-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_9992350-10164565

-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 HiQ_model.g15570.t1
Valid prediction for GeneMark_model.39763_t
Valid prediction for GeneMark_model.39773_t
Valid prediction for GlimmerHMM_glimmerT_23225-T1
Couldn't classify 20576, 20694
Couldn't classify 21406, 21508
Sorry, prediction pasa_asmbl_54256.p1 fails validation.
(CCA)	 CT	20576-20694	GT	AGG
(AGA)	 AG	21147-21293	GT	AGG
(GCA)	 AG	21406-21508	GC	TTG
-recovered pasa_asmbl_54256.p1, internal, 21147, 21293
-recovered pasa_asmbl_54256.p1, internal, 21406, 21508
Valid prediction for GeneMark_model.39765_t
Valid prediction for GlimmerHMM_glimmerT_23229-T1
Valid prediction for GeneMark_model.39769_t
Valid prediction for snap_scaffold_9-snap.2016-T1
Valid prediction for snap_scaffold_9-snap.2003-T1
Valid prediction for GlimmerHMM_glimmerT_23237-T1
Valid prediction for snap_scaffold_9-snap.1996-T1
Valid prediction for GeneMark_model.39778_t
Valid prediction for Augustus_model.g15571.t1
Valid prediction for GlimmerHMM_glimmerT_23233-T1
Valid prediction for GeneMark_model.39767_t
Valid prediction for GeneMark_model.39786_t
Valid prediction for GeneMark_model.39779_t
Valid prediction for Augustus_model.g15569.t1
Valid prediction for snap_scaffold_9-snap.2014-T1
Valid prediction for GlimmerHMM_glimmerT_23236-T1
Valid prediction for snap_scaffold_9-snap.1995-T1
Valid prediction for snap_scaffold_9-snap.2005-T1
Valid prediction for GlimmerHMM_glimmerT_23231-T1
Valid prediction for GeneMark_model.39762_t
Valid prediction for snap_scaffold_9-snap.1994-T1
Valid prediction for snap_scaffold_9-snap.2010-T1
Valid prediction for GlimmerHMM_glimmerT_23234-T1
Valid prediction for snap_scaffold_9-snap.2008-T1
Valid prediction for GlimmerHMM_glimmerT_23243-T1
Couldn't classify 55677, 56859
Sorry, prediction pasa_asmbl_54259.p1 fails validation.
(CCC)	 AC	55677-56859	GT	AGG
(GTT)	 AG	57637-57767	GT	AGG
(CAT)	 AG	58307-58433	GT	GGG
(GCA)	 AG	58624-58751	GT	GGG
(CTC)	 AG	59034-59211	GT	GGG
(TGG)	 AG	59423-59573	GT	AGG
(GTC)	 AG	59913-59980	GT	AGG
(GAG)	 AG	60155-60228	GT	AGG
(GTT)	 AG	60659-60724	GT	AGG
(CTG)	 AG	60932-60994	AC	GAA
-recovered pasa_asmbl_54259.p1, terminal, 60932, 60994
-recovered pasa_asmbl_54259.p1, internal, 57637, 57767
-recovered pasa_asmbl_54259.p1, internal, 58307, 58433
-recovered pasa_asmbl_54259.p1, internal, 58624, 58751
-recovered pasa_asmbl_54259.p1, internal, 59034, 59211
-recovered pasa_asmbl_54259.p1, internal, 59423, 59573
-recovered pasa_asmbl_54259.p1, internal, 59913, 59980
-recovered pasa_asmbl_54259.p1, internal, 60155, 60228
-recovered pasa_asmbl_54259.p1, internal, 60659, 60724
Valid prediction for Augustus_model.g15565.t1
Valid prediction for GlimmerHMM_glimmerT_23241-T1
Couldn't classify 41855, 41945
Couldn't classify 42416, 42534
Sorry, prediction pasa_asmbl_54257.p1 fails validation.
(CCC)	 AC	41855-41945	GT	GGG
(GCA)	 AG	42051-42173	GT	TGG
(AGA)	 AG	42416-42534	GT	TGG
-recovered pasa_asmbl_54257.p1, internal, 42051, 42173
-recovered pasa_asmbl_54257.p1, internal, 42416, 42534
Valid prediction for GlimmerHMM_glimmerT_23249-T1
Valid prediction for GeneMark_model.39788_t
Valid prediction for Augustus_model.g15573.t1
Valid prediction for GeneMark_model.39784_t
Valid prediction for Augustus_model.g15574.t1
Valid prediction for GeneMark_model.39774_t
Valid prediction for snap_scaffold_9-snap.2001-T1
Valid prediction for snap_scaffold_9-snap.2009-T1
Valid prediction for GlimmerHMM_glimmerT_23230-T1
Valid prediction for snap_scaffold_9-snap.2002-T1
Valid prediction for HiQ_model.g15572.t1
Valid prediction for snap_scaffold_9-snap.2004-T1
Valid prediction for snap_scaffold_9-snap.2012-T1
Valid prediction for snap_scaffold_9-snap.2015-T1
Valid prediction for snap_scaffold_9-snap.2021-T1
Valid prediction for GeneMark_model.39776_t
Valid prediction for GeneMark_model.39782_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 GeneMark_model.39777_t
Valid prediction for snap_scaffold_9-snap.2013-T1
Valid prediction for GlimmerHMM_glimmerT_23232-T1
Couldn't classify 143171, 143482
Sorry, prediction pasa_asmbl_55217.p2 fails validation.
(GAG)	 GG	143171-143482	GA	AAG
Valid prediction for GlimmerHMM_glimmerT_23247-T1
Valid prediction for snap_scaffold_9-snap.2019-T1
Valid prediction for Augustus_model.g15567.t1
Valid prediction for snap_scaffold_9-snap.2007-T1
Valid prediction for Augustus_model.g15578.t1
Valid prediction for GlimmerHMM_glimmerT_23235-T1
Valid prediction for GlimmerHMM_glimmerT_23244-T1
Valid prediction for GeneMark_model.39790_t
Valid prediction for snap_scaffold_9-snap.2022-T1
Valid prediction for GlimmerHMM_glimmerT_23238-T1
Valid prediction for GeneMark_model.39780_t
Valid prediction for snap_scaffold_9-snap.2020-T1
Valid prediction for snap_scaffold_9-snap.2011-T1
Valid prediction for CodingQuarry_transcript_62130-T1
Valid prediction for GeneMark_model.39787_t
Valid prediction for GlimmerHMM_glimmerT_23246-T1
Valid prediction for GlimmerHMM_glimmerT_23226-T1
Valid prediction for GlimmerHMM_glimmerT_23240-T1
Valid prediction for snap_scaffold_9-snap.1998-T1
Valid prediction for snap_scaffold_9-snap.2017-T1
Valid prediction for Augustus_model.g15577.t1
Valid prediction for snap_scaffold_9-snap.1997-T1
Valid prediction for snap_scaffold_9-snap.2018-T1
Valid prediction for GeneMark_model.39764_t
Valid prediction for GeneMark_model.39772_t
Valid prediction for GeneMark_model.39791_t
Valid prediction for snap_scaffold_9-snap.2000-T1
Valid prediction for GeneMark_model.39789_t
Valid prediction for GeneMark_model.39783_t
Valid prediction for Augustus_model.g15566.t1
Valid prediction for snap_scaffold_9-snap.2006-T1
Valid prediction for GlimmerHMM_glimmerT_23245-T1
Valid prediction for Augustus_model.g15576.t1
Valid prediction for Augustus_model.g15568.t1
Valid prediction for GeneMark_model.39770_t
Valid prediction for GeneMark_model.39771_t
Valid prediction for Augustus_model.g15575.t1
Valid prediction for GlimmerHMM_glimmerT_23227-T1
Valid prediction for GeneMark_model.39785_t
Valid prediction for GlimmerHMM_glimmerT_23242-T1
Valid prediction for GlimmerHMM_glimmerT_23248-T1
Valid prediction for snap_scaffold_9-snap.1999-T1
Valid prediction for GeneMark_model.39781_t
Valid prediction for GlimmerHMM_glimmerT_23239-T1
Valid prediction for GeneMark_model.39775_t
Valid prediction for GlimmerHMM_glimmerT_23228-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 82479, rend_intergenic: 76061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106035, rend_intergenic: 100435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116769, rend_intergenic: 112089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170785, rend_intergenic: 168593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 84964, rend_intergenic: 84961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172216
-exon list size: 436


building trellis

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0.9    
1.1    
1.4    
1.6    
1.8    
2.1    
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2.5    
2.7    
3.0    
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3.9    
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4.6    
4.8    
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5.9    
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8.9    
9.1    
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9.8    
10.0    
10.3    
10.5    
10.7    
11.0    
11.2    
11.4    
11.6    
11.9    
12.1    
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12.6    
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13.5    
13.7    
13.9    
14.2    
14.4    
14.6    
14.8    
15.1    
15.3    
15.5    
15.8    
16.0    
16.2    
16.4    
16.7    
16.9    
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17.6    
17.8    
18.0    
18.3    
18.5    
18.7    
18.9    
19.2    
19.4    
19.6    
19.9    
20.1    
20.3    
20.5    
20.8    
21.0    
21.2    
21.5    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
26.7    
26.9    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.1    
30.4    
30.6    
30.8    
31.1    
31.3    
31.5    
31.7    
32.0    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.2    
35.4    
35.6    
35.8    
36.1    
36.3    
36.5    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.7    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
47.9    
48.2    
48.4    
48.6    
48.9    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.1    
51.4    
51.6    
51.8    
52.1    
52.3    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.3    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.8    
57.1    
57.3    
57.5    
57.8    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
61.0    
61.2    
61.4    
61.6    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.5    
63.7    
63.9    
64.2    
64.4    
64.6    
64.8    
65.1    
65.3    
65.5    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.0    
68.3    
68.5    
68.7    
68.9    
69.2    
69.4    
69.6    
69.9    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.1    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.5    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.7    
82.0    
82.2    
82.4    
82.6    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 82479, rend_intergenic: 76061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106035, rend_intergenic: 100435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116769, rend_intergenic: 112089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170785, rend_intergenic: 168593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 84964, rend_intergenic: 84961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support