-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_4279810-4497115

-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.g37917.t1
Valid prediction for GlimmerHMM_glimmerT_57186-T1
Valid prediction for GlimmerHMM_glimmerT_57178-T1
Valid prediction for HiQ_model.g37908.t1
Valid prediction for pasa_asmbl_36270.p2
Valid prediction for pasa_asmbl_36279.p2
Valid prediction for snap_scaffold_27-snap.1056-T1
Valid prediction for snap_scaffold_27-snap.1024-T1
Valid prediction for snap_scaffold_27-snap.1031-T1
Valid prediction for snap_scaffold_27-snap.1051-T1
Valid prediction for snap_scaffold_27-snap.1037-T1
Valid prediction for CodingQuarry_transcript_41874-T1
Valid prediction for Augustus_model.g37911.t1
Valid prediction for snap_scaffold_27-snap.1018-T1
Valid prediction for GlimmerHMM_glimmerT_57185-T1
Valid prediction for pasa_asmbl_36269.p1
Valid prediction for GlimmerHMM_glimmerT_57190-T1
Valid prediction for pasa_asmbl_36280.p1
Valid prediction for snap_scaffold_27-snap.1032-T1
Valid prediction for CodingQuarry_transcript_41875-T1
Valid prediction for Augustus_model.g37915.t1
Valid prediction for snap_scaffold_27-snap.1050-T1
Valid prediction for GlimmerHMM_glimmerT_57191-T1
Valid prediction for snap_scaffold_27-snap.1039-T1
Valid prediction for HiQ_model.g37910.t1
Valid prediction for pasa_asmbl_36272.p1
Couldn't classify 121350, 121511
Couldn't classify 122651, 122810
Sorry, prediction pasa_asmbl_36283.p1 fails validation.
(TTT)	 AG	121350-121511	GT	GAG
(GTC)	 AG	122200-122296	GT	CAG
(GTA)	 AG	122377-122482	GT	TGG
(CGC)	 AG	122651-122810	CT	GCC
-recovered pasa_asmbl_36283.p1, internal, 121350, 121511
-recovered pasa_asmbl_36283.p1, internal, 122200, 122296
-recovered pasa_asmbl_36283.p1, internal, 122377, 122482
Valid prediction for snap_scaffold_27-snap.1041-T1
Valid prediction for pasa_asmbl_36284.p1
Valid prediction for snap_scaffold_27-snap.1030-T1
Valid prediction for GlimmerHMM_glimmerT_57181-T1
Valid prediction for Augustus_model.g37922.t1
Valid prediction for GlimmerHMM_glimmerT_57174-T1
Valid prediction for snap_scaffold_27-snap.1027-T1
Valid prediction for GlimmerHMM_glimmerT_57183-T1
Valid prediction for snap_scaffold_27-snap.1054-T1
Valid prediction for CodingQuarry_transcript_41876-T1
Valid prediction for GlimmerHMM_glimmerT_57194-T1
Valid prediction for GlimmerHMM_glimmerT_57199-T1
Valid prediction for GlimmerHMM_glimmerT_57193-T1
Valid prediction for HiQ_model.g37914.t1
Valid prediction for snap_scaffold_27-snap.1019-T1
Valid prediction for GlimmerHMM_glimmerT_57177-T1
Valid prediction for snap_scaffold_27-snap.1011-T1
Valid prediction for GlimmerHMM_glimmerT_57188-T1
Valid prediction for Augustus_model.g37916.t1
Valid prediction for GlimmerHMM_glimmerT_57192-T1
Valid prediction for Augustus_model.g37912.t1
Valid prediction for HiQ_model.g37913.t1
Valid prediction for snap_scaffold_27-snap.1023-T1
Valid prediction for snap_scaffold_27-snap.1044-T1
Valid prediction for snap_scaffold_27-snap.1017-T1
Valid prediction for GlimmerHMM_glimmerT_57189-T1
Valid prediction for HiQ_model.g37903.t1
Valid prediction for snap_scaffold_27-snap.1020-T1
Valid prediction for snap_scaffold_27-snap.1033-T1
Valid prediction for GlimmerHMM_glimmerT_57187-T1
Valid prediction for snap_scaffold_27-snap.1010-T1
Valid prediction for snap_scaffold_27-snap.1014-T1
Valid prediction for snap_scaffold_27-snap.1029-T1
Valid prediction for Augustus_model.g37907.t1
Valid prediction for snap_scaffold_27-snap.1013-T1
Valid prediction for CodingQuarry_transcript_41873-T1
Valid prediction for GlimmerHMM_glimmerT_57173-T1
Valid prediction for Augustus_model.g37905.t1
Valid prediction for snap_scaffold_27-snap.1035-T1
Valid prediction for GlimmerHMM_glimmerT_57182-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_27-snap.1046-T1
Valid prediction for GlimmerHMM_glimmerT_57195-T1
Valid prediction for snap_scaffold_27-snap.1045-T1
Valid prediction for Augustus_model.g37920.t1
Valid prediction for Augustus_model.g37918.t1
Valid prediction for pasa_asmbl_36959.p1
Valid prediction for snap_scaffold_27-snap.1015-T1
Valid prediction for GlimmerHMM_glimmerT_57180-T1
Valid prediction for pasa_asmbl_36956.p1
Valid prediction for Augustus_model.g37904.t1
Couldn't classify 192112, 192120
Sorry, prediction pasa_asmbl_36953.p3 fails validation.
(TAC)	 TC	192112-192120	GT	AGG
(GGT)	 AG	192286-192460	GT	CGG
(GCA)	 AG	192658-192773	AG	AGA
-recovered pasa_asmbl_36953.p3, terminal, 192658, 192773
-recovered pasa_asmbl_36953.p3, internal, 192286, 192460
Valid prediction for Augustus_model.g37906.t1
Valid prediction for snap_scaffold_27-snap.1038-T1
Valid prediction for snap_scaffold_27-snap.1025-T1
Valid prediction for GlimmerHMM_glimmerT_57179-T1
Valid prediction for HiQ_model.g37919.t1
Valid prediction for snap_scaffold_27-snap.1016-T1
Valid prediction for GlimmerHMM_glimmerT_57202-T1
Valid prediction for snap_scaffold_27-snap.1040-T1
Valid prediction for snap_scaffold_27-snap.1021-T1
Valid prediction for snap_scaffold_27-snap.1036-T1
Valid prediction for GlimmerHMM_glimmerT_57201-T1
Valid prediction for GlimmerHMM_glimmerT_57176-T1
Valid prediction for snap_scaffold_27-snap.1047-T1
Valid prediction for GlimmerHMM_glimmerT_57196-T1
Valid prediction for Augustus_model.g37909.t1
Valid prediction for HiQ_model.g37924.t1
Valid prediction for snap_scaffold_27-snap.1043-T1
Valid prediction for GlimmerHMM_glimmerT_57197-T1
Valid prediction for snap_scaffold_27-snap.1012-T1
Valid prediction for snap_scaffold_27-snap.1048-T1
Valid prediction for HiQ_model.g37921.t1
Valid prediction for snap_scaffold_27-snap.1052-T1
Valid prediction for GlimmerHMM_glimmerT_57198-T1
Valid prediction for GlimmerHMM_glimmerT_57184-T1
Valid prediction for snap_scaffold_27-snap.1034-T1
Valid prediction for snap_scaffold_27-snap.1028-T1
Valid prediction for snap_scaffold_27-snap.1022-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_57175-T1
Valid prediction for snap_scaffold_27-snap.1049-T1
Valid prediction for GlimmerHMM_glimmerT_57200-T1
Valid prediction for snap_scaffold_27-snap.1055-T1
Valid prediction for CodingQuarry_transcript_41877-T1
Valid prediction for Augustus_model.g37923.t1
Valid prediction for snap_scaffold_27-snap.1053-T1
Valid prediction for snap_scaffold_27-snap.1042-T1
Valid prediction for snap_scaffold_27-snap.1026-T1
Valid prediction for pasa_asmbl_36954.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32007, rend_intergenic: 25511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33980, rend_intergenic: 32092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59029, rend_intergenic: 56359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73133, rend_intergenic: 71039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83813, rend_intergenic: 75708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86027, rend_intergenic: 84139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90086, rend_intergenic: 88031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127553, rend_intergenic: 124192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127840, rend_intergenic: 127631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133246, rend_intergenic: 128429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138766, rend_intergenic: 133643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152034, rend_intergenic: 149387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157134, rend_intergenic: 152673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173202, rend_intergenic: 159544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196926, rend_intergenic: 191614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209415, rend_intergenic: 199258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215241, rend_intergenic: 213155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217306
-exon list size: 414


building trellis

0.2    
0.5    
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1.0    
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23.6    
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26.7    
26.9    
27.2    
27.4    
27.6    
27.9    
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28.4    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
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30.8    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.1    
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42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.0    
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44.5    
44.7    
45.0    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.6    
46.9    
47.1    
47.4    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
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51.0    
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52.6    
52.9    
53.1    
53.4    
53.6    
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54.1    
54.3    
54.6    
54.8    
55.0    
55.3    
55.5    
55.8    
56.0    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.7    
63.0    
63.2    
63.5    
63.7    
63.9    
64.2    
64.4    
64.7    
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65.1    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
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70.9    
71.2    
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71.6    
71.9    
72.1    
72.4    
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73.6    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.4    
76.7    
76.9    
77.2    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.9    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.6    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 32007, rend_intergenic: 25511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33980, rend_intergenic: 32092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59029, rend_intergenic: 56359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73133, rend_intergenic: 71039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83813, rend_intergenic: 75708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86027, rend_intergenic: 84139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90086, rend_intergenic: 88031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127553, rend_intergenic: 124192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127840, rend_intergenic: 127631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133246, rend_intergenic: 128429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138766, rend_intergenic: 133643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152034, rend_intergenic: 149387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157134, rend_intergenic: 152673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173202, rend_intergenic: 159544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196926, rend_intergenic: 191614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209415, rend_intergenic: 199258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215241, rend_intergenic: 213155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12225
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10933
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support