-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_1702378-1919592

-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.g30246.t1
Valid prediction for snap_scaffold_20-snap.398-T1
Valid prediction for GlimmerHMM_glimmerT_45520-T1
Valid prediction for snap_scaffold_20-snap.394-T1
Valid prediction for GlimmerHMM_glimmerT_45509-T1
Valid prediction for Augustus_model.g30249.t1
Valid prediction for Augustus_model.g30244.t1
Valid prediction for Augustus_model.g30243.t1
Valid prediction for snap_scaffold_20-snap.403-T1
Valid prediction for HiQ_model.g30248.t1
Valid prediction for GlimmerHMM_glimmerT_45513-T1
Valid prediction for GlimmerHMM_glimmerT_45522-T1
Valid prediction for HiQ_model.g30242.t1
Valid prediction for GlimmerHMM_glimmerT_45525-T1
Valid prediction for snap_scaffold_20-snap.412-T1
Valid prediction for Augustus_model.g30251.t1
Valid prediction for GlimmerHMM_glimmerT_45524-T1
Valid prediction for Augustus_model.g30253.t1
Valid prediction for GlimmerHMM_glimmerT_45507-T1
Valid prediction for snap_scaffold_20-snap.393-T1
Valid prediction for GlimmerHMM_glimmerT_45517-T1
Valid prediction for snap_scaffold_20-snap.392-T1
Valid prediction for snap_scaffold_20-snap.396-T1
Couldn't classify 164888, 165011
Sorry, prediction pasa_asmbl_27209.p2 fails validation.
(ATG)	 AC	163010-163073	GT	CCG
(AAA)	 AG	163429-163533	GT	AGG
(GCA)	 AG	164135-164357	GT	TGG
(GTG)	 AG	164665-164772	GT	AGG
(GGT)	 AG	164888-165011	GG	GGG
-recovered pasa_asmbl_27209.p2, initial, 163010, 163073
-recovered pasa_asmbl_27209.p2, internal, 163429, 163533
-recovered pasa_asmbl_27209.p2, internal, 164135, 164357
-recovered pasa_asmbl_27209.p2, internal, 164665, 164772
Valid prediction for snap_scaffold_20-snap.415-T1
Valid prediction for CodingQuarry_transcript_30436-T1
Valid prediction for Augustus_model.g30252.t1
Valid prediction for snap_scaffold_20-snap.385-T1
Valid prediction for GlimmerHMM_glimmerT_45514-T1
Valid prediction for snap_scaffold_20-snap.399-T1
Valid prediction for snap_scaffold_20-snap.390-T1
Valid prediction for GlimmerHMM_glimmerT_45521-T1
Couldn't classify 166473, 166629
Couldn't classify 166742, 166778
Couldn't classify 167578, 167664
Couldn't classify 167884, 167926
Sorry, prediction CodingQuarry_transcript_30439-T1 fails validation.
(ATG)	 AC	163010-163073	GT	CCG
(AAA)	 AG	163429-163533	GT	AGG
(GCA)	 AG	164135-164357	GT	TGG
(GTG)	 AG	164665-164772	GT	AGG
(GGT)	 AG	164888-165112	GT	ATG
(ACC)	 AG	166013-166088	GT	CGG
(GGT)	 AG	166473-166629	AC	CAA
(ACA)	 AC	166742-166778	GT	ACG
(CCA)	 AG	167578-167664	TC	TTT
(CCA)	 CC	167884-167926	TC	GAT
-recovered CodingQuarry_transcript_30439-T1, initial, 163010, 163073
-recovered CodingQuarry_transcript_30439-T1, internal, 163429, 163533
-recovered CodingQuarry_transcript_30439-T1, internal, 164135, 164357
-recovered CodingQuarry_transcript_30439-T1, internal, 164665, 164772
-recovered CodingQuarry_transcript_30439-T1, internal, 164888, 165112
-recovered CodingQuarry_transcript_30439-T1, internal, 166013, 166088
Valid prediction for snap_scaffold_20-snap.419-T1
Valid prediction for snap_scaffold_20-snap.388-T1
Valid prediction for snap_scaffold_20-snap.386-T1
Valid prediction for CodingQuarry_transcript_30440-T1
Valid prediction for snap_scaffold_20-snap.420-T1
Valid prediction for HiQ_model.g30250.t1
Valid prediction for snap_scaffold_20-snap.389-T1
Valid prediction for snap_scaffold_20-snap.406-T1
Valid prediction for snap_scaffold_20-snap.423-T1
Valid prediction for pasa_asmbl_26454.p1
Valid prediction for GlimmerHMM_glimmerT_45515-T1
Valid prediction for GlimmerHMM_glimmerT_45519-T1
Couldn't classify 51717, 51766
Sorry, prediction pasa_asmbl_26450.p1 fails validation.
(CAT)	 AA	51717-51766	GT	GAG
(TTC)	 AG	51911-51986	GT	AGG
(AAG)	 AG	52233-52325	GT	ACG
(TTT)	 AG	53056-53157	CT	GAC
-recovered pasa_asmbl_26450.p1, terminal, 53056, 53157
-recovered pasa_asmbl_26450.p1, internal, 51911, 51986
-recovered pasa_asmbl_26450.p1, internal, 52233, 52325
Couldn't classify 166473, 166662
Couldn't classify 167574, 167664
Couldn't classify 167884, 167926
Sorry, prediction CodingQuarry_transcript_30438-T1 fails validation.
(ATG)	 AC	163010-163073	GT	CCG
(AAA)	 AG	163429-163533	GT	AGG
(GCA)	 AG	164135-164357	GT	TGG
(GTG)	 AG	164665-164772	GT	AGG
(GGT)	 AG	164888-165112	GT	ATG
(ACC)	 AG	166013-166088	GT	CGG
(GGT)	 AG	166473-166662	AT	CAA
(TCA)	 CC	167574-167664	TC	TTT
(CCA)	 CC	167884-167926	TC	GAT
-recovered CodingQuarry_transcript_30438-T1, initial, 163010, 163073
-recovered CodingQuarry_transcript_30438-T1, internal, 163429, 163533
-recovered CodingQuarry_transcript_30438-T1, internal, 164135, 164357
-recovered CodingQuarry_transcript_30438-T1, internal, 164665, 164772
-recovered CodingQuarry_transcript_30438-T1, internal, 164888, 165112
-recovered CodingQuarry_transcript_30438-T1, internal, 166013, 166088
Valid prediction for snap_scaffold_20-snap.411-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 Augustus_model.g30241.t1
Valid prediction for snap_scaffold_20-snap.391-T1
Valid prediction for snap_scaffold_20-snap.407-T1
Valid prediction for GlimmerHMM_glimmerT_45526-T1
Valid prediction for snap_scaffold_20-snap.414-T1
Valid prediction for pasa_asmbl_25615.p1
Valid prediction for GlimmerHMM_glimmerT_45506-T1
Valid prediction for snap_scaffold_20-snap.417-T1
Valid prediction for snap_scaffold_20-snap.421-T1
Couldn't classify 213733, 214197
Sorry, prediction pasa_asmbl_25603.p1 fails validation.
(GGA)	 GG	213733-214197	AA	GAA
Couldn't classify 202829, 202867
Couldn't classify 206089, 206184
Sorry, prediction pasa_asmbl_25610.p1 fails validation.
(GAC)	 CG	202829-202867	GT	AGG
(ACA)	 AG	203240-203328	GT	CAG
(TTA)	 AG	203483-203579	GT	TGG
(GAT)	 AG	203990-204126	GT	GCG
(CGA)	 AG	204883-205055	GT	CTG
(GCA)	 AG	205696-205799	GT	AGG
(GCG)	 AG	206089-206184	AC	GAA
-recovered pasa_asmbl_25610.p1, internal, 203240, 203328
-recovered pasa_asmbl_25610.p1, internal, 203483, 203579
-recovered pasa_asmbl_25610.p1, internal, 203990, 204126
-recovered pasa_asmbl_25610.p1, internal, 204883, 205055
-recovered pasa_asmbl_25610.p1, internal, 205696, 205799
Valid prediction for GlimmerHMM_glimmerT_45510-T1
Valid prediction for CodingQuarry_transcript_30437-T1
Valid prediction for snap_scaffold_20-snap.409-T1
Valid prediction for snap_scaffold_20-snap.405-T1
Valid prediction for snap_scaffold_20-snap.404-T1
Valid prediction for GlimmerHMM_glimmerT_45508-T1
Couldn't classify 210850, 211335
Couldn't classify 211456, 211956
Sorry, prediction pasa_asmbl_25607.p1 fails validation.
(CAT)	 CC	210850-211335	GT	AGG
(GTG)	 AG	211456-211956	GA	GGG
Couldn't classify 212095, 212225
Couldn't classify 213113, 213461
Sorry, prediction pasa_asmbl_25606.p1 fails validation.
(ACA)	 CG	212095-212225	GT	AGG
(GCC)	 AG	212329-212417	GT	AGG
(GAG)	 AG	212727-212811	GT	AGG
(GTG)	 AG	213113-213461	GC	AGG
-recovered pasa_asmbl_25606.p1, internal, 212329, 212417
-recovered pasa_asmbl_25606.p1, internal, 212727, 212811
-recovered pasa_asmbl_25606.p1, internal, 213113, 213461
Valid prediction for Augustus_model.g30239.t1
Couldn't classify 195378, 195686
Sorry, prediction pasa_asmbl_25612.p2 fails validation.
(TCC)	 GC	195378-195686	AA	AAA
Valid prediction for Augustus_model.g30240.t1
Valid prediction for snap_scaffold_20-snap.416-T1
Valid prediction for GlimmerHMM_glimmerT_45516-T1
Valid prediction for snap_scaffold_20-snap.408-T1
Valid prediction for GlimmerHMM_glimmerT_45523-T1
Valid prediction for GlimmerHMM_glimmerT_45512-T1
Valid prediction for snap_scaffold_20-snap.395-T1
Couldn't classify 209776, 210780
Sorry, prediction pasa_asmbl_25608.p1 fails validation.
(GAC)	 GG	209776-210780	CC	CCC
Valid prediction for snap_scaffold_20-snap.410-T1
Valid prediction for snap_scaffold_20-snap.418-T1
Valid prediction for GlimmerHMM_glimmerT_45518-T1
Valid prediction for Augustus_model.g30247.t1
Valid prediction for snap_scaffold_20-snap.397-T1
Valid prediction for snap_scaffold_20-snap.400-T1
Valid prediction for CodingQuarry_transcript_30435-T1
Valid prediction for snap_scaffold_20-snap.387-T1
Valid prediction for GlimmerHMM_glimmerT_45511-T1
Valid prediction for snap_scaffold_20-snap.413-T1
Valid prediction for snap_scaffold_20-snap.422-T1
Valid prediction for snap_scaffold_20-snap.401-T1
Valid prediction for snap_scaffold_20-snap.402-T1
Valid prediction for HiQ_model.g30245.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10396, rend_intergenic: 3019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18864, rend_intergenic: 11391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21833, rend_intergenic: 20153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32645, rend_intergenic: 21951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34368, rend_intergenic: 33985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48438, rend_intergenic: 34841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51164, rend_intergenic: 48589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53913, rend_intergenic: 51918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84616, rend_intergenic: 55185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115279, rend_intergenic: 86000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143550, rend_intergenic: 116526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159776, rend_intergenic: 150355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170051, rend_intergenic: 163556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180146, rend_intergenic: 175794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192086, rend_intergenic: 186265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213043, rend_intergenic: 193178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217215
-exon list size: 394


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
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2.0    
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2.5    
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3.0    
3.3    
3.5    
3.8    
4.0    
4.3    
4.5    
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5.1    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.8    
8.1    
8.3    
8.6    
8.8    
9.1    
9.3    
9.6    
9.8    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.6    
11.9    
12.1    
12.4    
12.6    
12.9    
13.1    
13.4    
13.6    
13.9    
14.1    
14.4    
14.6    
14.9    
15.2    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.7    
22.0    
22.2    
22.5    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.8    
28.0    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.9    
62.1    
62.4    
62.6    
62.9    
63.1    
63.4    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.2    
65.4    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.7    
72.0    
72.2    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.1    
87.4    
87.6    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.5    
95.7    
96.0    
96.2    
96.5    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 10396, rend_intergenic: 3019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18864, rend_intergenic: 11391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21833, rend_intergenic: 20153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32645, rend_intergenic: 21951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34368, rend_intergenic: 33985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48438, rend_intergenic: 34841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51164, rend_intergenic: 48589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53913, rend_intergenic: 51918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84616, rend_intergenic: 55185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115279, rend_intergenic: 86000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143550, rend_intergenic: 116526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159776, rend_intergenic: 150355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170051, rend_intergenic: 163556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180146, rend_intergenic: 175794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192086, rend_intergenic: 186265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213043, rend_intergenic: 193178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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