction for snap_scaffold_20-snap.602-T1
Valid prediction for GlimmerHMM_glimmerT_45662-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_20-snap.627-T1
Valid prediction for snap_scaffold_20-snap.621-T1
Valid prediction for GlimmerHMM_glimmerT_45653-T1
Valid prediction for HiQ_model.g30332.t1
Valid prediction for HiQ_model.g30329.t1
Valid prediction for pasa_asmbl_25682.p1
Valid prediction for GlimmerHMM_glimmerT_45652-T1
Valid prediction for snap_scaffold_20-snap.599-T1
Valid prediction for CodingQuarry_transcript_30467-T1
Valid prediction for GlimmerHMM_glimmerT_45670-T1
Valid prediction for pasa_asmbl_25677.p1
Valid prediction for GlimmerHMM_glimmerT_45665-T1
Valid prediction for snap_scaffold_20-snap.617-T1
Valid prediction for Augustus_model.g30338.t1
Valid prediction for GlimmerHMM_glimmerT_45659-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.622-T1
Valid prediction for snap_scaffold_20-snap.595-T1
Valid prediction for snap_scaffold_20-snap.605-T1
Valid prediction for snap_scaffold_20-snap.613-T1
Valid prediction for snap_scaffold_20-snap.635-T1
Valid prediction for snap_scaffold_20-snap.629-T1
Valid prediction for snap_scaffold_20-snap.612-T1
Valid prediction for GlimmerHMM_glimmerT_45667-T1
Valid prediction for GlimmerHMM_glimmerT_45664-T1
Valid prediction for snap_scaffold_20-snap.597-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g30342.t1
Valid prediction for Augustus_model.g30339.t1
Valid prediction for Augustus_model.g30330.t1
Couldn't classify 69272, 69303
Couldn't classify 70408, 70875
Sorry, prediction pasa_asmbl_25684.p1 fails validation.
(TTC)	 AC	69272-69303	GT	CGG
(GTT)	 AG	69877-70159	GT	AGG
(TCT)	 AG	70408-70875	AT	ACA
-recovered pasa_asmbl_25684.p1, internal, 69877, 70159
Valid prediction for pasa_asmbl_25679.p1
Valid prediction for GlimmerHMM_glimmerT_45654-T1
Valid prediction for GlimmerHMM_glimmerT_45671-T1
Valid prediction for snap_scaffold_20-snap.610-T1
Valid prediction for snap_scaffold_20-snap.614-T1
Valid prediction for snap_scaffold_20-snap.607-T1
Valid prediction for snap_scaffold_20-snap.615-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.618-T1
Valid prediction for snap_scaffold_20-snap.603-T1
Valid prediction for GlimmerHMM_glimmerT_45663-T1
Valid prediction for CodingQuarry_transcript_30468-T1
Valid prediction for GlimmerHMM_glimmerT_45655-T1
Valid prediction for Augustus_model.g30341.t1
Valid prediction for snap_scaffold_20-snap.596-T1
Valid prediction for Augustus_model.g30331.t1
Couldn't classify 36591, 36682
Sorry, prediction pasa_asmbl_25687.p1 fails validation.
(ATG)	 AG	29211-29243	GT	GCG
(AAC)	 AG	29812-29942	GT	CGG
(AGG)	 AG	30450-30603	GT	AGG
(GCG)	 AG	30957-31043	GT	AGG
(GGG)	 AG	31724-31862	GT	GGG
(GTA)	 AG	33103-33219	GT	GGG
(GTC)	 AG	33676-33787	GT	AGG
(CAC)	 AG	34575-34719	GT	AGG
(GAA)	 AG	35506-35719	GT	GGG
(GAG)	 AG	36591-36682	GN	AAG
-recovered pasa_asmbl_25687.p1, initial, 29211, 29243
-recovered pasa_asmbl_25687.p1, internal, 29211, 29243
-recovered pasa_asmbl_25687.p1, internal, 29812, 29942
-recovered pasa_asmbl_25687.p1, internal, 30450, 30603
-recovered pasa_asmbl_25687.p1, internal, 30957, 31043
-recovered pasa_asmbl_25687.p1, internal, 31724, 31862
-recovered pasa_asmbl_25687.p1, internal, 33103, 33219
-recovered pasa_asmbl_25687.p1, internal, 33676, 33787
-recovered pasa_asmbl_25687.p1, internal, 34575, 34719
-recovered pasa_asmbl_25687.p1, internal, 35506, 35719
Valid prediction for snap_scaffold_20-snap.631-T1
Valid prediction for GlimmerHMM_glimmerT_45666-T1
Valid prediction for CodingQuarry_transcript_30466-T1
Valid prediction for Augustus_model.g30337.t1
Valid prediction for HiQ_model.g30340.t1
Valid prediction for GlimmerHMM_glimmerT_45657-T1
Valid prediction for snap_scaffold_20-snap.606-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19292, rend_intergenic: 16420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19993, rend_intergenic: 19751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24433, rend_intergenic: 20431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26626, rend_intergenic: 25229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62637, rend_intergenic: 51786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89503, rend_intergenic: 63762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91232, rend_intergenic: 89576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98518, rend_intergenic: 91419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105018, rend_intergenic: 98955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107798, rend_intergenic: 105130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136803, rend_intergenic: 107989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137459, rend_intergenic: 137358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144984, rend_intergenic: 140020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148693, rend_intergenic: 145008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159323, rend_intergenic: 153139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170975, rend_intergenic: 162552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178366
-exon list size: 405


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.2    
4.4    
4.7    
4.9    
5.2    
5.4    
5.7    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.6    
8.8    
9.1    
9.3    
9.6    
9.8    
10.1    
10.3    
10.6    
10.8    
11.1    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.8    
13.0    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.7    
15.0    
15.2    
15.5    
15.7    
16.0    
16.2    
16.5    
16.7    
17.0    
17.2    
17.4    
17.7    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.3    
23.6    
23.8    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.8    
28.0    
28.3    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.4    
31.7    
31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.5    
54.8    
55.0    
55.3    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
62.9    
63.1    
63.4    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.1    
68.3    
68.6    
68.8    
69.0    
69.3    
69.5    
69.8    
70.0    
70.3    
70.5    
70.8    
71.0    
71.3    
71.5    
71.7    
72.0    
72.2    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.4    
76.7    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.0    
83.3    
83.5    
83.8    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 19292, rend_intergenic: 16420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19993, rend_intergenic: 19751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24433, rend_intergenic: 20431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26626, rend_intergenic: 25229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62637, rend_intergenic: 51786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89503, rend_intergenic: 63762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91232, rend_intergenic: 89576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98518, rend_intergenic: 91419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105018, rend_intergenic: 98955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107798, rend_intergenic: 105130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136803, rend_intergenic: 107989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137459, rend_intergenic: 137358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144984, rend_intergenic: 140020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148693, rend_intergenic: 145008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159323, rend_intergenic: 153139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170975, rend_intergenic: 162552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support