-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_408402-575241

-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.g16418.t1
Valid prediction for GeneMark_model.41865_t
Valid prediction for GeneMark_model.41862_t
Valid prediction for snap_scaffold_10-snap.114-T1
Valid prediction for GeneMark_model.41853_t
Valid prediction for Augustus_model.g16432.t1
Valid prediction for Augustus_model.g16413.t1
Valid prediction for GeneMark_model.41866_t
Valid prediction for Augustus_model.g16407.t1
Valid prediction for snap_scaffold_10-snap.111-T1
Valid prediction for snap_scaffold_10-snap.100-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.41872_t
Valid prediction for GlimmerHMM_glimmerT_24505-T1
Valid prediction for GeneMark_model.41874_t
Valid prediction for snap_scaffold_10-snap.104-T1
Valid prediction for GeneMark_model.41878_t
Valid prediction for Augustus_model.g16399.t1
Valid prediction for snap_scaffold_10-snap.127-T1
Valid prediction for snap_scaffold_10-snap.89-T1
Valid prediction for GlimmerHMM_glimmerT_24503-T1
Valid prediction for GlimmerHMM_glimmerT_24504-T1
Valid prediction for snap_scaffold_10-snap.97-T1
Valid prediction for snap_scaffold_10-snap.110-T1
Valid prediction for Augustus_model.g16427.t1
Valid prediction for Augustus_model.g16419.t1
Valid prediction for GeneMark_model.41859_t
Valid prediction for GlimmerHMM_glimmerT_24515-T1
Valid prediction for GlimmerHMM_glimmerT_24514-T1
Valid prediction for GlimmerHMM_glimmerT_24496-T1
Valid prediction for GeneMark_model.41877_t
Valid prediction for Augustus_model.g16414.t1
Valid prediction for GlimmerHMM_glimmerT_24510-T1
Valid prediction for snap_scaffold_10-snap.115-T1
Valid prediction for Augustus_model.g16417.t1
Valid prediction for snap_scaffold_10-snap.118-T1
Couldn't classify 4258, 4599
Sorry, prediction pasa_asmbl_4142.p1 fails validation.
(CAG)	 TG	4258-4599	AC	GGA
Valid prediction for GlimmerHMM_glimmerT_24486-T1
Valid prediction for snap_scaffold_10-snap.112-T1
Valid prediction for Augustus_model.g16428.t1
Valid prediction for snap_scaffold_10-snap.98-T1
Valid prediction for snap_scaffold_10-snap.113-T1
Valid prediction for GlimmerHMM_glimmerT_24501-T1
Valid prediction for GlimmerHMM_glimmerT_24509-T1
Valid prediction for GlimmerHMM_glimmerT_24518-T1
Valid prediction for snap_scaffold_10-snap.99-T1
Valid prediction for snap_scaffold_10-snap.96-T1
Valid prediction for GeneMark_model.41863_t
Valid prediction for GlimmerHMM_glimmerT_24483-T1
Valid prediction for snap_scaffold_10-snap.116-T1
Valid prediction for Augustus_model.g16416.t1
Valid prediction for snap_scaffold_10-snap.131-T1
Valid prediction for Augustus_model.g16425.t1
Valid prediction for snap_scaffold_10-snap.123-T1
Valid prediction for GeneMark_model.41870_t
Valid prediction for GeneMark_model.41875_t
Valid prediction for GeneMark_model.41873_t
Valid prediction for snap_scaffold_10-snap.117-T1
Valid prediction for GlimmerHMM_glimmerT_24492-T1
Valid prediction for GlimmerHMM_glimmerT_24500-T1
Valid prediction for GeneMark_model.41867_t
Valid prediction for snap_scaffold_10-snap.130-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 Augustus_model.g16405.t1
Valid prediction for Augustus_model.g16412.t1
Valid prediction for HiQ_model.g16430.t1
Valid prediction for Augustus_model.g16411.t1
Valid prediction for Augustus_model.g16420.t1
Valid prediction for GlimmerHMM_glimmerT_24521-T1
Valid prediction for Augustus_model.g16424.t1
Valid prediction for CodingQuarry_transcript_5245-T1
Valid prediction for GlimmerHMM_glimmerT_24517-T1
Valid prediction for Augustus_model.g16406.t1
Valid prediction for snap_scaffold_10-snap.122-T1
Valid prediction for snap_scaffold_10-snap.106-T1
Couldn't classify 34781, 35089
Sorry, prediction pasa_asmbl_2877.p1 fails validation.
(CAG)	 TC	34781-35089	GT	CAG
(GTT)	 AG	35265-35423	AA	AGA
-recovered pasa_asmbl_2877.p1, terminal, 35265, 35423
Valid prediction for GeneMark_model.41868_t
Valid prediction for Augustus_model.g16434.t1
Valid prediction for Augustus_model.g16401.t1
Valid prediction for GeneMark_model.41861_t
Valid prediction for GlimmerHMM_glimmerT_24519-T1
Valid prediction for GeneMark_model.41857_t
Valid prediction for GlimmerHMM_glimmerT_24487-T1
Valid prediction for Augustus_model.g16404.t1
Valid prediction for Augustus_model.g16402.t1
Valid prediction for CodingQuarry_transcript_5243-T1
Valid prediction for GeneMark_model.41860_t
Valid prediction for GeneMark_model.41871_t
Valid prediction for GlimmerHMM_glimmerT_24488-T1
Valid prediction for CodingQuarry_transcript_5246-T1
Couldn't classify 43614, 43908
Sorry, prediction pasa_asmbl_2873.p1 fails validation.
(ACT)	 AC	43614-43908	GT	AGG
(CTC)	 AG	45539-45664	GT	GCG
(ACA)	 AG	45778-45968	GT	AGG
(GTG)	 AG	46101-46291	GT	ATG
(GCT)	 AG	46463-46679	AA	AAA
-recovered pasa_asmbl_2873.p1, terminal, 46463, 46679
-recovered pasa_asmbl_2873.p1, internal, 45539, 45664
-recovered pasa_asmbl_2873.p1, internal, 45778, 45968
-recovered pasa_asmbl_2873.p1, internal, 46101, 46291
Valid prediction for GeneMark_model.41881_t
Valid prediction for GeneMark_model.41876_t
Valid prediction for snap_scaffold_10-snap.102-T1
Valid prediction for Augustus_model.g16433.t1
Valid prediction for GlimmerHMM_glimmerT_24494-T1
Valid prediction for snap_scaffold_10-snap.120-T1
Valid prediction for snap_scaffold_10-snap.101-T1
Valid prediction for GeneMark_model.41856_t
Valid prediction for GlimmerHMM_glimmerT_24520-T1
Valid prediction for Augustus_model.g16429.t1
Valid prediction for snap_scaffold_10-snap.90-T1
Valid prediction for Augustus_model.g16408.t1
Valid prediction for GlimmerHMM_glimmerT_24489-T1
Valid prediction for snap_scaffold_10-snap.105-T1
Valid prediction for Augustus_model.g16410.t1
Valid prediction for GeneMark_model.41858_t
Valid prediction for snap_scaffold_10-snap.109-T1
Valid prediction for GeneMark_model.41880_t
Valid prediction for pasa_asmbl_2880.p1
Valid prediction for snap_scaffold_10-snap.119-T1
Valid prediction for GlimmerHMM_glimmerT_24516-T1
Valid prediction for GeneMark_model.41854_t
Valid prediction for Augustus_model.g16415.t1
Valid prediction for snap_scaffold_10-snap.121-T1
Valid prediction for Augustus_model.g16435.t1
Valid prediction for GlimmerHMM_glimmerT_24507-T1
Valid prediction for GlimmerHMM_glimmerT_24490-T1
Valid prediction for GlimmerHMM_glimmerT_24499-T1
Valid prediction for Augustus_model.g16409.t1
Valid prediction for Augustus_model.g16431.t1
Valid prediction for GlimmerHMM_glimmerT_24508-T1
Valid prediction for Augustus_model.g16421.t1
Valid prediction for snap_scaffold_10-snap.95-T1
Valid prediction for Augustus_model.g16403.t1
Valid prediction for GlimmerHMM_glimmerT_24495-T1
Valid prediction for snap_scaffold_10-snap.133-T1
Valid prediction for Augustus_model.g16422.t1
Valid prediction for GeneMark_model.41869_t
Valid prediction for GlimmerHMM_glimmerT_24484-T1
Valid prediction for snap_scaffold_10-snap.92-T1
Valid prediction for snap_scaffold_10-snap.132-T1
Couldn't classify 65828, 66565
Sorry, prediction pasa_asmbl_2872.p1 fails validation.
(GAA)	 AG	65828-66565	GG	GGG
Valid prediction for snap_scaffold_10-snap.125-T1
Couldn't classify 69958, 71046
Sorry, prediction pasa_asmbl_2871.p1 fails validation.
(CTA)	 GG	69958-71046	CC	GAC
Valid prediction for snap_scaffold_10-snap.124-T1
Couldn't classify 110865, 111314
Sorry, prediction pasa_asmbl_2870.p1 fails validation.
(GCA)	 GG	110865-111314	CA	CAC
Valid prediction for GlimmerHMM_glimmerT_24485-T1
Valid prediction for snap_scaffold_10-snap.126-T1
Valid prediction for snap_scaffold_10-snap.91-T1
Valid prediction for snap_scaffold_10-snap.93-T1
Valid prediction for GlimmerHMM_glimmerT_24502-T1
Valid prediction for GlimmerHMM_glimmerT_24491-T1
Valid prediction for snap_scaffold_10-snap.94-T1
Valid prediction for Augustus_model.g16426.t1
Valid prediction for snap_scaffold_10-snap.129-T1
Valid prediction for snap_scaffold_10-snap.88-T1
Valid prediction for GlimmerHMM_glimmerT_24511-T1
Valid prediction for Augustus_model.g16400.t1
Valid prediction for GlimmerHMM_glimmerT_24498-T1
Valid prediction for snap_scaffold_10-snap.128-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g16423.t1
Valid prediction for snap_scaffold_10-snap.107-T1
Valid prediction for GlimmerHMM_glimmerT_24506-T1
Valid prediction for GlimmerHMM_glimmerT_24512-T1
Valid prediction for GlimmerHMM_glimmerT_24493-T1
Valid prediction for snap_scaffold_10-snap.108-T1
Valid prediction for GlimmerHMM_glimmerT_24497-T1
Valid prediction for snap_scaffold_10-snap.134-T1
Valid prediction for snap_scaffold_10-snap.103-T1
Valid prediction for GeneMark_model.41879_t
Valid prediction for GlimmerHMM_glimmerT_24513-T1
Valid prediction for GeneMark_model.41855_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 148346, rend_intergenic: 148343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166840
-exon list size: 485


building trellis

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11.9    
12.1    
12.3    
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13.6    
13.8    
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14.8    
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17.9    
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18.9    
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20.9    
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21.6    
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22.0    
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22.8    
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25.9    
26.1    
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26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
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52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
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70.4    
70.6    
70.8    
71.0    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 53 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 148346, rend_intergenic: 148343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 48 predictions persist after filtering for low support