-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_573633-860241

-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.g34639.t1
Valid prediction for GlimmerHMM_glimmerT_51582-T1
Valid prediction for GlimmerHMM_glimmerT_51590-T1
Valid prediction for GlimmerHMM_glimmerT_51571-T1
Valid prediction for snap_scaffold_23-snap.101-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.115-T1
Valid prediction for GlimmerHMM_glimmerT_51569-T1
Valid prediction for GlimmerHMM_glimmerT_51599-T1
Valid prediction for Augustus_model.g34620.t1
Valid prediction for GeneMark_model.89722_t
Valid prediction for snap_scaffold_23-snap.95-T1
Valid prediction for snap_scaffold_23-snap.92-T1
Valid prediction for snap_scaffold_23-snap.112-T1
Valid prediction for Augustus_model.g34628.t1
Valid prediction for snap_scaffold_23-snap.100-T1
Valid prediction for GlimmerHMM_glimmerT_51593-T1
Valid prediction for GeneMark_model.89739_t
Valid prediction for GeneMark_model.89749_t
Valid prediction for Augustus_model.g34637.t1
Valid prediction for snap_scaffold_23-snap.117-T1
Valid prediction for snap_scaffold_23-snap.98-T1
Valid prediction for GlimmerHMM_glimmerT_51585-T1
Valid prediction for GeneMark_model.89726_t
Valid prediction for snap_scaffold_23-snap.94-T1
Valid prediction for GlimmerHMM_glimmerT_51579-T1
Valid prediction for Augustus_model.g34642.t1
Valid prediction for Augustus_model.g34616.t1
Valid prediction for Augustus_model.g34636.t1
Valid prediction for GeneMark_model.89724_t
Valid prediction for snap_scaffold_23-snap.99-T1
Valid prediction for GeneMark_model.89737_t
Valid prediction for snap_scaffold_23-snap.97-T1
Valid prediction for GeneMark_model.89725_t
Valid prediction for GlimmerHMM_glimmerT_51577-T1
Valid prediction for GeneMark_model.89734_t
Valid prediction for snap_scaffold_23-snap.91-T1
Couldn't classify 14730, 15326
Sorry, prediction pasa_asmbl_30603.p1 fails validation.
(AAG)	 CT	14730-15326	GT	CTG
Valid prediction for GeneMark_model.89727_t
Valid prediction for Augustus_model.g34615.t1
Valid prediction for GeneMark_model.89748_t
Valid prediction for GlimmerHMM_glimmerT_51574-T1
Valid prediction for Augustus_model.g34644.t1
Couldn't classify 13890, 14249
Sorry, prediction pasa_asmbl_30602.p1 fails validation.
(ATG)	 TC	13890-14249	CT	ACC
Valid prediction for Augustus_model.g34621.t1
Valid prediction for snap_scaffold_23-snap.108-T1
Valid prediction for Augustus_model.g34625.t1
Valid prediction for GeneMark_model.89750_t
Valid prediction for snap_scaffold_23-snap.111-T1
Valid prediction for GlimmerHMM_glimmerT_51576-T1
Valid prediction for snap_scaffold_23-snap.106-T1
Valid prediction for GeneMark_model.89729_t
Valid prediction for snap_scaffold_23-snap.93-T1
Valid prediction for GeneMark_model.89731_t
Valid prediction for snap_scaffold_23-snap.103-T1
Valid prediction for GeneMark_model.89736_t
Couldn't classify 15582, 15938
Sorry, prediction pasa_asmbl_30604.p1 fails validation.
(ATT)	 AT	15582-15938	GG	AGG
Valid prediction for GlimmerHMM_glimmerT_51580-T1
Valid prediction for Augustus_model.g34622.t1
Valid prediction for Augustus_model.g34640.t1
Valid prediction for Augustus_model.g34619.t1
Valid prediction for snap_scaffold_23-snap.82-T1
Valid prediction for Augustus_model.g34626.t1
Valid prediction for GlimmerHMM_glimmerT_51572-T1
Valid prediction for GlimmerHMM_glimmerT_51591-T1
Valid prediction for Augustus_model.g34623.t1
Valid prediction for Augustus_model.g34618.t1
Valid prediction for GlimmerHMM_glimmerT_51594-T1
Valid prediction for GlimmerHMM_glimmerT_51596-T1
Valid prediction for snap_scaffold_23-snap.114-T1
Valid prediction for snap_scaffold_23-snap.86-T1
Valid prediction for Augustus_model.g34630.t1
Valid prediction for GeneMark_model.89751_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_23-snap.84-T1
Valid prediction for snap_scaffold_23-snap.118-T1
Couldn't classify 99235, 99400
Couldn't classify 102291, 102439
Sorry, prediction pasa_asmbl_31323.p1 fails validation.
(GTA)	 AG	99235-99400	GT	GGG
(GAA)	 AG	100882-101056	GT	CGG
(TTA)	 AG	101288-101393	GT	GTG
(TCC)	 AG	101669-101867	GT	AGG
(ACA)	 AG	102291-102439	GT	AGG
-recovered pasa_asmbl_31323.p1, internal, 99235, 99400
-recovered pasa_asmbl_31323.p1, internal, 100882, 101056
-recovered pasa_asmbl_31323.p1, internal, 101288, 101393
-recovered pasa_asmbl_31323.p1, internal, 101669, 101867
-recovered pasa_asmbl_31323.p1, internal, 102291, 102439
Valid prediction for GlimmerHMM_glimmerT_51583-T1
Valid prediction for Augustus_model.g34634.t1
Valid prediction for Augustus_model.g34624.t1
Valid prediction for Augustus_model.g34617.t1
Valid prediction for snap_scaffold_23-snap.83-T1
Valid prediction for GeneMark_model.89730_t
Valid prediction for snap_scaffold_23-snap.90-T1
Valid prediction for GeneMark_model.89738_t
Valid prediction for GeneMark_model.89747_t
Valid prediction for GlimmerHMM_glimmerT_51586-T1
Valid prediction for GlimmerHMM_glimmerT_51598-T1
Valid prediction for GeneMark_model.89743_t
Valid prediction for snap_scaffold_23-snap.119-T1
Valid prediction for GeneMark_model.89742_t
Couldn't classify 19870, 20025
Couldn't classify 21397, 21510
Sorry, prediction pasa_asmbl_31928.p1 fails validation.
(AAG)	 TG	19870-20025	GT	AGG
(CGT)	 AG	20224-20339	GT	AGG
(AAA)	 AG	20542-20697	GT	AGG
(AGT)	 AG	20842-20950	GT	AGG
(ATT)	 AG	21397-21510	GG	AAG
-recovered pasa_asmbl_31928.p1, internal, 20224, 20339
-recovered pasa_asmbl_31928.p1, internal, 20542, 20697
-recovered pasa_asmbl_31928.p1, internal, 20842, 20950
Valid prediction for GlimmerHMM_glimmerT_51600-T1
Valid prediction for Augustus_model.g34641.t1
Valid prediction for Augustus_model.g34632.t1
Valid prediction for GeneMark_model.89746_t
Valid prediction for GlimmerHMM_glimmerT_51581-T1
Valid prediction for CodingQuarry_transcript_35475-T1
Valid prediction for GeneMark_model.89733_t
Couldn't classify 58928, 59245
Sorry, prediction pasa_asmbl_31329.p5 fails validation.
(ATG)	 AG	58928-59245	AA	GCA
Valid prediction for snap_scaffold_23-snap.113-T1
Valid prediction for snap_scaffold_23-snap.120-T1
Valid prediction for Augustus_model.g34631.t1
Valid prediction for GlimmerHMM_glimmerT_51587-T1
Valid prediction for GeneMark_model.89753_t
Valid prediction for GeneMark_model.89741_t
Valid prediction for snap_scaffold_23-snap.116-T1
Valid prediction for Augustus_model.g34635.t1
Valid prediction for Augustus_model.g34645.t1
Valid prediction for GlimmerHMM_glimmerT_51578-T1
Valid prediction for GlimmerHMM_glimmerT_51584-T1
Valid prediction for GeneMark_model.89740_t
Valid prediction for GlimmerHMM_glimmerT_51592-T1
Valid prediction for snap_scaffold_23-snap.87-T1
Couldn't classify 35745, 35913
Couldn't classify 37681, 37881
Sorry, prediction pasa_asmbl_31331.p1 fails validation.
(AAG)	 AG	35745-35913	GT	AGG
(ATT)	 AG	36152-36357	GT	AGG
(ATC)	 AG	37681-37881	CC	TGC
add_exon() Sorry, pasa_asmbl_31331.p1 35745-35913-terminal-3 is invalid.
-recovered pasa_asmbl_31331.p1, terminal, 35745, 35913
-recovered pasa_asmbl_31331.p1, internal, 35745, 35913
-recovered pasa_asmbl_31331.p1, internal, 36152, 36357
Valid prediction for HiQ_model.g34629.t1
Valid prediction for GlimmerHMM_glimmerT_51575-T1
Valid prediction for Augustus_model.g34627.t1
Valid prediction for snap_scaffold_23-snap.105-T1
Valid prediction for HiQ_model.g34633.t1
Valid prediction for GlimmerHMM_glimmerT_51588-T1
Valid prediction for GlimmerHMM_glimmerT_51589-T1
Valid prediction for snap_scaffold_23-snap.104-T1
Valid prediction for GeneMark_model.89735_t
Valid prediction for GlimmerHMM_glimmerT_51597-T1
Valid prediction for Augustus_model.g34638.t1
Valid prediction for snap_scaffold_23-snap.107-T1
Valid prediction for snap_scaffold_23-snap.110-T1
Valid prediction for GlimmerHMM_glimmerT_51573-T1
Valid prediction for GeneMark_model.89752_t
Valid prediction for GlimmerHMM_glimmerT_51595-T1
Valid prediction for snap_scaffold_23-snap.96-T1
Valid prediction for snap_scaffold_23-snap.102-T1
Couldn't classify 258943, 259635
Sorry, prediction pasa_asmbl_31321.p1 fails validation.
(GCA)	 TT	258943-259635	AC	GAA
Couldn't classify 109142, 109372
Sorry, prediction pasa_asmbl_31322.p1 fails validation.
(ATC)	 AG	109142-109372	GT	AGG
(AAA)	 AG	109537-109603	GT	AAG
(GAC)	 AG	112135-112242	GT	TGG
(GAT)	 AG	112355-112402	GT	AGG
(GAT)	 AG	113893-114014	GG	GAG
-recovered pasa_asmbl_31322.p1, terminal, 113893, 114014
-recovered pasa_asmbl_31322.p1, internal, 109142, 109372
-recovered pasa_asmbl_31322.p1, internal, 109537, 109603
-recovered pasa_asmbl_31322.p1, internal, 112135, 112242
-recovered pasa_asmbl_31322.p1, internal, 112355, 112402
Valid prediction for snap_scaffold_23-snap.85-T1
Valid prediction for GlimmerHMM_glimmerT_51570-T1
Valid prediction for snap_scaffold_23-snap.88-T1
Valid prediction for snap_scaffold_23-snap.89-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g34643.t1
Valid prediction for snap_scaffold_23-snap.109-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 227213, rend_intergenic: 226349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 286609
-exon list size: 399


building trellis

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21.9    
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22.7    
22.9    
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23.9    
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24.9    
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26.9    
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31.7    
31.9    
32.2    
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33.4    
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34.2    
34.4    
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34.9    
35.2    
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35.9    
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36.4    
36.7    
36.9    
37.2    
37.4    
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37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
46.9    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.6    
51.9    
52.1    
52.4    
52.6    
52.9    
53.1    
53.4    
53.6    
53.9    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.6    
63.8    
64.1    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.1    
68.3    
68.6    
68.8    
69.1    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.3    
73.6    
73.8    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.8    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 227213, rend_intergenic: 226349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 39 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13889
-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

-building DP trellis

-building trellis in range 1 - 13459
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 1 - 11605
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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