-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_3178449-3374371

-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 Augustus_model.g25390.t1
Valid prediction for snap_scaffold_16-snap.613-T1
Valid prediction for GlimmerHMM_glimmerT_38063-T1
Valid prediction for snap_scaffold_16-snap.596-T1
Valid prediction for GlimmerHMM_glimmerT_38060-T1
Valid prediction for snap_scaffold_16-snap.627-T1
Valid prediction for CodingQuarry_transcript_19918-T1
Valid prediction for GlimmerHMM_glimmerT_38058-T1
Valid prediction for snap_scaffold_16-snap.608-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.599-T1
Valid prediction for GlimmerHMM_glimmerT_38070-T1
Valid prediction for Augustus_model.g25385.t1
Valid prediction for snap_scaffold_16-snap.614-T1
Valid prediction for GlimmerHMM_glimmerT_38056-T1
Valid prediction for snap_scaffold_16-snap.607-T1
Valid prediction for Augustus_model.g25392.t1
Valid prediction for Augustus_model.g25396.t1
Valid prediction for snap_scaffold_16-snap.595-T1
Valid prediction for snap_scaffold_16-snap.592-T1
Valid prediction for snap_scaffold_16-snap.593-T1
Valid prediction for Augustus_model.g25391.t1
Valid prediction for GlimmerHMM_glimmerT_38077-T1
Valid prediction for snap_scaffold_16-snap.615-T1
Valid prediction for snap_scaffold_16-snap.617-T1
Valid prediction for snap_scaffold_16-snap.628-T1
Couldn't classify 108906, 109094
Sorry, prediction pasa_asmbl_16141.p1 fails validation.
(ATG)	 CC	106705-107018	GT	GAG
(GGA)	 AG	107111-107176	GT	CAG
(GAG)	 AG	107377-107551	GT	AGG
(GAG)	 AG	107919-107998	GT	GAG
(TTA)	 AG	108128-108246	GT	AGG
(ATC)	 AG	108395-108477	GT	AGG
(ATC)	 AG	108906-109094	CA	AGC
-recovered pasa_asmbl_16141.p1, initial, 106705, 107018
add_exon() Sorry, pasa_asmbl_16141.p1 107919-107998-terminal-2 is invalid.
-recovered pasa_asmbl_16141.p1, terminal, 107919, 107998
-recovered pasa_asmbl_16141.p1, internal, 107111, 107176
-recovered pasa_asmbl_16141.p1, internal, 107377, 107551
-recovered pasa_asmbl_16141.p1, internal, 107919, 107998
-recovered pasa_asmbl_16141.p1, internal, 108128, 108246
-recovered pasa_asmbl_16141.p1, internal, 108395, 108477
Valid prediction for GlimmerHMM_glimmerT_38054-T1
Valid prediction for snap_scaffold_16-snap.604-T1
Valid prediction for snap_scaffold_16-snap.590-T1
Valid prediction for GlimmerHMM_glimmerT_38074-T1
Valid prediction for snap_scaffold_16-snap.624-T1
Valid prediction for GlimmerHMM_glimmerT_38067-T1
Valid prediction for snap_scaffold_16-snap.630-T1
Valid prediction for Augustus_model.g25398.t1
Valid prediction for Augustus_model.g25383.t1
Valid prediction for GlimmerHMM_glimmerT_38072-T1
Valid prediction for snap_scaffold_16-snap.619-T1
Valid prediction for GlimmerHMM_glimmerT_38053-T1
Valid prediction for Augustus_model.g25394.t1
Valid prediction for snap_scaffold_16-snap.623-T1
Valid prediction for snap_scaffold_16-snap.597-T1
Valid prediction for snap_scaffold_16-snap.618-T1
Valid prediction for snap_scaffold_16-snap.601-T1
Valid prediction for GlimmerHMM_glimmerT_38066-T1
Valid prediction for snap_scaffold_16-snap.609-T1
Valid prediction for HiQ_model.g25387.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_38068-T1
Valid prediction for snap_scaffold_16-snap.606-T1
Valid prediction for Augustus_model.g25386.t1
Valid prediction for snap_scaffold_16-snap.594-T1
Valid prediction for GlimmerHMM_glimmerT_38055-T1
Valid prediction for snap_scaffold_16-snap.631-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g25382.t1
Valid prediction for GlimmerHMM_glimmerT_38075-T1
Valid prediction for Augustus_model.g25384.t1
Valid prediction for GlimmerHMM_glimmerT_38071-T1
Valid prediction for GlimmerHMM_glimmerT_38076-T1
Valid prediction for snap_scaffold_16-snap.591-T1
Valid prediction for Augustus_model.g25388.t1
Valid prediction for GlimmerHMM_glimmerT_38057-T1
Couldn't classify 70586, 70680
Sorry, prediction pasa_asmbl_16981.p1 fails validation.
(GAA)	 TG	70586-70680	GT	CGG
(CTC)	 AG	70823-70914	GT	AGG
(CCC)	 AG	71772-71951	GT	AGG
(GTT)	 AG	72274-72372	GT	AGG
(GTC)	 AG	72861-72953	GT	AGG
(GAT)	 AG	73094-73250	GT	AGG
(GTT)	 AG	73370-73485	GT	CGG
(GCC)	 AG	73706-73782	GG	GAG
-recovered pasa_asmbl_16981.p1, terminal, 73706, 73782
-recovered pasa_asmbl_16981.p1, internal, 70823, 70914
-recovered pasa_asmbl_16981.p1, internal, 71772, 71951
-recovered pasa_asmbl_16981.p1, internal, 72274, 72372
-recovered pasa_asmbl_16981.p1, internal, 72861, 72953
-recovered pasa_asmbl_16981.p1, internal, 73094, 73250
-recovered pasa_asmbl_16981.p1, internal, 73370, 73485
Valid prediction for snap_scaffold_16-snap.632-T1
Valid prediction for snap_scaffold_16-snap.610-T1
Valid prediction for snap_scaffold_16-snap.616-T1
Valid prediction for GlimmerHMM_glimmerT_38062-T1
Valid prediction for GlimmerHMM_glimmerT_38059-T1
Valid prediction for snap_scaffold_16-snap.622-T1
Valid prediction for snap_scaffold_16-snap.611-T1
Valid prediction for snap_scaffold_16-snap.605-T1
Valid prediction for snap_scaffold_16-snap.598-T1
Valid prediction for snap_scaffold_16-snap.626-T1
Valid prediction for snap_scaffold_16-snap.589-T1
Valid prediction for snap_scaffold_16-snap.602-T1
Valid prediction for GlimmerHMM_glimmerT_38065-T1
Valid prediction for snap_scaffold_16-snap.588-T1
Valid prediction for Augustus_model.g25389.t1
Valid prediction for Augustus_model.g25395.t1
Valid prediction for snap_scaffold_16-snap.625-T1
Valid prediction for snap_scaffold_16-snap.621-T1
Valid prediction for snap_scaffold_16-snap.603-T1
Valid prediction for GlimmerHMM_glimmerT_38061-T1
Valid prediction for GlimmerHMM_glimmerT_38064-T1
Valid prediction for snap_scaffold_16-snap.600-T1
Valid prediction for snap_scaffold_16-snap.620-T1
Valid prediction for snap_scaffold_16-snap.612-T1
Valid prediction for GlimmerHMM_glimmerT_38073-T1
Valid prediction for GlimmerHMM_glimmerT_38069-T1
Valid prediction for Augustus_model.g25393.t1
Valid prediction for Augustus_model.g25381.t1
Valid prediction for Augustus_model.g25397.t1
Valid prediction for snap_scaffold_16-snap.629-T1
Sorry, intron length (7) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18943, rend_intergenic: 13432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55397, rend_intergenic: 26407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69313, rend_intergenic: 56171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102002, rend_intergenic: 100480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117837, rend_intergenic: 106112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126742, rend_intergenic: 124904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137026, rend_intergenic: 134256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146302, rend_intergenic: 140851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157695, rend_intergenic: 149694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170104, rend_intergenic: 158667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174091, rend_intergenic: 170695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179429, rend_intergenic: 175938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181137, rend_intergenic: 179991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190054, rend_intergenic: 181432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195923
-exon list size: 408


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.4    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.1    
4.4    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.8    
8.0    
8.3    
8.5    
8.8    
9.0    
9.3    
9.5    
9.8    
10.0    
10.2    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.7    
22.0    
22.2    
22.4    
22.7    
22.9    
23.2    
23.4    
23.7    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.0    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.3    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.5    
69.8    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.7    
72.0    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 18943, rend_intergenic: 13432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55397, rend_intergenic: 26407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69313, rend_intergenic: 56171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102002, rend_intergenic: 100480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117837, rend_intergenic: 106112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126742, rend_intergenic: 124904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137026, rend_intergenic: 134256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146302, rend_intergenic: 140851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157695, rend_intergenic: 149694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170104, rend_intergenic: 158667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174091, rend_intergenic: 170695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179429, rend_intergenic: 175938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181137, rend_intergenic: 179991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190054, rend_intergenic: 181432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support