-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_3382952-3521195

-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 GlimmerHMM_glimmerT_58526-T1
Valid prediction for GlimmerHMM_glimmerT_58535-T1
Valid prediction for snap_scaffold_28-snap.876-T1
Valid prediction for GlimmerHMM_glimmerT_58552-T1
Valid prediction for Augustus_model.g38770.t1
Valid prediction for GlimmerHMM_glimmerT_58534-T1
Valid prediction for GlimmerHMM_glimmerT_58548-T1
Valid prediction for Augustus_model.g38777.t1
Valid prediction for GlimmerHMM_glimmerT_58533-T1
Valid prediction for snap_scaffold_28-snap.865-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.883-T1
Valid prediction for GlimmerHMM_glimmerT_58549-T1
Valid prediction for GlimmerHMM_glimmerT_58551-T1
Valid prediction for Augustus_model.g38775.t1
Couldn't classify 3471, 3509
Sorry, prediction pasa_asmbl_37480.p1 fails validation.
(CTT)	 TC	3471-3509	GT	AGG
(GTC)	 AG	4216-4260	GT	AGG
(ACG)	 AG	4503-4724	GC	AGG
(GCT)	 AG	4749-5054	GT	AGG
(GTC)	 AG	5662-5703	GT	TGG
(GTG)	 AG	6074-6145	GT	AGG
(GTC)	 AG	6284-6397	GT	AGG
(GTG)	 AG	6609-6713	GT	AGG
(GCT)	 AG	7504-7542	GT	AGG
(GAC)	 AG	7682-7810	GT	TGG
(GAA)	 AG	8196-8255	GT	AGG
-recovered pasa_asmbl_37480.p1, terminal, 8196, 8255
-recovered pasa_asmbl_37480.p1, internal, 4216, 4260
-recovered pasa_asmbl_37480.p1, internal, 4503, 4724
-recovered pasa_asmbl_37480.p1, internal, 4749, 5054
-recovered pasa_asmbl_37480.p1, internal, 5662, 5703
-recovered pasa_asmbl_37480.p1, internal, 6074, 6145
-recovered pasa_asmbl_37480.p1, internal, 6284, 6397
-recovered pasa_asmbl_37480.p1, internal, 6609, 6713
-recovered pasa_asmbl_37480.p1, internal, 7504, 7542
-recovered pasa_asmbl_37480.p1, internal, 7682, 7810
-recovered pasa_asmbl_37480.p1, internal, 8196, 8255
Couldn't classify 21173, 21309
Sorry, prediction pasa_asmbl_37485.p1 fails validation.
(ACA)	 AA	21173-21309	GT	AGG
(AAT)	 AG	21640-21835	GT	AGG
(GAC)	 AG	22004-22170	GT	TAG
(TGA)	 AG	22276-22416	GT	AGG
(ATG)	 AG	22674-22852	GT	AAG
(ACT)	 AG	22957-23070	GT	GGG
(GGC)	 AG	23393-23496	GT	AGG
(GTG)	 AG	23849-24040	CG	GAC
add_exon() Sorry, pasa_asmbl_37485.p1 22674-22852-initial-1 is invalid.
-recovered pasa_asmbl_37485.p1, initial, 22674, 22852
-recovered pasa_asmbl_37485.p1, terminal, 23849, 24040
-recovered pasa_asmbl_37485.p1, internal, 21640, 21835
-recovered pasa_asmbl_37485.p1, internal, 22004, 22170
-recovered pasa_asmbl_37485.p1, internal, 22276, 22416
-recovered pasa_asmbl_37485.p1, internal, 22674, 22852
-recovered pasa_asmbl_37485.p1, internal, 22957, 23070
-recovered pasa_asmbl_37485.p1, internal, 23393, 23496
Couldn't classify 37057, 37165
Couldn't classify 38069, 38129
Sorry, prediction pasa_asmbl_37486.p1 fails validation.
(CCT)	 GG	37057-37165	GT	CAG
(AGT)	 AG	37406-37538	GT	CGG
(GAC)	 AG	38069-38129	AG	ACA
-recovered pasa_asmbl_37486.p1, internal, 37406, 37538
Valid prediction for GlimmerHMM_glimmerT_58531-T1
Valid prediction for snap_scaffold_28-snap.872-T1
Valid prediction for Augustus_model.g38773.t1
Valid prediction for snap_scaffold_28-snap.877-T1
Valid prediction for Augustus_model.g38768.t1
Valid prediction for Augustus_model.g38778.t1
Valid prediction for GlimmerHMM_glimmerT_58528-T1
Valid prediction for snap_scaffold_28-snap.862-T1
Valid prediction for HiQ_model.g38771.t1
Valid prediction for snap_scaffold_28-snap.864-T1
Valid prediction for snap_scaffold_28-snap.860-T1
Valid prediction for snap_scaffold_28-snap.853-T1
Valid prediction for GlimmerHMM_glimmerT_58544-T1
Valid prediction for HiQ_model.g38772.t1
Valid prediction for snap_scaffold_28-snap.881-T1
Valid prediction for GlimmerHMM_glimmerT_58530-T1
Valid prediction for GlimmerHMM_glimmerT_58532-T1
Valid prediction for Augustus_model.g38776.t1
Valid prediction for GlimmerHMM_glimmerT_58529-T1
Valid prediction for GlimmerHMM_glimmerT_58527-T1
Valid prediction for snap_scaffold_28-snap.854-T1
Valid prediction for snap_scaffold_28-snap.884-T1
Valid prediction for snap_scaffold_28-snap.882-T1
Valid prediction for GlimmerHMM_glimmerT_58539-T1
Valid prediction for CodingQuarry_transcript_43608-T1
Valid prediction for GlimmerHMM_glimmerT_58536-T1
Valid prediction for GlimmerHMM_glimmerT_58541-T1
Valid prediction for snap_scaffold_28-snap.869-T1
Valid prediction for snap_scaffold_28-snap.855-T1
Valid prediction for snap_scaffold_28-snap.879-T1
Valid prediction for snap_scaffold_28-snap.878-T1
Valid prediction for pasa_asmbl_37484.p1
Valid prediction for Augustus_model.g38779.t1
Valid prediction for snap_scaffold_28-snap.856-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_28-snap.871-T1
Valid prediction for HiQ_model.g38769.t1
Valid prediction for GlimmerHMM_glimmerT_58525-T1
Valid prediction for snap_scaffold_28-snap.863-T1
Valid prediction for pasa_asmbl_38150.p1
Valid prediction for GlimmerHMM_glimmerT_58553-T1
Valid prediction for snap_scaffold_28-snap.861-T1
Valid prediction for GlimmerHMM_glimmerT_58540-T1
Valid prediction for snap_scaffold_28-snap.874-T1
Valid prediction for GlimmerHMM_glimmerT_58550-T1
Valid prediction for GlimmerHMM_glimmerT_58537-T1
Valid prediction for snap_scaffold_28-snap.875-T1
Valid prediction for GlimmerHMM_glimmerT_58542-T1
Valid prediction for GlimmerHMM_glimmerT_58546-T1
Valid prediction for snap_scaffold_28-snap.870-T1
Valid prediction for GlimmerHMM_glimmerT_58524-T1
Valid prediction for snap_scaffold_28-snap.868-T1
Valid prediction for snap_scaffold_28-snap.852-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.858-T1
Valid prediction for snap_scaffold_28-snap.880-T1
Valid prediction for snap_scaffold_28-snap.873-T1
Valid prediction for Augustus_model.g38774.t1
Valid prediction for snap_scaffold_28-snap.857-T1
Valid prediction for GlimmerHMM_glimmerT_58545-T1
Valid prediction for snap_scaffold_28-snap.867-T1
Valid prediction for Augustus_model.g38782.t1
Valid prediction for GlimmerHMM_glimmerT_58543-T1
Valid prediction for GlimmerHMM_glimmerT_58547-T1
Valid prediction for snap_scaffold_28-snap.850-T1
Couldn't classify 2399, 2986
Sorry, prediction pasa_asmbl_38152.p2 fails validation.
(ATG)	 CG	2399-2986	GG	GGG
Valid prediction for snap_scaffold_28-snap.859-T1
Valid prediction for GlimmerHMM_glimmerT_58538-T1
Couldn't classify 9280, 9428
Sorry, prediction pasa_asmbl_38151.p1 fails validation.
(GGT)	 CA	9280-9428	GT	AGG
(TAC)	 AG	11451-11551	GT	AGG
(CTA)	 AG	13749-13858	GT	AGG
(GCC)	 AG	16810-17013	AC	GAA
-recovered pasa_asmbl_38151.p1, terminal, 16810, 17013
-recovered pasa_asmbl_38151.p1, internal, 11451, 11551
-recovered pasa_asmbl_38151.p1, internal, 13749, 13858
Valid prediction for snap_scaffold_28-snap.851-T1
Valid prediction for Augustus_model.g38780.t1
Valid prediction for snap_scaffold_28-snap.885-T1
Valid prediction for snap_scaffold_28-snap.866-T1
Valid prediction for Augustus_model.g38781.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 44967, rend_intergenic: 28013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49126, rend_intergenic: 44970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63605, rend_intergenic: 54394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68255, rend_intergenic: 66170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81695, rend_intergenic: 70950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95968, rend_intergenic: 90624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104710, rend_intergenic: 97267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108710, rend_intergenic: 106234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117760, rend_intergenic: 110290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123508, rend_intergenic: 121232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133827, rend_intergenic: 123863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135906, rend_intergenic: 134021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 138244
-exon list size: 377


building trellis

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1.1    
1.3    
1.6    
1.8    
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2.4    
2.6    
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3.4    
3.7    
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6.3    
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6.9    
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10.6    
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11.3    
11.6    
11.9    
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14.2    
14.5    
14.8    
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15.6    
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16.6    
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17.2    
17.4    
17.7    
17.9    
18.2    
18.5    
18.7    
19.0    
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19.5    
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20.6    
20.8    
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21.4    
21.6    
21.9    
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22.4    
22.7    
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24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
31.9    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.3    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.2    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.7    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
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68.1    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
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70.2    
70.4    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.6    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.5    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.4    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
90.0    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.5    
94.7    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 44967, rend_intergenic: 28013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49126, rend_intergenic: 44970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63605, rend_intergenic: 54394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68255, rend_intergenic: 66170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81695, rend_intergenic: 70950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95968, rend_intergenic: 90624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104710, rend_intergenic: 97267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108710, rend_intergenic: 106234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117760, rend_intergenic: 110290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123508, rend_intergenic: 121232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133827, rend_intergenic: 123863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135906, rend_intergenic: 134021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support