-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_11835206-11988438

-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 snap_scaffold_10-snap.2341-T1
Valid prediction for CodingQuarry_transcript_5587-T1
Valid prediction for CodingQuarry_transcript_5579-T1
Valid prediction for GlimmerHMM_glimmerT_25506-T1
Valid prediction for GlimmerHMM_glimmerT_25516-T1
Valid prediction for snap_scaffold_10-snap.2317-T1
Couldn't classify 116477, 116653
Sorry, prediction pasa_asmbl_3506.p1 fails validation.
(AAC)	 CA	116477-116653	GT	AGG
(CGC)	 AG	116904-117015	GT	CGG
(TTG)	 AG	117221-117297	GT	AGG
(AGC)	 AG	117390-117481	GT	AGG
(GGG)	 AG	117599-117698	GT	AGG
(AAA)	 AG	118019-118094	GT	AGG
(GGG)	 AG	118191-118306	GT	CTG
(GGG)	 AG	118433-118537	GA	GAG
-recovered pasa_asmbl_3506.p1, terminal, 118019, 118094
-recovered pasa_asmbl_3506.p1, terminal, 118433, 118537
-recovered pasa_asmbl_3506.p1, internal, 116904, 117015
-recovered pasa_asmbl_3506.p1, internal, 117221, 117297
-recovered pasa_asmbl_3506.p1, internal, 117390, 117481
-recovered pasa_asmbl_3506.p1, internal, 117599, 117698
-recovered pasa_asmbl_3506.p1, internal, 118019, 118094
-recovered pasa_asmbl_3506.p1, internal, 118191, 118306
Valid prediction for snap_scaffold_10-snap.2338-T1
Valid prediction for pasa_asmbl_3508.p1
Valid prediction for CodingQuarry_transcript_5588-T1
Valid prediction for GlimmerHMM_glimmerT_25509-T1
Valid prediction for snap_scaffold_10-snap.2323-T1
Valid prediction for CodingQuarry_transcript_5590-T1
Valid prediction for snap_scaffold_10-snap.2315-T1
Valid prediction for snap_scaffold_10-snap.2320-T1
Valid prediction for snap_scaffold_10-snap.2309-T1
Valid prediction for HiQ_model.g16974.t1
Valid prediction for HiQ_model.g16964.t1
Valid prediction for GlimmerHMM_glimmerT_25507-T1
Valid prediction for snap_scaffold_10-snap.2333-T1
Valid prediction for snap_scaffold_10-snap.2329-T1
Valid prediction for HiQ_model.g16961.t1
Valid prediction for pasa_asmbl_3501.p1
Valid prediction for Augustus_model.g16963.t1
Valid prediction for GlimmerHMM_glimmerT_25512-T1
Valid prediction for snap_scaffold_10-snap.2326-T1
Valid prediction for snap_scaffold_10-snap.2335-T1
Valid prediction for snap_scaffold_10-snap.2319-T1
Valid prediction for snap_scaffold_10-snap.2314-T1
Valid prediction for snap_scaffold_10-snap.2325-T1
Valid prediction for HiQ_model.g16970.t1
Couldn't classify 35896, 35955
Sorry, prediction pasa_asmbl_3499.p1 fails validation.
(TTC)	 AG	35896-35955	GT	AGG
(TAT)	 AG	36132-36279	GT	TGG
(GTC)	 AG	36406-36654	GT	CGG
(GTG)	 AG	36795-36957	GT	AGG
(TTT)	 AG	37263-37351	GT	TGG
(ACT)	 AG	37443-37529	GT	AGG
(CCA)	 AG	37619-37727	GT	ATG
(GAT)	 AG	37862-37938	GT	AAG
(GTT)	 AG	38253-38299	GT	TGG
(GAT)	 AG	38418-38660	TG	AAT
-recovered pasa_asmbl_3499.p1, terminal, 38418, 38660
-recovered pasa_asmbl_3499.p1, internal, 35896, 35955
-recovered pasa_asmbl_3499.p1, internal, 36132, 36279
-recovered pasa_asmbl_3499.p1, internal, 36406, 36654
-recovered pasa_asmbl_3499.p1, internal, 36795, 36957
-recovered pasa_asmbl_3499.p1, internal, 37263, 37351
-recovered pasa_asmbl_3499.p1, internal, 37443, 37529
-recovered pasa_asmbl_3499.p1, internal, 37619, 37727
-recovered pasa_asmbl_3499.p1, internal, 37862, 37938
-recovered pasa_asmbl_3499.p1, internal, 38253, 38299
Valid prediction for GlimmerHMM_glimmerT_25504-T1
Valid prediction for Augustus_model.g16966.t1
Valid prediction for snap_scaffold_10-snap.2311-T1
Valid prediction for snap_scaffold_10-snap.2339-T1
Valid prediction for CodingQuarry_transcript_5589-T1
Valid prediction for snap_scaffold_10-snap.2336-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_10-snap.2327-T1
Valid prediction for snap_scaffold_10-snap.2316-T1
Valid prediction for GlimmerHMM_glimmerT_25503-T1
Valid prediction for Augustus_model.g16972.t1
Valid prediction for CodingQuarry_transcript_5584-T1
Valid prediction for HiQ_model.g16960.t1
Valid prediction for snap_scaffold_10-snap.2321-T1
Valid prediction for GlimmerHMM_glimmerT_25501-T1
Valid prediction for GlimmerHMM_glimmerT_25517-T1
Valid prediction for pasa_asmbl_4792.p1
Valid prediction for pasa_asmbl_4801.p1
Valid prediction for Augustus_model.g16969.t1
Couldn't classify 129826, 129979
Couldn't classify 130195, 130787
Sorry, prediction pasa_asmbl_4789.p1 fails validation.
(GGT)	 CA	129826-129979	GT	AGG
(GTG)	 AG	130195-130787	CA	GAC
Valid prediction for pasa_asmbl_4804.p1
Valid prediction for snap_scaffold_10-snap.2334-T1
Valid prediction for snap_scaffold_10-snap.2308-T1
Couldn't classify 131139, 132332
Sorry, prediction pasa_asmbl_4788.p1 fails validation.
(GAT)	 GG	131139-132332	TT	ACT
Valid prediction for HiQ_model.g16962.t1
Valid prediction for snap_scaffold_10-snap.2324-T1
Valid prediction for snap_scaffold_10-snap.2318-T1
Valid prediction for snap_scaffold_10-snap.2313-T1
Couldn't classify 22527, 22602
Couldn't classify 22740, 22814
Sorry, prediction CodingQuarry_transcript_5586-T1 fails validation.
(ATG)	 TA	21812-21900	GT	CTG
(TAA)	 AG	22527-22602	AT	ATA
(CTA)	 AT	22740-22814	GT	ATG
(GCT)	 AG	22932-23047	GT	AGG
(AGC)	 AG	23185-23317	CA	AAC
-recovered CodingQuarry_transcript_5586-T1, initial, 21812, 21900
-recovered CodingQuarry_transcript_5586-T1, terminal, 23185, 23317
-recovered CodingQuarry_transcript_5586-T1, internal, 22932, 23047
Valid prediction for Augustus_model.g16971.t1
Valid prediction for snap_scaffold_10-snap.2328-T1
Valid prediction for GlimmerHMM_glimmerT_25514-T1
Valid prediction for snap_scaffold_10-snap.2310-T1
Valid prediction for CodingQuarry_transcript_5585-T1
Valid prediction for Augustus_model.g16958.t1
Valid prediction for snap_scaffold_10-snap.2331-T1
Valid prediction for CodingQuarry_transcript_5582-T1
Valid prediction for Augustus_model.g16957.t1
Valid prediction for snap_scaffold_10-snap.2312-T1
Valid prediction for CodingQuarry_transcript_5578-T1
Valid prediction for snap_scaffold_10-snap.2337-T1
Valid prediction for Augustus_model.g16975.t1
Valid prediction for GlimmerHMM_glimmerT_25505-T1
Valid prediction for Augustus_model.g16973.t1
Valid prediction for snap_scaffold_10-snap.2332-T1
Valid prediction for pasa_asmbl_4793.p1
Valid prediction for GlimmerHMM_glimmerT_25515-T1
Valid prediction for HiQ_model.g16965.t1
Valid prediction for snap_scaffold_10-snap.2322-T1
Valid prediction for Augustus_model.g16967.t1
Couldn't classify 26017, 26077
Sorry, prediction pasa_asmbl_5196.p1 fails validation.
(ATG)	 GC	24259-24352	GT	AGG
(GTA)	 AG	24455-24610	GT	TGG
(GCC)	 AG	24813-24935	GT	AGG
(GTA)	 AG	25422-25521	GT	AGG
(GTT)	 AG	25648-25728	GT	AGG
(TGC)	 AG	26017-26077	GC	AGG
-recovered pasa_asmbl_5196.p1, initial, 24259, 24352
-recovered pasa_asmbl_5196.p1, internal, 24455, 24610
-recovered pasa_asmbl_5196.p1, internal, 24813, 24935
-recovered pasa_asmbl_5196.p1, internal, 25422, 25521
-recovered pasa_asmbl_5196.p1, internal, 25648, 25728
-recovered pasa_asmbl_5196.p1, internal, 26017, 26077
Valid prediction for GlimmerHMM_glimmerT_25511-T1
Valid prediction for GlimmerHMM_glimmerT_25508-T1
Valid prediction for CodingQuarry_transcript_5577-T1
Valid prediction for Augustus_model.g16968.t1
Valid prediction for Augustus_model.g16959.t1
Valid prediction for CodingQuarry_transcript_5581-T1
Valid prediction for GlimmerHMM_glimmerT_25513-T1
Valid prediction for GlimmerHMM_glimmerT_25502-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for pasa_asmbl_4799.p1
Valid prediction for GlimmerHMM_glimmerT_25500-T1
Couldn't classify 76794, 77028
Sorry, prediction pasa_asmbl_4800.p1 fails validation.
(CAT)	 AT	76794-77028	GT	AGG
(GAA)	 AG	77190-77335	GA	AGG
-recovered pasa_asmbl_4800.p1, terminal, 77190, 77335
Valid prediction for CodingQuarry_transcript_5583-T1
Valid prediction for snap_scaffold_10-snap.2330-T1
Valid prediction for GlimmerHMM_glimmerT_25510-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24642, rend_intergenic: 24129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98273, rend_intergenic: 90157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111396, rend_intergenic: 105295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124326, rend_intergenic: 116835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128905, rend_intergenic: 124465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 153233
-exon list size: 405


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
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2.5    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.2    
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4.9    
5.2    
5.4    
5.7    
5.9    
6.1    
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8.4    
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8.8    
9.1    
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10.1    
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10.6    
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11.1    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.8    
13.0    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.7    
15.0    
15.2    
15.5    
15.7    
16.0    
16.2    
16.5    
16.7    
17.0    
17.2    
17.4    
17.7    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.3    
23.6    
23.8    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.8    
28.0    
28.3    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.4    
31.7    
31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
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    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.5    
54.8    
55.0    
55.3    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
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61.9    
62.2    
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62.9    
63.1    
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63.6    
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64.4    
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66.3    
66.6    
66.8    
67.1    
67.3    
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68.1    
68.3    
68.6    
68.8    
69.0    
69.3    
69.5    
69.8    
70.0    
70.3    
70.5    
70.8    
71.0    
71.3    
71.5    
71.7    
72.0    
72.2    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.4    
76.7    
76.9    
77.1    
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77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.0    
83.3    
83.5    
83.8    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 24642, rend_intergenic: 24129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98273, rend_intergenic: 90157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111396, rend_intergenic: 105295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124326, rend_intergenic: 116835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128905, rend_intergenic: 124465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support