-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_8069027-8222933

-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 GlimmerHMM_glimmerT_54622-T1
Valid prediction for snap_scaffold_25-snap.1756-T1
Valid prediction for snap_scaffold_25-snap.1775-T1
Valid prediction for Augustus_model.g36226.t1
Valid prediction for snap_scaffold_25-snap.1757-T1
Couldn't classify 44205, 44297
Couldn't classify 44841, 45084
Sorry, prediction pasa_asmbl_33724.p1 fails validation.
(GGC)	 AC	44205-44297	GT	TGG
(GTG)	 AG	44647-44723	GT	CCG
(GGC)	 AG	44841-45084	TG	ACT
-recovered pasa_asmbl_33724.p1, internal, 44647, 44723
Valid prediction for GlimmerHMM_glimmerT_54614-T1
Valid prediction for snap_scaffold_25-snap.1786-T1
Valid prediction for snap_scaffold_25-snap.1768-T1
Valid prediction for snap_scaffold_25-snap.1773-T1
Valid prediction for Augustus_model.g36227.t1
Valid prediction for Augustus_model.g36239.t1
Valid prediction for snap_scaffold_25-snap.1778-T1
Valid prediction for snap_scaffold_25-snap.1755-T1
Couldn't classify 45824, 45977
Sorry, prediction pasa_asmbl_33726.p1 fails validation.
(CAG)	 TC	45824-45977	GT	CGG
(GCA)	 AG	46111-46187	GT	AGG
(TCC)	 AG	46692-46799	GA	GAG
-recovered pasa_asmbl_33726.p1, terminal, 46692, 46799
-recovered pasa_asmbl_33726.p1, internal, 46111, 46187
Valid prediction for GlimmerHMM_glimmerT_54627-T1
Valid prediction for GlimmerHMM_glimmerT_54612-T1
Valid prediction for Augustus_model.g36236.t1
Valid prediction for snap_scaffold_25-snap.1759-T1
Valid prediction for Augustus_model.g36225.t1
Valid prediction for Augustus_model.g36237.t1
Valid prediction for snap_scaffold_25-snap.1782-T1
Valid prediction for GlimmerHMM_glimmerT_54626-T1
Valid prediction for Augustus_model.g36240.t1
Valid prediction for snap_scaffold_25-snap.1783-T1
Valid prediction for Augustus_model.g36230.t1
Valid prediction for snap_scaffold_25-snap.1788-T1
Valid prediction for GlimmerHMM_glimmerT_54623-T1
Valid prediction for GlimmerHMM_glimmerT_54631-T1
Valid prediction for GlimmerHMM_glimmerT_54630-T1
Valid prediction for GlimmerHMM_glimmerT_54632-T1
Valid prediction for snap_scaffold_25-snap.1780-T1
Valid prediction for snap_scaffold_25-snap.1764-T1
Valid prediction for CodingQuarry_transcript_38803-T1
Valid prediction for snap_scaffold_25-snap.1784-T1
Valid prediction for GlimmerHMM_glimmerT_54619-T1
Valid prediction for snap_scaffold_25-snap.1767-T1
Valid prediction for snap_scaffold_25-snap.1762-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_25-snap.1771-T1
Valid prediction for snap_scaffold_25-snap.1760-T1
Valid prediction for GlimmerHMM_glimmerT_54613-T1
Valid prediction for snap_scaffold_25-snap.1776-T1
Valid prediction for Augustus_model.g36231.t1
Valid prediction for GlimmerHMM_glimmerT_54616-T1
Valid prediction for Augustus_model.g36229.t1
Valid prediction for GlimmerHMM_glimmerT_54629-T1
Valid prediction for snap_scaffold_25-snap.1766-T1
Couldn't classify 44250, 44393
Sorry, prediction pasa_asmbl_34563.p1 fails validation.
(AGT)	 AC	44250-44393	GT	AGG
(GCT)	 AG	44595-44676	GT	TGG
(AGG)	 AG	44966-45108	AT	AAA
-recovered pasa_asmbl_34563.p1, terminal, 44966, 45108
-recovered pasa_asmbl_34563.p1, internal, 44595, 44676
Valid prediction for snap_scaffold_25-snap.1787-T1
Valid prediction for snap_scaffold_25-snap.1765-T1
Valid prediction for GlimmerHMM_glimmerT_54625-T1
Couldn't classify 46994, 47437
Sorry, prediction pasa_asmbl_34423.p2 fails validation.
(GTT)	 CT	46994-47437	GG	GAG
Valid prediction for CodingQuarry_transcript_38804-T1
Valid prediction for GlimmerHMM_glimmerT_54620-T1
Valid prediction for snap_scaffold_25-snap.1781-T1
Valid prediction for snap_scaffold_25-snap.1770-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for HiQ_model.g36232.t1
Valid prediction for snap_scaffold_25-snap.1769-T1
Valid prediction for Augustus_model.g36234.t1
Couldn't classify 101764, 102012
Couldn't classify 102732, 102848
Sorry, prediction pasa_asmbl_34574.p1 fails validation.
(GCG)	 GG	101764-102012	GT	TGG
(AAC)	 AG	102101-102348	GT	AGG
(GCA)	 AG	102441-102588	GT	AGG
(ATC)	 AG	102732-102848	AG	AGA
-recovered pasa_asmbl_34574.p1, internal, 102101, 102348
-recovered pasa_asmbl_34574.p1, internal, 102441, 102588
Valid prediction for snap_scaffold_25-snap.1772-T1
Valid prediction for Augustus_model.g36235.t1
Valid prediction for GlimmerHMM_glimmerT_54618-T1
Valid prediction for snap_scaffold_25-snap.1758-T1
Couldn't classify 60142, 60255
Sorry, prediction pasa_asmbl_34421.p1 fails validation.
(CCG)	 GG	60142-60255	GT	TCG
(ATC)	 AG	60547-60809	GT	AGG
(GCT)	 AG	61115-61172	GT	CGG
(CTC)	 AG	62601-62777	GT	ACG
(GTG)	 AG	63284-63433	CA	GAC
-recovered pasa_asmbl_34421.p1, terminal, 63284, 63433
-recovered pasa_asmbl_34421.p1, internal, 60547, 60809
-recovered pasa_asmbl_34421.p1, internal, 61115, 61172
-recovered pasa_asmbl_34421.p1, internal, 62601, 62777
Valid prediction for Augustus_model.g36233.t1
Valid prediction for GlimmerHMM_glimmerT_54617-T1
Valid prediction for GlimmerHMM_glimmerT_54624-T1
Valid prediction for Augustus_model.g36238.t1
Valid prediction for GlimmerHMM_glimmerT_54621-T1
Valid prediction for snap_scaffold_25-snap.1761-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1777-T1
Valid prediction for snap_scaffold_25-snap.1779-T1
Valid prediction for snap_scaffold_25-snap.1763-T1
Valid prediction for snap_scaffold_25-snap.1754-T1
Valid prediction for GlimmerHMM_glimmerT_54615-T1
Valid prediction for snap_scaffold_25-snap.1785-T1
Couldn't classify 40452, 40470
Couldn't classify 43859, 43909
Sorry, prediction pasa_asmbl_34424.p1 fails validation.
(CAG)	 CG	40452-40470	GT	AGG
(CTG)	 AG	41913-42061	GT	CCG
(TGT)	 AG	42843-42968	GT	AGG
(GAT)	 AG	43342-43456	GT	AGG
(CCT)	 AG	43625-43719	GT	AGG
(GAT)	 AG	43859-43909	TG	CCT
-recovered pasa_asmbl_34424.p1, internal, 41913, 42061
-recovered pasa_asmbl_34424.p1, internal, 42843, 42968
-recovered pasa_asmbl_34424.p1, internal, 43342, 43456
-recovered pasa_asmbl_34424.p1, internal, 43625, 43719
Valid prediction for snap_scaffold_25-snap.1774-T1
Valid prediction for GlimmerHMM_glimmerT_54628-T1
Valid prediction for Augustus_model.g36228.t1
Valid prediction for GlimmerHMM_glimmerT_54611-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9865, rend_intergenic: 1831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23543, rend_intergenic: 17571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28179, rend_intergenic: 24697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47027, rend_intergenic: 28279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49370, rend_intergenic: 47057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55663, rend_intergenic: 50630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60106, rend_intergenic: 55728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67424, rend_intergenic: 60494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76469, rend_intergenic: 69854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98336, rend_intergenic: 90499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109622, rend_intergenic: 108451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116344, rend_intergenic: 114278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119230, rend_intergenic: 116910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119468, rend_intergenic: 119366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131444, rend_intergenic: 125366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141522, rend_intergenic: 138473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144578, rend_intergenic: 142954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148127, rend_intergenic: 144868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 153907
-exon list size: 336


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
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    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
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    
46.4    
46.7    
47.0    
47.3    
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    
52.7    
53.0    
53.3    
53.6    
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    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
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    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 9865, rend_intergenic: 1831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23543, rend_intergenic: 17571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28179, rend_intergenic: 24697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47027, rend_intergenic: 28279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49370, rend_intergenic: 47057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55663, rend_intergenic: 50630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60106, rend_intergenic: 55728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67424, rend_intergenic: 60494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76469, rend_intergenic: 69854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98336, rend_intergenic: 90499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109622, rend_intergenic: 108451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116344, rend_intergenic: 114278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119230, rend_intergenic: 116910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119468, rend_intergenic: 119366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131444, rend_intergenic: 125366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141522, rend_intergenic: 138473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144578, rend_intergenic: 142954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148127, rend_intergenic: 144868  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