-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_2541642-2839348

-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_19410-T1
Valid prediction for snap_scaffold_8-snap.481-T1
Valid prediction for snap_scaffold_8-snap.522-T1
Valid prediction for pasa_asmbl_52728.p1
Valid prediction for snap_scaffold_8-snap.486-T1
Valid prediction for GlimmerHMM_glimmerT_19402-T1
Valid prediction for snap_scaffold_8-snap.476-T1
Valid prediction for snap_scaffold_8-snap.505-T1
Valid prediction for GlimmerHMM_glimmerT_19407-T1
Valid prediction for snap_scaffold_8-snap.520-T1
Valid prediction for snap_scaffold_8-snap.491-T1
Valid prediction for snap_scaffold_8-snap.492-T1
Valid prediction for CodingQuarry_transcript_59602-T1
Valid prediction for pasa_asmbl_52735.p1
Valid prediction for snap_scaffold_8-snap.478-T1
Valid prediction for Augustus_model.g12921.t1
Valid prediction for GlimmerHMM_glimmerT_19415-T1
Valid prediction for snap_scaffold_8-snap.482-T1
Valid prediction for Augustus_model.g12924.t1
Valid prediction for Augustus_model.g12923.t1
Valid prediction for GlimmerHMM_glimmerT_19421-T1
Couldn't classify 101516, 102020
Couldn't classify 102631, 102849
Sorry, prediction pasa_asmbl_52723.p1 fails validation.
(AAC)	 GG	101516-102020	GT	AGG
(GGT)	 AG	102283-102395	GT	AGG
(AAG)	 AG	102631-102849	TT	GCT
-recovered pasa_asmbl_52723.p1, internal, 102283, 102395
Valid prediction for GlimmerHMM_glimmerT_19416-T1
Valid prediction for snap_scaffold_8-snap.487-T1
Valid prediction for GlimmerHMM_glimmerT_19401-T1
Valid prediction for snap_scaffold_8-snap.485-T1
Valid prediction for snap_scaffold_8-snap.516-T1
Valid prediction for Augustus_model.g12916.t1
Valid prediction for snap_scaffold_8-snap.506-T1
Valid prediction for snap_scaffold_8-snap.503-T1
Valid prediction for GlimmerHMM_glimmerT_19404-T1
Couldn't classify 66894, 67235
Sorry, prediction pasa_asmbl_52640.p1 fails validation.
(TAC)	 TC	66894-67235	CC	CTC
Valid prediction for snap_scaffold_8-snap.517-T1
Valid prediction for snap_scaffold_8-snap.511-T1
Valid prediction for snap_scaffold_8-snap.498-T1
Valid prediction for Augustus_model.g12920.t1
Valid prediction for GlimmerHMM_glimmerT_19414-T1
Valid prediction for snap_scaffold_8-snap.514-T1
Valid prediction for GlimmerHMM_glimmerT_19417-T1
Valid prediction for snap_scaffold_8-snap.479-T1
Valid prediction for GlimmerHMM_glimmerT_19426-T1
Valid prediction for snap_scaffold_8-snap.495-T1
Valid prediction for Augustus_model.g12911.t1
Valid prediction for snap_scaffold_8-snap.493-T1
Valid prediction for snap_scaffold_8-snap.507-T1
Valid prediction for GlimmerHMM_glimmerT_19418-T1
Valid prediction for snap_scaffold_8-snap.501-T1
Valid prediction for snap_scaffold_8-snap.496-T1
Valid prediction for snap_scaffold_8-snap.474-T1
Valid prediction for snap_scaffold_8-snap.510-T1
Valid prediction for Augustus_model.g12917.t1
Valid prediction for HiQ_model.g12915.t1
Couldn't classify 105860, 106193
Couldn't classify 107410, 107505
Sorry, prediction pasa_asmbl_53633.p1 fails validation.
(GGC)	 CG	105860-106193	GT	AGG
(ATC)	 AG	107012-107115	GT	GGG
(GAG)	 AG	107410-107505	CA	CCC
-recovered pasa_asmbl_53633.p1, internal, 107012, 107115
Valid prediction for snap_scaffold_8-snap.483-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 GlimmerHMM_glimmerT_19409-T1
Valid prediction for Augustus_model.g12908.t1
Valid prediction for GlimmerHMM_glimmerT_19413-T1
Valid prediction for GlimmerHMM_glimmerT_19408-T1
Valid prediction for GlimmerHMM_glimmerT_19424-T1
Valid prediction for Augustus_model.g12907.t1
Valid prediction for snap_scaffold_8-snap.475-T1
Valid prediction for Augustus_model.g12910.t1
Valid prediction for GlimmerHMM_glimmerT_19427-T1
Valid prediction for snap_scaffold_8-snap.500-T1
Valid prediction for snap_scaffold_8-snap.518-T1
Valid prediction for snap_scaffold_8-snap.509-T1
Valid prediction for snap_scaffold_8-snap.513-T1
Valid prediction for Augustus_model.g12912.t1
Valid prediction for HiQ_model.g12913.t1
Valid prediction for snap_scaffold_8-snap.480-T1
Valid prediction for Augustus_model.g12922.t1
Valid prediction for HiQ_model.g12914.t1
Valid prediction for snap_scaffold_8-snap.521-T1
Valid prediction for GlimmerHMM_glimmerT_19420-T1
Valid prediction for snap_scaffold_8-snap.497-T1
Valid prediction for GlimmerHMM_glimmerT_19431-T1
Valid prediction for snap_scaffold_8-snap.499-T1
Valid prediction for Augustus_model.g12918.t1
Valid prediction for GlimmerHMM_glimmerT_19419-T1
Valid prediction for GlimmerHMM_glimmerT_19430-T1
Valid prediction for Augustus_model.g12919.t1
Valid prediction for snap_scaffold_8-snap.519-T1
Valid prediction for GlimmerHMM_glimmerT_19429-T1
Valid prediction for pasa_asmbl_51715.p1
Valid prediction for snap_scaffold_8-snap.488-T1
Valid prediction for snap_scaffold_8-snap.484-T1
Valid prediction for snap_scaffold_8-snap.515-T1
Valid prediction for GlimmerHMM_glimmerT_19412-T1
Valid prediction for GlimmerHMM_glimmerT_19422-T1
Couldn't classify 181062, 181143
Sorry, prediction pasa_asmbl_51714.p1 fails validation.
(GTC)	 CC	181062-181143	GT	TGG
(ACA)	 AG	181477-181576	GT	CAG
(CGC)	 AG	181866-181992	GT	AGG
(CTG)	 AG	182325-182453	CC	GAC
-recovered pasa_asmbl_51714.p1, terminal, 182325, 182453
-recovered pasa_asmbl_51714.p1, internal, 181477, 181576
-recovered pasa_asmbl_51714.p1, internal, 181866, 181992
Valid prediction for CodingQuarry_transcript_59601-T1
Valid prediction for snap_scaffold_8-snap.477-T1
Valid prediction for Augustus_model.g12909.t1
Valid prediction for snap_scaffold_8-snap.512-T1
Valid prediction for GlimmerHMM_glimmerT_19411-T1
Valid prediction for GlimmerHMM_glimmerT_19406-T1
Valid prediction for snap_scaffold_8-snap.490-T1
Valid prediction for GlimmerHMM_glimmerT_19403-T1
Valid prediction for GlimmerHMM_glimmerT_19405-T1
Valid prediction for snap_scaffold_8-snap.494-T1
Valid prediction for GlimmerHMM_glimmerT_19425-T1
Valid prediction for snap_scaffold_8-snap.502-T1
Valid prediction for snap_scaffold_8-snap.508-T1
Valid prediction for GlimmerHMM_glimmerT_19428-T1
Valid prediction for GlimmerHMM_glimmerT_19423-T1
Valid prediction for snap_scaffold_8-snap.504-T1
Valid prediction for snap_scaffold_8-snap.489-T1
Valid prediction for CodingQuarry_transcript_59600-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29666, rend_intergenic: 8455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31416, rend_intergenic: 29925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37298, rend_intergenic: 32448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43068, rend_intergenic: 38154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57896, rend_intergenic: 43136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71948, rend_intergenic: 59554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87986, rend_intergenic: 72119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108157, rend_intergenic: 88900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138445, rend_intergenic: 130394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148086, rend_intergenic: 145854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152205, rend_intergenic: 149349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156337, rend_intergenic: 153704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177110, rend_intergenic: 164596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185982, rend_intergenic: 180895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212400, rend_intergenic: 186413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215523, rend_intergenic: 212415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233344, rend_intergenic: 217858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240055, rend_intergenic: 235529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243965, rend_intergenic: 242026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246220, rend_intergenic: 244889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260496, rend_intergenic: 247110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 274335, rend_intergenic: 260904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 287884, rend_intergenic: 280146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 297707
-exon list size: 394


building trellis

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1.0    
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2.0    
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8.1    
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8.8    
9.1    
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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    
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16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.4    
18.7    
18.9    
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19.4    
19.7    
19.9    
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20.5    
20.7    
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22.7    
23.0    
23.2    
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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    
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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 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 29666, rend_intergenic: 8455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31416, rend_intergenic: 29925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37298, rend_intergenic: 32448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43068, rend_intergenic: 38154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57896, rend_intergenic: 43136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71948, rend_intergenic: 59554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87986, rend_intergenic: 72119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108157, rend_intergenic: 88900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138445, rend_intergenic: 130394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148086, rend_intergenic: 145854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152205, rend_intergenic: 149349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156337, rend_intergenic: 153704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177110, rend_intergenic: 164596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185982, rend_intergenic: 180895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212400, rend_intergenic: 186413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215523, rend_intergenic: 212415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233344, rend_intergenic: 217858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240055, rend_intergenic: 235529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243965, rend_intergenic: 242026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246220, rend_intergenic: 244889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260496, rend_intergenic: 247110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 274335, rend_intergenic: 260904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 287884, rend_intergenic: 280146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10511
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support