-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_9498742-9700710

-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_27-snap.2183-T1
Valid prediction for snap_scaffold_27-snap.2206-T1
Valid prediction for GlimmerHMM_glimmerT_57863-T1
Valid prediction for CodingQuarry_transcript_41970-T1
Valid prediction for GlimmerHMM_glimmerT_57864-T1
Valid prediction for GlimmerHMM_glimmerT_57856-T1
Valid prediction for snap_scaffold_27-snap.2219-T1
Valid prediction for snap_scaffold_27-snap.2195-T1
Valid prediction for snap_scaffold_27-snap.2192-T1
Valid prediction for GlimmerHMM_glimmerT_57880-T1
Valid prediction for snap_scaffold_27-snap.2191-T1
Valid prediction for GlimmerHMM_glimmerT_57855-T1
Valid prediction for snap_scaffold_27-snap.2215-T1
Valid prediction for snap_scaffold_27-snap.2197-T1
Valid prediction for GlimmerHMM_glimmerT_57882-T1
Valid prediction for GlimmerHMM_glimmerT_57875-T1
Valid prediction for GlimmerHMM_glimmerT_57877-T1
Valid prediction for snap_scaffold_27-snap.2187-T1
Valid prediction for snap_scaffold_27-snap.2185-T1
Valid prediction for snap_scaffold_27-snap.2196-T1
Valid prediction for snap_scaffold_27-snap.2204-T1
Valid prediction for HiQ_model.g38301.t1
Valid prediction for snap_scaffold_27-snap.2210-T1
Valid prediction for snap_scaffold_27-snap.2201-T1
Valid prediction for GlimmerHMM_glimmerT_57862-T1
Valid prediction for snap_scaffold_27-snap.2189-T1
Valid prediction for GlimmerHMM_glimmerT_57870-T1
Valid prediction for snap_scaffold_27-snap.2205-T1
Valid prediction for snap_scaffold_27-snap.2208-T1
Valid prediction for GlimmerHMM_glimmerT_57872-T1
Valid prediction for GlimmerHMM_glimmerT_57866-T1
Valid prediction for snap_scaffold_27-snap.2213-T1
Valid prediction for snap_scaffold_27-snap.2217-T1
Valid prediction for snap_scaffold_27-snap.2199-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.2202-T1
Valid prediction for snap_scaffold_27-snap.2184-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_57871-T1
Valid prediction for GlimmerHMM_glimmerT_57874-T1
Valid prediction for Augustus_model.g38304.t1
Valid prediction for GlimmerHMM_glimmerT_57873-T1
Valid prediction for snap_scaffold_27-snap.2186-T1
Valid prediction for GlimmerHMM_glimmerT_57860-T1
Valid prediction for Augustus_model.g38309.t1
Valid prediction for GlimmerHMM_glimmerT_57861-T1
Valid prediction for snap_scaffold_27-snap.2220-T1
Couldn't classify 106466, 106631
Couldn't classify 113060, 113268
Sorry, prediction pasa_asmbl_37145.p1 fails validation.
(GTG)	 GT	106466-106631	GT	TGG
(TCC)	 AG	108958-109060	GT	CGG
(GCA)	 AG	109595-109739	GT	CAG
(GAG)	 AG	109995-110077	GT	AGG
(GAC)	 AG	110432-110539	GT	AGG
(GTC)	 AG	110624-110769	GT	AGG
(GCC)	 AG	110845-111046	GT	AGG
(GAA)	 AG	111185-111324	GT	AGG
(GTG)	 AG	112227-112301	GT	AGG
(GAG)	 AG	113060-113268	CC	CCC
-recovered pasa_asmbl_37145.p1, internal, 108958, 109060
-recovered pasa_asmbl_37145.p1, internal, 109595, 109739
-recovered pasa_asmbl_37145.p1, internal, 109995, 110077
-recovered pasa_asmbl_37145.p1, internal, 110432, 110539
-recovered pasa_asmbl_37145.p1, internal, 110624, 110769
-recovered pasa_asmbl_37145.p1, internal, 110845, 111046
-recovered pasa_asmbl_37145.p1, internal, 111185, 111324
-recovered pasa_asmbl_37145.p1, internal, 112227, 112301
Valid prediction for GlimmerHMM_glimmerT_57883-T1
Valid prediction for snap_scaffold_27-snap.2203-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.2190-T1
Valid prediction for Augustus_model.g38303.t1
Valid prediction for GlimmerHMM_glimmerT_57858-T1
Valid prediction for Augustus_model.g38306.t1
Valid prediction for CodingQuarry_transcript_41969-T1
Valid prediction for GlimmerHMM_glimmerT_57865-T1
Couldn't classify 94944, 95024
Sorry, prediction pasa_asmbl_37146.p1 fails validation.
(ATG)	 GG	92621-92746	GT	AGG
(GCC)	 AG	93089-93181	GT	AGG
(GTG)	 AG	93643-93765	GT	AGG
(GTT)	 AG	94150-94227	GT	AGG
(GTT)	 AG	94944-95024	GG	CAG
-recovered pasa_asmbl_37146.p1, initial, 92621, 92746
-recovered pasa_asmbl_37146.p1, internal, 93089, 93181
-recovered pasa_asmbl_37146.p1, internal, 93643, 93765
-recovered pasa_asmbl_37146.p1, internal, 94150, 94227
Valid prediction for snap_scaffold_27-snap.2221-T1
Valid prediction for GlimmerHMM_glimmerT_57859-T1
Valid prediction for snap_scaffold_27-snap.2209-T1
Valid prediction for snap_scaffold_27-snap.2194-T1
Valid prediction for snap_scaffold_27-snap.2198-T1
Valid prediction for Augustus_model.g38308.t1
Valid prediction for snap_scaffold_27-snap.2182-T1
Valid prediction for snap_scaffold_27-snap.2200-T1
Valid prediction for GlimmerHMM_glimmerT_57876-T1
Valid prediction for snap_scaffold_27-snap.2193-T1
Valid prediction for GlimmerHMM_glimmerT_57868-T1
Valid prediction for snap_scaffold_27-snap.2216-T1
Valid prediction for snap_scaffold_27-snap.2214-T1
Couldn't classify 113506, 113899
Couldn't classify 114238, 114302
Sorry, prediction pasa_asmbl_37144.p1 fails validation.
(AAA)	 CC	113506-113899	GT	AGG
(GAT)	 AG	114238-114302	AG	AGA
Valid prediction for GlimmerHMM_glimmerT_57881-T1
Valid prediction for GlimmerHMM_glimmerT_57857-T1
Valid prediction for Augustus_model.g38299.t1
Valid prediction for GlimmerHMM_glimmerT_57879-T1
Valid prediction for GlimmerHMM_glimmerT_57869-T1
Valid prediction for HiQ_model.g38300.t1
Valid prediction for Augustus_model.g38305.t1
Valid prediction for Augustus_model.g38302.t1
Valid prediction for GlimmerHMM_glimmerT_57867-T1
Valid prediction for snap_scaffold_27-snap.2207-T1
Valid prediction for snap_scaffold_27-snap.2212-T1
Valid prediction for pasa_asmbl_37142.p1
Valid prediction for CodingQuarry_transcript_41972-T1
Valid prediction for snap_scaffold_27-snap.2188-T1
Valid prediction for GlimmerHMM_glimmerT_57878-T1
Valid prediction for snap_scaffold_27-snap.2211-T1
Couldn't classify 115089, 115205
Sorry, prediction pasa_asmbl_37143.p1 fails validation.
(GAC)	 CC	115089-115205	GT	AGG
(GTA)	 AG	116311-118284	GA	GAG
-recovered pasa_asmbl_37143.p1, terminal, 116311, 118284
Valid prediction for Augustus_model.g38307.t1
Valid prediction for snap_scaffold_27-snap.2218-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11083, rend_intergenic: 6392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20694, rend_intergenic: 15121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30363, rend_intergenic: 20804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39712, rend_intergenic: 32044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56908, rend_intergenic: 41977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60928, rend_intergenic: 57261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73653, rend_intergenic: 64619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91148, rend_intergenic: 83686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98233, rend_intergenic: 91263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102055, rend_intergenic: 100220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126347, rend_intergenic: 102131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132342, rend_intergenic: 130256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146232, rend_intergenic: 140658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160801, rend_intergenic: 156852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166574, rend_intergenic: 161585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171230, rend_intergenic: 167112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172230, rend_intergenic: 171373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172499, rend_intergenic: 172238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187658, rend_intergenic: 175682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201969
-exon list size: 326


building trellis

0.3    
0.6    
0.9    
1.2    
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1.8    
2.1    
2.4    
2.7    
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3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
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    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
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    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
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    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
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    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
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    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 11083, rend_intergenic: 6392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20694, rend_intergenic: 15121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30363, rend_intergenic: 20804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39712, rend_intergenic: 32044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56908, rend_intergenic: 41977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60928, rend_intergenic: 57261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73653, rend_intergenic: 64619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91148, rend_intergenic: 83686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98233, rend_intergenic: 91263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102055, rend_intergenic: 100220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126347, rend_intergenic: 102131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132342, rend_intergenic: 130256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146232, rend_intergenic: 140658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160801, rend_intergenic: 156852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166574, rend_intergenic: 161585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171230, rend_intergenic: 167112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172230, rend_intergenic: 171373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172499, rend_intergenic: 172238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187658, rend_intergenic: 175682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 189529 - 201969
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 189987 - 201969
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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