-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_2090016-2281239

-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_16-snap.353-T1
Valid prediction for GlimmerHMM_glimmerT_37893-T1
Valid prediction for Augustus_model.g25283.t1
Valid prediction for GlimmerHMM_glimmerT_37915-T1
Valid prediction for snap_scaffold_16-snap.368-T1
Valid prediction for CodingQuarry_transcript_19904-T1
Valid prediction for snap_scaffold_16-snap.349-T1
Valid prediction for snap_scaffold_16-snap.342-T1
Valid prediction for GlimmerHMM_glimmerT_37902-T1
Valid prediction for snap_scaffold_16-snap.344-T1
Valid prediction for snap_scaffold_16-snap.339-T1
Valid prediction for GlimmerHMM_glimmerT_37910-T1
Valid prediction for snap_scaffold_16-snap.361-T1
Valid prediction for pasa_asmbl_16112.p1
Valid prediction for snap_scaffold_16-snap.331-T1
Valid prediction for GlimmerHMM_glimmerT_37908-T1
Valid prediction for snap_scaffold_16-snap.356-T1
Valid prediction for GlimmerHMM_glimmerT_37900-T1
Valid prediction for Augustus_model.g25273.t1
Valid prediction for snap_scaffold_16-snap.346-T1
Valid prediction for Augustus_model.g25269.t1
Valid prediction for GlimmerHMM_glimmerT_37904-T1
Valid prediction for GlimmerHMM_glimmerT_37903-T1
Valid prediction for pasa_asmbl_16123.p2
Valid prediction for Augustus_model.g25280.t1
Valid prediction for Augustus_model.g25276.t1
Valid prediction for snap_scaffold_16-snap.333-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g25272.t1
Valid prediction for GlimmerHMM_glimmerT_37917-T1
Valid prediction for snap_scaffold_16-snap.355-T1
Valid prediction for CodingQuarry_transcript_19908-T1
Valid prediction for GlimmerHMM_glimmerT_37898-T1
Valid prediction for snap_scaffold_16-snap.332-T1
Valid prediction for snap_scaffold_16-snap.343-T1
Valid prediction for GlimmerHMM_glimmerT_37907-T1
Valid prediction for snap_scaffold_16-snap.365-T1
Valid prediction for Augustus_model.g25277.t1
Valid prediction for CodingQuarry_transcript_19906-T1
Valid prediction for snap_scaffold_16-snap.359-T1
Valid prediction for snap_scaffold_16-snap.354-T1
Valid prediction for snap_scaffold_16-snap.340-T1
Valid prediction for GlimmerHMM_glimmerT_37909-T1
Valid prediction for CodingQuarry_transcript_19907-T1
Valid prediction for Augustus_model.g25271.t1
Valid prediction for snap_scaffold_16-snap.337-T1
Valid prediction for snap_scaffold_16-snap.351-T1
Valid prediction for Augustus_model.g25265.t1
Valid prediction for GlimmerHMM_glimmerT_37911-T1
Valid prediction for Augustus_model.g25278.t1
Valid prediction for snap_scaffold_16-snap.350-T1
Valid prediction for HiQ_model.g25275.t1
Valid prediction for GlimmerHMM_glimmerT_37899-T1
Valid prediction for GlimmerHMM_glimmerT_37912-T1
Valid prediction for GlimmerHMM_glimmerT_37916-T1
Valid prediction for snap_scaffold_16-snap.362-T1
Valid prediction for Augustus_model.g25270.t1
Valid prediction for snap_scaffold_16-snap.338-T1
Valid prediction for Augustus_model.g25282.t1
Couldn't classify 99783, 99805
Sorry, prediction pasa_asmbl_16122.p1 fails validation.
(CTA)	 AC	99783-99805	GT	AGG
(TAG)	 AG	100348-100502	GT	AGG
(GCT)	 AG	101174-101384	GT	GGG
(GAG)	 AG	101707-101876	GT	GGG
(GTT)	 AG	102705-102908	GT	AGG
(CGG)	 AG	105121-105302	GT	AGG
(GCC)	 AG	105580-105691	GT	AGG
(GTA)	 AG	105986-106112	GT	CGG
(TAA)	 AG	106283-106385	GT	AGG
(GCA)	 AG	106470-106567	GT	AGG
(ATA)	 AG	106662-106801	GT	TGG
(GCT)	 AG	107222-107409	GT	AGG
(GCA)	 AG	107663-107786	GT	AGG
(AGG)	 AG	110061-110224	GT	AGG
(ATC)	 AG	110341-110442	GT	AGG
(ATT)	 AG	110651-110806	GT	AGG
(GTC)	 AG	110916-111066	GT	AGG
(GTA)	 AG	111263-111387	GT	AGG
(CTG)	 AG	111912-112024	GT	AGG
(GGT)	 AG	112143-112277	GT	TTG
(TAT)	 AG	112435-112565	GT	AGG
(GTC)	 AG	112721-112857	GT	AGG
(GTG)	 AG	113103-113236	GT	AGG
(CTT)	 AG	113417-113592	GT	AGG
(GCC)	 AG	113739-113841	GT	AGG
(GAA)	 AG	114199-114424	GT	GGG
(GAC)	 AG	114649-114760	GC	AGG
(GCT)	 AG	115091-115226	GT	AGG
(AGA)	 AG	115393-115505	GT	AGG
(ATC)	 AG	115739-115950	GT	TGG
(GCC)	 AG	116286-116383	GT	GAG
(TGA)	 AG	116611-116698	GT	CTG
(GAG)	 AG	116806-116939	GT	AGG
(GTC)	 AG	117123-117240	CC	GAC
-recovered pasa_asmbl_16122.p1, terminal, 117123, 117240
-recovered pasa_asmbl_16122.p1, internal, 100348, 100502
-recovered pasa_asmbl_16122.p1, internal, 101174, 101384
-recovered pasa_asmbl_16122.p1, internal, 101707, 101876
-recovered pasa_asmbl_16122.p1, internal, 102705, 102908
-recovered pasa_asmbl_16122.p1, internal, 105121, 105302
-recovered pasa_asmbl_16122.p1, internal, 105580, 105691
-recovered pasa_asmbl_16122.p1, internal, 105986, 106112
-recovered pasa_asmbl_16122.p1, internal, 106283, 106385
-recovered pasa_asmbl_16122.p1, internal, 106470, 106567
-recovered pasa_asmbl_16122.p1, internal, 106662, 106801
-recovered pasa_asmbl_16122.p1, internal, 107222, 107409
-recovered pasa_asmbl_16122.p1, internal, 107663, 107786
-recovered pasa_asmbl_16122.p1, internal, 110061, 110224
-recovered pasa_asmbl_16122.p1, internal, 110341, 110442
-recovered pasa_asmbl_16122.p1, internal, 110651, 110806
-recovered pasa_asmbl_16122.p1, internal, 110916, 111066
-recovered pasa_asmbl_16122.p1, internal, 111263, 111387
-recovered pasa_asmbl_16122.p1, internal, 111912, 112024
-recovered pasa_asmbl_16122.p1, internal, 112143, 112277
-recovered pasa_asmbl_16122.p1, internal, 112435, 112565
-recovered pasa_asmbl_16122.p1, internal, 112721, 112857
-recovered pasa_asmbl_16122.p1, internal, 113103, 113236
-recovered pasa_asmbl_16122.p1, internal, 113417, 113592
-recovered pasa_asmbl_16122.p1, internal, 113739, 113841
-recovered pasa_asmbl_16122.p1, internal, 114199, 114424
-recovered pasa_asmbl_16122.p1, internal, 114649, 114760
-recovered pasa_asmbl_16122.p1, internal, 115091, 115226
-recovered pasa_asmbl_16122.p1, internal, 115393, 115505
-recovered pasa_asmbl_16122.p1, internal, 115739, 115950
-recovered pasa_asmbl_16122.p1, internal, 116286, 116383
-recovered pasa_asmbl_16122.p1, internal, 116611, 116698
-recovered pasa_asmbl_16122.p1, internal, 116806, 116939
Valid prediction for snap_scaffold_16-snap.347-T1
Valid prediction for snap_scaffold_16-snap.335-T1
Valid prediction for snap_scaffold_16-snap.345-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_16-snap.330-T1
Valid prediction for snap_scaffold_16-snap.366-T1
Valid prediction for snap_scaffold_16-snap.363-T1
Valid prediction for Augustus_model.g25267.t1
Valid prediction for Augustus_model.g25279.t1
Valid prediction for pasa_asmbl_16958.p1
Valid prediction for GlimmerHMM_glimmerT_37906-T1
Valid prediction for CodingQuarry_transcript_19905-T1
Valid prediction for snap_scaffold_16-snap.348-T1
Valid prediction for Augustus_model.g25268.t1
Valid prediction for snap_scaffold_16-snap.341-T1
Valid prediction for snap_scaffold_16-snap.357-T1
Valid prediction for snap_scaffold_16-snap.358-T1
Valid prediction for Augustus_model.g25266.t1
Valid prediction for snap_scaffold_16-snap.360-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.334-T1
Valid prediction for Augustus_model.g25264.t1
Valid prediction for GlimmerHMM_glimmerT_37895-T1
Valid prediction for GlimmerHMM_glimmerT_37913-T1
Valid prediction for snap_scaffold_16-snap.367-T1
Valid prediction for snap_scaffold_16-snap.364-T1
Valid prediction for GlimmerHMM_glimmerT_37896-T1
Valid prediction for snap_scaffold_16-snap.369-T1
Valid prediction for GlimmerHMM_glimmerT_37914-T1
Valid prediction for GlimmerHMM_glimmerT_37897-T1
Valid prediction for Augustus_model.g25281.t1
Valid prediction for GlimmerHMM_glimmerT_37905-T1
Couldn't classify 1696, 1740
Couldn't classify 9188, 9327
Sorry, prediction pasa_asmbl_16961.p1 fails validation.
(GTC)	 AC	1696-1740	GT	TGG
(CAC)	 AG	3080-3180	GT	AGG
(GTC)	 AG	3547-3675	GT	AGG
(GGA)	 AG	4023-4124	GT	GCG
(GAT)	 AG	4402-4522	GT	AGG
(GGG)	 AG	6177-6258	GT	AGG
(GCT)	 AG	6634-6754	GT	AGG
(TTT)	 AG	8593-8768	GT	AGG
(ACC)	 AG	9188-9327	GC	AGG
-recovered pasa_asmbl_16961.p1, terminal, 6177, 6258
-recovered pasa_asmbl_16961.p1, internal, 3080, 3180
-recovered pasa_asmbl_16961.p1, internal, 3547, 3675
-recovered pasa_asmbl_16961.p1, internal, 4023, 4124
-recovered pasa_asmbl_16961.p1, internal, 4402, 4522
-recovered pasa_asmbl_16961.p1, internal, 6177, 6258
-recovered pasa_asmbl_16961.p1, internal, 6634, 6754
-recovered pasa_asmbl_16961.p1, internal, 8593, 8768
-recovered pasa_asmbl_16961.p1, internal, 9188, 9327
Valid prediction for snap_scaffold_16-snap.336-T1
Valid prediction for GlimmerHMM_glimmerT_37918-T1
Valid prediction for snap_scaffold_16-snap.352-T1
Valid prediction for GlimmerHMM_glimmerT_37901-T1
Valid prediction for HiQ_model.g25274.t1
Valid prediction for GlimmerHMM_glimmerT_37892-T1
Valid prediction for GlimmerHMM_glimmerT_37894-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18889, rend_intergenic: 16362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70657, rend_intergenic: 60792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86571, rend_intergenic: 84223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172798, rend_intergenic: 166756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184988, rend_intergenic: 181772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186909, rend_intergenic: 186625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191224
-exon list size: 404


building trellis

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1.0    
1.2    
1.5    
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2.5    
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3.4    
3.7    
3.9    
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4.9    
5.2    
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10.6    
10.8    
11.1    
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11.6    
11.8    
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14.5    
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15.3    
15.5    
15.8    
16.0    
16.3    
16.5    
16.7    
17.0    
17.2    
17.5    
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18.5    
18.7    
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19.5    
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20.0    
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20.4    
20.7    
20.9    
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21.9    
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22.4    
22.7    
22.9    
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23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.7    
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    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
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51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
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56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
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59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
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61.6    
61.8    
62.1    
62.3    
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63.1    
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64.0    
64.3    
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65.3    
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66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
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72.9    
73.2    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
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    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
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87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.4    
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90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
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93.1    
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93.6    
93.8    
94.1    
94.3    
94.6    
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95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
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 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 18889, rend_intergenic: 16362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70657, rend_intergenic: 60792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86571, rend_intergenic: 84223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172798, rend_intergenic: 166756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184988, rend_intergenic: 181772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186909, rend_intergenic: 186625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support