-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_10828682-11049144

-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 GeneMark_model.83548_t
Valid prediction for pasa_asmbl_26157.p1
Valid prediction for snap_scaffold_20-snap.2357-T1
Valid prediction for GeneMark_model.83554_t
Valid prediction for GlimmerHMM_glimmerT_47951-T1
Valid prediction for GlimmerHMM_glimmerT_47933-T1
Valid prediction for Augustus_model.g32000.t1
Valid prediction for GlimmerHMM_glimmerT_47948-T1
Valid prediction for Augustus_model.g32005.t1
Valid prediction for Augustus_model.g32008.t1
Valid prediction for GeneMark_model.83562_t
Valid prediction for GlimmerHMM_glimmerT_47929-T1
Valid prediction for snap_scaffold_20-snap.2326-T1
Valid prediction for snap_scaffold_20-snap.2333-T1
Valid prediction for snap_scaffold_20-snap.2356-T1
Valid prediction for GeneMark_model.83561_t
Valid prediction for GlimmerHMM_glimmerT_47941-T1
Valid prediction for GeneMark_model.83551_t
Valid prediction for snap_scaffold_20-snap.2325-T1
Valid prediction for Augustus_model.g32003.t1
Valid prediction for GeneMark_model.83550_t
Valid prediction for HiQ_model.g32011.t1
Valid prediction for GlimmerHMM_glimmerT_47943-T1
Couldn't classify 44971, 45060
Couldn't classify 45936, 46051
Sorry, prediction pasa_asmbl_26154.p1 fails validation.
(GAA)	 AT	44971-45060	GT	GGG
(ATG)	 AG	45200-45279	GT	AGG
(GCG)	 AG	45369-45411	GT	AGG
(ACC)	 AG	45533-45612	GT	AGG
(ACT)	 AG	45748-45818	GT	AGG
(AGC)	 AG	45936-46051	GG	GGG
-recovered pasa_asmbl_26154.p1, initial, 45200, 45279
-recovered pasa_asmbl_26154.p1, internal, 45200, 45279
-recovered pasa_asmbl_26154.p1, internal, 45369, 45411
-recovered pasa_asmbl_26154.p1, internal, 45533, 45612
-recovered pasa_asmbl_26154.p1, internal, 45748, 45818
Valid prediction for GlimmerHMM_glimmerT_47949-T1
Valid prediction for snap_scaffold_20-snap.2346-T1
Valid prediction for snap_scaffold_20-snap.2354-T1
Valid prediction for CodingQuarry_transcript_30597-T1
Valid prediction for snap_scaffold_20-snap.2353-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g32014.t1
Valid prediction for GlimmerHMM_glimmerT_47931-T1
Valid prediction for Augustus_model.g32004.t1
Valid prediction for GlimmerHMM_glimmerT_47938-T1
Valid prediction for GlimmerHMM_glimmerT_47934-T1
Valid prediction for HiQ_model.g32009.t1
Valid prediction for Augustus_model.g32010.t1
Valid prediction for CodingQuarry_transcript_30596-T1
Valid prediction for GlimmerHMM_glimmerT_47940-T1
Valid prediction for CodingQuarry_transcript_30595-T1
Valid prediction for GeneMark_model.83547_t
Valid prediction for GlimmerHMM_glimmerT_47928-T1
Valid prediction for GeneMark_model.83559_t
Valid prediction for snap_scaffold_20-snap.2330-T1
Valid prediction for snap_scaffold_20-snap.2332-T1
Valid prediction for GeneMark_model.83567_t
Valid prediction for snap_scaffold_20-snap.2334-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.2335-T1
Valid prediction for GlimmerHMM_glimmerT_47936-T1
Valid prediction for GlimmerHMM_glimmerT_47924-T1
Valid prediction for snap_scaffold_20-snap.2331-T1
Valid prediction for pasa_asmbl_26150.p1
Valid prediction for GlimmerHMM_glimmerT_47926-T1
Valid prediction for HiQ_model.g32001.t1
Valid prediction for snap_scaffold_20-snap.2350-T1
Valid prediction for GeneMark_model.83549_t

-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.2337-T1
Valid prediction for snap_scaffold_20-snap.2351-T1
Valid prediction for snap_scaffold_20-snap.2348-T1
Valid prediction for GlimmerHMM_glimmerT_47942-T1
Valid prediction for GeneMark_model.83565_t
Valid prediction for snap_scaffold_20-snap.2340-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.83546_t
Valid prediction for GlimmerHMM_glimmerT_47945-T1
Valid prediction for Augustus_model.g32012.t1
Couldn't classify 133278, 133353
Couldn't classify 140351, 140370
Sorry, prediction pasa_asmbl_27051.p1 fails validation.
(AGG)	 TC	133278-133353	GT	TGG
(ATG)	 AG	133762-133846	GT	CAG
(GTA)	 AG	136568-136738	GT	AGG
(TAA)	 AG	136965-137100	GT	CAG
(ATA)	 AG	137644-137806	GT	GGG
(CTG)	 AG	140351-140370	CC	CCC
add_exon() Sorry, pasa_asmbl_27051.p1 133762-133846-initial-1 is invalid.
-recovered pasa_asmbl_27051.p1, initial, 133762, 133846
-recovered pasa_asmbl_27051.p1, internal, 133762, 133846
-recovered pasa_asmbl_27051.p1, internal, 136568, 136738
-recovered pasa_asmbl_27051.p1, internal, 136965, 137100
-recovered pasa_asmbl_27051.p1, internal, 137644, 137806
Valid prediction for Augustus_model.g31999.t1
Valid prediction for snap_scaffold_20-snap.2328-T1
Valid prediction for GeneMark_model.83555_t
Valid prediction for GlimmerHMM_glimmerT_47950-T1
Valid prediction for Augustus_model.g32006.t1
Valid prediction for snap_scaffold_20-snap.2327-T1
Valid prediction for GeneMark_model.83544_t
Valid prediction for snap_scaffold_20-snap.2339-T1
Valid prediction for GeneMark_model.83552_t
Valid prediction for GlimmerHMM_glimmerT_47937-T1
Valid prediction for GlimmerHMM_glimmerT_47946-T1
Valid prediction for GlimmerHMM_glimmerT_47927-T1
Valid prediction for snap_scaffold_20-snap.2345-T1
Valid prediction for snap_scaffold_20-snap.2329-T1
Valid prediction for snap_scaffold_20-snap.2355-T1
Valid prediction for snap_scaffold_20-snap.2352-T1
Valid prediction for snap_scaffold_20-snap.2344-T1
Valid prediction for GlimmerHMM_glimmerT_47932-T1
Valid prediction for GeneMark_model.83566_t
Valid prediction for GlimmerHMM_glimmerT_47947-T1
Valid prediction for snap_scaffold_20-snap.2338-T1
Valid prediction for GlimmerHMM_glimmerT_47925-T1
Valid prediction for GeneMark_model.83558_t
Valid prediction for GlimmerHMM_glimmerT_47939-T1
Valid prediction for GeneMark_model.83545_t
Couldn't classify 142324, 142347
Sorry, prediction pasa_asmbl_27050.p1 fails validation.
(GAG)	 AC	142324-142347	GT	ATG
(CTT)	 AG	145012-145187	GT	AAG
(GTG)	 AG	145760-145807	GT	CGG
(AGG)	 AG	145943-146064	GT	TGG
(AGC)	 AG	146274-146441	GT	AGG
(AGC)	 AG	147028-147168	GT	AGG
(GAC)	 AG	147421-147522	GT	AGG
(GGA)	 AG	147723-147809	GT	CAG
(GTC)	 AG	148112-148281	TT	GAT
-recovered pasa_asmbl_27050.p1, terminal, 148112, 148281
-recovered pasa_asmbl_27050.p1, internal, 145012, 145187
-recovered pasa_asmbl_27050.p1, internal, 145760, 145807
-recovered pasa_asmbl_27050.p1, internal, 145943, 146064
-recovered pasa_asmbl_27050.p1, internal, 146274, 146441
-recovered pasa_asmbl_27050.p1, internal, 147028, 147168
-recovered pasa_asmbl_27050.p1, internal, 147421, 147522
-recovered pasa_asmbl_27050.p1, internal, 147723, 147809
Valid prediction for pasa_asmbl_27048.p1
Valid prediction for Augustus_model.g32016.t1
Valid prediction for Augustus_model.g32007.t1
Valid prediction for HiQ_model.g32002.t1
Valid prediction for GeneMark_model.83563_t
Valid prediction for snap_scaffold_20-snap.2336-T1
Valid prediction for Augustus_model.g32015.t1
Valid prediction for GeneMark_model.83560_t
Valid prediction for snap_scaffold_20-snap.2347-T1
Valid prediction for GlimmerHMM_glimmerT_47944-T1
Valid prediction for snap_scaffold_20-snap.2342-T1
Valid prediction for snap_scaffold_20-snap.2343-T1
Valid prediction for snap_scaffold_20-snap.2349-T1
Valid prediction for GlimmerHMM_glimmerT_47935-T1
Valid prediction for GlimmerHMM_glimmerT_47930-T1
Valid prediction for Augustus_model.g32013.t1
Valid prediction for GeneMark_model.83553_t
Valid prediction for GeneMark_model.83564_t
Valid prediction for GeneMark_model.83543_t
Valid prediction for snap_scaffold_20-snap.2341-T1
Valid prediction for GeneMark_model.83557_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 213789, rend_intergenic: 212667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220463
-exon list size: 372


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.0    
8.3    
8.6    
8.8    
9.1    
9.4    
9.6    
9.9    
10.2    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.0    
12.3    
12.6    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.1    
21.4    
21.7    
21.9    
22.2    
22.5    
22.7    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.5    
27.8    
28.1    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.2    
42.5    
42.8    
43.0    
43.3    
43.6    
43.9    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.1    
56.4    
56.7    
57.0    
57.2    
57.5    
57.8    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.2    
61.5    
61.8    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.4    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
71.9    
72.2    
72.5    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.3    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 213789, rend_intergenic: 212667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12081
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support