-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_1-230646

-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_16-snap.18-T1
Valid prediction for Augustus_model.g25067.t1
Valid prediction for snap_scaffold_16-snap.31-T1
Valid prediction for snap_scaffold_16-snap.24-T1
Valid prediction for GlimmerHMM_glimmerT_37647-T1
Valid prediction for GlimmerHMM_glimmerT_37661-T1
Valid prediction for snap_scaffold_16-snap.23-T1
Valid prediction for pasa_asmbl_15994.p1
Valid prediction for snap_scaffold_16-snap.33-T1
Valid prediction for GlimmerHMM_glimmerT_37658-T1
Valid prediction for snap_scaffold_16-snap.10-T1
Valid prediction for Augustus_model.g25078.t1
Valid prediction for HiQ_model.g25080.t1
Valid prediction for GlimmerHMM_glimmerT_37651-T1
Valid prediction for Augustus_model.g25091.t1
Valid prediction for Augustus_model.g25065.t1
Valid prediction for GlimmerHMM_glimmerT_37642-T1
Valid prediction for snap_scaffold_16-snap.7-T1
Valid prediction for snap_scaffold_16-snap.21-T1
Valid prediction for snap_scaffold_16-snap.6-T1
Valid prediction for Augustus_model.g25070.t1
Valid prediction for GlimmerHMM_glimmerT_37671-T1
Valid prediction for snap_scaffold_16-snap.13-T1
Valid prediction for snap_scaffold_16-snap.3-T1
Valid prediction for Augustus_model.g25081.t1
Valid prediction for GlimmerHMM_glimmerT_37645-T1
Valid prediction for snap_scaffold_16-snap.19-T1
Valid prediction for pasa_asmbl_16007.p1
Valid prediction for Augustus_model.g25089.t1
Valid prediction for GlimmerHMM_glimmerT_37644-T1
Valid prediction for HiQ_model.g25090.t1
Valid prediction for snap_scaffold_16-snap.15-T1
Couldn't classify 137443, 137557
Couldn't classify 138725, 138869
Sorry, prediction pasa_asmbl_16757.p1 fails validation.
(AGA)	 TC	137443-137557	GT	CGG
(TTG)	 AG	138105-138177	GT	TGG
(CTG)	 AG	138725-138869	GG	ATG
-recovered pasa_asmbl_16757.p1, internal, 138105, 138177
Valid prediction for Augustus_model.g25076.t1
Valid prediction for snap_scaffold_16-snap.5-T1
Valid prediction for Augustus_model.g25066.t1
Valid prediction for Augustus_model.g25077.t1
Valid prediction for GlimmerHMM_glimmerT_37655-T1
Valid prediction for GlimmerHMM_glimmerT_37667-T1
Couldn't classify 205452, 205535
Couldn't classify 207250, 207336
Sorry, prediction pasa_asmbl_16005.p1 fails validation.
(ACT)	 AG	205452-205535	GT	GCG
(AGG)	 AG	205756-205906	GT	GGG
(GGG)	 AG	206194-206266	GT	GAG
(AGA)	 AG	206972-207026	GT	TGG
(ACC)	 AG	207250-207336	AT	GCA
-recovered pasa_asmbl_16005.p1, internal, 205452, 205535
-recovered pasa_asmbl_16005.p1, internal, 205756, 205906
-recovered pasa_asmbl_16005.p1, internal, 206194, 206266
-recovered pasa_asmbl_16005.p1, internal, 206972, 207026
Valid prediction for snap_scaffold_16-snap.11-T1
Valid prediction for snap_scaffold_16-snap.1-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_19869-T1
Valid prediction for Augustus_model.g25079.t1
Valid prediction for CodingQuarry_transcript_19868-T1
Valid prediction for GlimmerHMM_glimmerT_37654-T1
Valid prediction for pasa_asmbl_15996.p1
Valid prediction for GlimmerHMM_glimmerT_37662-T1
Valid prediction for GlimmerHMM_glimmerT_37641-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.20-T1
Valid prediction for snap_scaffold_16-snap.26-T1
Valid prediction for snap_scaffold_16-snap.32-T1
Valid prediction for snap_scaffold_16-snap.16-T1
Valid prediction for CodingQuarry_transcript_19870-T1
Couldn't classify 104620, 104792
Couldn't classify 105135, 105266
Sorry, prediction pasa_asmbl_16774.p1 fails validation.
(GTT)	 AG	104620-104792	GT	AGG
(CAC)	 AG	104930-105023	GT	AGG
(GTA)	 AG	105135-105266	TG	AGT
-recovered pasa_asmbl_16774.p1, internal, 104620, 104792
-recovered pasa_asmbl_16774.p1, internal, 104930, 105023
Valid prediction for GlimmerHMM_glimmerT_37652-T1
Valid prediction for snap_scaffold_16-snap.2-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g25064.t1
Couldn't classify 145376, 145465
Sorry, prediction pasa_asmbl_16002.p1 fails validation.
(AGC)	 GT	145376-145465	GT	TAG
(TAC)	 AG	145546-145687	GT	AGG
(GTT)	 AG	145808-145908	TG	GAT
-recovered pasa_asmbl_16002.p1, terminal, 145808, 145908
-recovered pasa_asmbl_16002.p1, internal, 145546, 145687
Valid prediction for GlimmerHMM_glimmerT_37669-T1
Valid prediction for Augustus_model.g25072.t1
Valid prediction for snap_scaffold_16-snap.27-T1
Valid prediction for snap_scaffold_16-snap.34-T1
Valid prediction for GlimmerHMM_glimmerT_37664-T1
Couldn't classify 109020, 109170
Couldn't classify 109555, 109626
Sorry, prediction pasa_asmbl_16807.p1 fails validation.
(AGG)	 TT	109020-109170	GT	AGG
(AGC)	 AG	109344-109432	GT	CGG
(GAT)	 AG	109555-109626	TG	CTT
-recovered pasa_asmbl_16807.p1, internal, 109344, 109432
Valid prediction for CodingQuarry_transcript_19871-T1
Valid prediction for GlimmerHMM_glimmerT_37648-T1
Valid prediction for snap_scaffold_16-snap.25-T1
Valid prediction for Augustus_model.g25074.t1
Valid prediction for Augustus_model.g25083.t1
Valid prediction for snap_scaffold_16-snap.22-T1
Valid prediction for GlimmerHMM_glimmerT_37640-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_37643-T1
Valid prediction for GlimmerHMM_glimmerT_37660-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: -)Couldn't classify 144517, 144613
Sorry, prediction pasa_asmbl_16828.p1 fails validation.
(AAG)	 GA	144517-144613	GT	AGG
(GAA)	 AG	144703-144760	GT	AGG
(TGG)	 AG	144864-144943	GT	AGG
(GAT)	 AG	146034-146076	GT	GGG
(CGT)	 AG	146167-146265	GT	GGG
(CAT)	 AG	149228-149308	GT	AAG
(GGC)	 AG	149424-149614	GT	AGG
(GCA)	 AG	149761-149940	GT	AGG
(GAC)	 AG	150141-150196	GT	AGG
(GCA)	 AG	150295-150440	GT	AGG
(GGC)	 AG	151684-151759	AT	GAA
-recovered pasa_asmbl_16828.p1, terminal, 151684, 151759
-recovered pasa_asmbl_16828.p1, internal, 144703, 144760
-recovered pasa_asmbl_16828.p1, internal, 144864, 144943
-recovered pasa_asmbl_16828.p1, internal, 146034, 146076
-recovered pasa_asmbl_16828.p1, internal, 146167, 146265
-recovered pasa_asmbl_16828.p1, internal, 149228, 149308
-recovered pasa_asmbl_16828.p1, internal, 149424, 149614
-recovered pasa_asmbl_16828.p1, internal, 149761, 149940
-recovered pasa_asmbl_16828.p1, internal, 150141, 150196
-recovered pasa_asmbl_16828.p1, internal, 150295, 150440
Valid prediction for Augustus_model.g25073.t1
Valid prediction for Augustus_model.g25068.t1
Valid prediction for snap_scaffold_16-snap.35-T1
Valid prediction for GlimmerHMM_glimmerT_37657-T1
Valid prediction for Augustus_model.g25069.t1
Valid prediction for Augustus_model.g25086.t1
Valid prediction for snap_scaffold_16-snap.17-T1
Valid prediction for GlimmerHMM_glimmerT_37646-T1
Valid prediction for snap_scaffold_16-snap.30-T1
Valid prediction for Augustus_model.g25085.t1
Valid prediction for GlimmerHMM_glimmerT_37672-T1
Valid prediction for snap_scaffold_16-snap.4-T1
Valid prediction for HiQ_model.g25075.t1
Valid prediction for snap_scaffold_16-snap.14-T1
Valid prediction for GlimmerHMM_glimmerT_37673-T1
Valid prediction for Augustus_model.g25087.t1
Valid prediction for snap_scaffold_16-snap.36-T1
Valid prediction for snap_scaffold_16-snap.29-T1
Valid prediction for GlimmerHMM_glimmerT_37668-T1
Valid prediction for GlimmerHMM_glimmerT_37665-T1
Valid prediction for snap_scaffold_16-snap.28-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.8-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_37649-T1
Valid prediction for snap_scaffold_16-snap.12-T1
Valid prediction for HiQ_model.g25084.t1
Valid prediction for Augustus_model.g25088.t1
Valid prediction for GlimmerHMM_glimmerT_37666-T1
Valid prediction for pasa_asmbl_16841.p1
Valid prediction for GlimmerHMM_glimmerT_37653-T1
Valid prediction for snap_scaffold_16-snap.9-T1
Valid prediction for GlimmerHMM_glimmerT_37670-T1
Valid prediction for GlimmerHMM_glimmerT_37650-T1
Valid prediction for CodingQuarry_transcript_19867-T1
Valid prediction for GlimmerHMM_glimmerT_37656-T1
Valid prediction for Augustus_model.g25093.t1
Valid prediction for Augustus_model.g25071.t1
Valid prediction for Augustus_model.g25092.t1
Valid prediction for Augustus_model.g25082.t1
Valid prediction for GlimmerHMM_glimmerT_37663-T1
Valid prediction for GlimmerHMM_glimmerT_37659-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 28336, rend_intergenic: 28333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 230646
-exon list size: 382


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.9    
3.1    
3.4    
3.6    
3.9    
4.2    
4.4    
4.7    
4.9    
5.2    
5.5    
5.7    
6.0    
6.2    
6.5    
6.8    
7.0    
7.3    
7.6    
7.8    
8.1    
8.3    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.5    
13.8    
14.1    
14.3    
14.6    
14.8    
15.1    
15.4    
15.6    
15.9    
16.1    
16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
18.0    
18.2    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.7    
22.9    
23.2    
23.4    
23.7    
24.0    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.7    
41.9    
42.2    
42.4    
42.7    
43.0    
43.2    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.1    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.9    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.8    
57.0    
57.3    
57.6    
57.8    
58.1    
58.3    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.5    
63.8    
64.1    
64.3    
64.6    
64.8    
65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
68.0    
68.2    
68.5    
68.8    
69.0    
69.3    
69.5    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.8    
82.0    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.6    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.7    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.4    
96.6    
96.9    
97.1    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 44 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 28336, rend_intergenic: 28333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 42 predictions persist after filtering for low support