-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_16078471-16288549

-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 pasa_asmbl_9121.p1
Valid prediction for GeneMark_model.54246_t
Valid prediction for GeneMark_model.54239_t
Valid prediction for GeneMark_model.54241_t
Valid prediction for snap_scaffold_12-snap.3110-T1
Valid prediction for GlimmerHMM_glimmerT_31447-T1
Valid prediction for Augustus_model.g20966.t1
Valid prediction for snap_scaffold_12-snap.3127-T1
Valid prediction for GeneMark_model.54245_t
Valid prediction for GlimmerHMM_glimmerT_31429-T1
Valid prediction for snap_scaffold_12-snap.3153-T1
Valid prediction for snap_scaffold_12-snap.3114-T1
Valid prediction for snap_scaffold_12-snap.3139-T1
Valid prediction for GlimmerHMM_glimmerT_31426-T1
Valid prediction for GlimmerHMM_glimmerT_31452-T1
Valid prediction for snap_scaffold_12-snap.3126-T1
Valid prediction for snap_scaffold_12-snap.3134-T1
Valid prediction for snap_scaffold_12-snap.3129-T1
Valid prediction for GeneMark_model.54235_t
Valid prediction for snap_scaffold_12-snap.3116-T1
Valid prediction for GeneMark_model.54260_t
Valid prediction for Augustus_model.g20968.t1
Couldn't classify 152583, 152927
Sorry, prediction pasa_asmbl_8250.p1 fails validation.
(GTC)	 TT	152583-152927	AT	AGA
Valid prediction for Augustus_model.g20955.t1
Valid prediction for GeneMark_model.54236_t
Valid prediction for GlimmerHMM_glimmerT_31436-T1
Valid prediction for GlimmerHMM_glimmerT_31425-T1
Valid prediction for snap_scaffold_12-snap.3125-T1
Valid prediction for snap_scaffold_12-snap.3132-T1
Valid prediction for snap_scaffold_12-snap.3150-T1
Valid prediction for GlimmerHMM_glimmerT_31444-T1
Valid prediction for snap_scaffold_12-snap.3123-T1
Valid prediction for snap_scaffold_12-snap.3151-T1
Valid prediction for Augustus_model.g20963.t1
Valid prediction for Augustus_model.g20969.t1
Valid prediction for snap_scaffold_12-snap.3112-T1
Valid prediction for Augustus_model.g20979.t1
Valid prediction for GlimmerHMM_glimmerT_31427-T1
Valid prediction for GeneMark_model.54258_t
Valid prediction for Augustus_model.g20956.t1
Valid prediction for GlimmerHMM_glimmerT_31446-T1
Valid prediction for snap_scaffold_12-snap.3124-T1
Valid prediction for GeneMark_model.54238_t
Valid prediction for GlimmerHMM_glimmerT_31434-T1
Couldn't classify 32404, 32460
Sorry, prediction pasa_asmbl_9107.p1 fails validation.
(AAA)	 TG	32404-32460	GT	AGG
(GAC)	 AG	33940-34185	GG	AAG
-recovered pasa_asmbl_9107.p1, terminal, 33940, 34185
Valid prediction for Augustus_model.g20967.t1
Valid prediction for GlimmerHMM_glimmerT_31428-T1
Valid prediction for GeneMark_model.54253_t
Valid prediction for GeneMark_model.54257_t
Valid prediction for snap_scaffold_12-snap.3128-T1
Valid prediction for GlimmerHMM_glimmerT_31433-T1
Valid prediction for GeneMark_model.54234_t
Valid prediction for GlimmerHMM_glimmerT_31430-T1
Valid prediction for GeneMark_model.54249_t
Valid prediction for Augustus_model.g20960.t1
Valid prediction for GeneMark_model.54248_t
Valid prediction for GeneMark_model.54232_t
Valid prediction for snap_scaffold_12-snap.3121-T1
Valid prediction for Augustus_model.g20965.t1
Valid prediction for GeneMark_model.54243_t
Valid prediction for GlimmerHMM_glimmerT_31435-T1
Valid prediction for Augustus_model.g20988.t1
Valid prediction for GlimmerHMM_glimmerT_31442-T1
Valid prediction for GlimmerHMM_glimmerT_31450-T1
Valid prediction for GlimmerHMM_glimmerT_31445-T1
Valid prediction for snap_scaffold_12-snap.3141-T1
Valid prediction for snap_scaffold_12-snap.3142-T1
Valid prediction for Augustus_model.g20980.t1
Valid prediction for Augustus_model.g20978.t1
Valid prediction for Augustus_model.g20985.t1
Valid prediction for Augustus_model.g20957.t1
Valid prediction for GlimmerHMM_glimmerT_31437-T1
Valid prediction for snap_scaffold_12-snap.3122-T1
Valid prediction for Augustus_model.g20982.t1
Valid prediction for snap_scaffold_12-snap.3144-T1
Valid prediction for Augustus_model.g20959.t1
Valid prediction for snap_scaffold_12-snap.3115-T1
Valid prediction for GlimmerHMM_glimmerT_31454-T1
Valid prediction for Augustus_model.g20986.t1
Valid prediction for GlimmerHMM_glimmerT_31448-T1
Valid prediction for Augustus_model.g20975.t1
Valid prediction for GeneMark_model.54237_t
Valid prediction for snap_scaffold_12-snap.3136-T1
Valid prediction for Augustus_model.g20964.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 snap_scaffold_12-snap.3145-T1
Couldn't classify 81436, 81543
Sorry, prediction pasa_asmbl_8247.p1 fails validation.
(TCA)	 TT	81436-81543	GT	AGG
(AAC)	 AG	82733-82840	GT	AGG
(GGT)	 AG	83417-83641	GA	GAG
-recovered pasa_asmbl_8247.p1, terminal, 83417, 83641
-recovered pasa_asmbl_8247.p1, internal, 82733, 82840
Valid prediction for GeneMark_model.54254_t
Valid prediction for snap_scaffold_12-snap.3148-T1
Valid prediction for Augustus_model.g20976.t1
Valid prediction for CodingQuarry_transcript_10487-T1
Valid prediction for GlimmerHMM_glimmerT_31455-T1
Valid prediction for CodingQuarry_transcript_10485-T1
Valid prediction for CodingQuarry_transcript_10488-T1
Valid prediction for GlimmerHMM_glimmerT_31440-T1
Valid prediction for HiQ_model.g20970.t1
Valid prediction for GeneMark_model.54231_t
Valid prediction for GeneMark_model.54255_t
Couldn't classify 14235, 14367
Sorry, prediction pasa_asmbl_8253.p1 fails validation.
(GGG)	 AG	14235-14367	GT	GGG
(AGG)	 AG	14527-14653	GT	AGG
(CCA)	 AG	14891-15006	GT	AGG
(ATC)	 AG	15178-15215	AG	AAA
-recovered pasa_asmbl_8253.p1, terminal, 14891, 15006
-recovered pasa_asmbl_8253.p1, terminal, 15178, 15215
-recovered pasa_asmbl_8253.p1, internal, 14235, 14367
-recovered pasa_asmbl_8253.p1, internal, 14527, 14653
-recovered pasa_asmbl_8253.p1, internal, 14891, 15006
Valid prediction for GlimmerHMM_glimmerT_31449-T1
Valid prediction for snap_scaffold_12-snap.3120-T1
Valid prediction for snap_scaffold_12-snap.3138-T1
Valid prediction for Augustus_model.g20958.t1
Valid prediction for snap_scaffold_12-snap.3113-T1
Valid prediction for snap_scaffold_12-snap.3143-T1
Valid prediction for Augustus_model.g20974.t1
Valid prediction for Augustus_model.g20981.t1
Valid prediction for Augustus_model.g20977.t1
Valid prediction for Augustus_model.g20972.t1
Valid prediction for GeneMark_model.54240_t
Valid prediction for snap_scaffold_12-snap.3154-T1
Valid prediction for GlimmerHMM_glimmerT_31443-T1
Valid prediction for snap_scaffold_12-snap.3152-T1
Valid prediction for GeneMark_model.54242_t
Valid prediction for GeneMark_model.54251_t
Valid prediction for snap_scaffold_12-snap.3137-T1
Valid prediction for Augustus_model.g20989.t1
Valid prediction for GlimmerHMM_glimmerT_31438-T1
Valid prediction for snap_scaffold_12-snap.3118-T1
Couldn't classify 73683, 73846
Couldn't classify 77369, 77587
Sorry, prediction pasa_asmbl_8248.p1 fails validation.
(GAA)	 AG	73683-73846	GT	GGG
(GAA)	 AG	76743-76872	GT	AGG
(GAT)	 AG	77369-77587	AA	GGA
-recovered pasa_asmbl_8248.p1, internal, 73683, 73846
-recovered pasa_asmbl_8248.p1, internal, 76743, 76872
Valid prediction for snap_scaffold_12-snap.3119-T1
Valid prediction for snap_scaffold_12-snap.3146-T1
Valid prediction for Augustus_model.g20973.t1
Valid prediction for GeneMark_model.54261_t
Valid prediction for GeneMark_model.54266_t
Valid prediction for GlimmerHMM_glimmerT_31441-T1
Couldn't classify 54910, 55067
Sorry, prediction pasa_asmbl_8251.p1 fails validation.
(ATG)	 CA	51706-51738	GT	TGG
(TAT)	 AG	52354-52442	GT	AGG
(GAC)	 AG	52667-52754	GT	AAG
(TAT)	 AG	54498-54672	GT	TGG
(GGA)	 AG	54910-55067	GT	AGG
-recovered pasa_asmbl_8251.p1, initial, 51706, 51738
-recovered pasa_asmbl_8251.p1, internal, 52354, 52442
-recovered pasa_asmbl_8251.p1, internal, 52667, 52754
-recovered pasa_asmbl_8251.p1, internal, 54498, 54672
-recovered pasa_asmbl_8251.p1, internal, 54910, 55067
Valid prediction for GlimmerHMM_glimmerT_31431-T1
Valid prediction for Augustus_model.g20962.t1
Valid prediction for GlimmerHMM_glimmerT_31451-T1
Valid prediction for snap_scaffold_12-snap.3130-T1
Valid prediction for snap_scaffold_12-snap.3111-T1
Valid prediction for snap_scaffold_12-snap.3149-T1
Valid prediction for Augustus_model.g20983.t1
Valid prediction for GlimmerHMM_glimmerT_31453-T1
Valid prediction for GlimmerHMM_glimmerT_31439-T1
Valid prediction for Augustus_model.g20971.t1
Valid prediction for snap_scaffold_12-snap.3133-T1
Valid prediction for GeneMark_model.54233_t
Valid prediction for snap_scaffold_12-snap.3135-T1
Valid prediction for GeneMark_model.54252_t
Valid prediction for GeneMark_model.54263_t
Valid prediction for GeneMark_model.54259_t
Valid prediction for snap_scaffold_12-snap.3140-T1
Valid prediction for snap_scaffold_12-snap.3117-T1
Valid prediction for snap_scaffold_12-snap.3131-T1
Valid prediction for snap_scaffold_12-snap.3147-T1
Valid prediction for GeneMark_model.54262_t
Valid prediction for Augustus_model.g20984.t1
Valid prediction for CodingQuarry_transcript_10486-T1
Valid prediction for GeneMark_model.54265_t
Valid prediction for GlimmerHMM_glimmerT_31432-T1
Valid prediction for GeneMark_model.54264_t
Valid prediction for Augustus_model.g20961.t1
Valid prediction for HiQ_model.g20987.t1
Valid prediction for GeneMark_model.54250_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16383, rend_intergenic: 8968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25584, rend_intergenic: 25015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210079
-exon list size: 445


building trellis

0.2    
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1.6    
1.8    
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2.9    
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3.8    
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13.9    
14.1    
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14.5    
14.8    
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15.2    
15.4    
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15.9    
16.1    
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16.6    
16.8    
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17.4    
17.7    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.2    
19.5    
19.7    
19.9    
20.1    
20.4    
20.6    
20.8    
21.0    
21.3    
21.5    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
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23.3    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
26.0    
26.2    
26.4    
26.6    
26.8    
27.1    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.5    
29.8    
30.0    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.5    
31.8    
32.0    
32.2    
32.4    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.5    
36.7    
36.9    
37.1    
37.4    
37.6    
37.8    
38.0    
38.3    
38.5    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.8    
42.1    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.8    
47.0    
47.2    
47.4    
47.7    
47.9    
48.1    
48.3    
48.5    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.5    
51.7    
51.9    
52.1    
52.3    
52.6    
52.8    
53.0    
53.2    
53.5    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
57.9    
58.2    
58.4    
58.6    
58.8    
59.1    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.9    
61.1    
61.3    
61.5    
61.7    
62.0    
62.2    
62.4    
62.6    
62.9    
63.1    
63.3    
63.5    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.3    
65.5    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.3    
67.6    
67.8    
68.0    
68.2    
68.5    
68.7    
68.9    
69.1    
69.4    
69.6    
69.8    
70.0    
70.2    
70.5    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.0    
72.3    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.8    
74.0    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.5    
78.7    
79.0    
79.2    
79.4    
79.6    
79.9    
80.1    
80.3    
80.5    
80.8    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.3    
82.6    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.3    
84.6    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.4    
86.6    
86.8    
87.0    
87.2    
87.5    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
89.9    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.8    
93.1    
93.3    
93.5    
93.7    
94.0    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 16383, rend_intergenic: 8968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25584, rend_intergenic: 25015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 41 predictions persist after filtering for low support