-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_7811732-7991824

-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_18-snap.1669-T1
Valid prediction for snap_scaffold_18-snap.1660-T1
Valid prediction for GlimmerHMM_glimmerT_42685-T1
Valid prediction for GlimmerHMM_glimmerT_42695-T1
Couldn't classify 62400, 62559
Sorry, prediction pasa_asmbl_20810.p1 fails validation.
(GCC)	 GA	62400-62559	GT	AGG
(AAA)	 AG	63016-63160	GT	AGG
(GTA)	 AG	63300-63455	GT	AAG
(ATG)	 AG	63675-63774	GT	CTG
(TTC)	 AG	64140-64293	GT	AGG
(AAA)	 AG	65013-65182	TA	GAT
add_exon() Sorry, pasa_asmbl_20810.p1 63675-63774-initial-1 is invalid.
-recovered pasa_asmbl_20810.p1, initial, 63675, 63774
-recovered pasa_asmbl_20810.p1, terminal, 65013, 65182
-recovered pasa_asmbl_20810.p1, internal, 63016, 63160
-recovered pasa_asmbl_20810.p1, internal, 63300, 63455
-recovered pasa_asmbl_20810.p1, internal, 63675, 63774
-recovered pasa_asmbl_20810.p1, internal, 64140, 64293
Valid prediction for HiQ_model.g28471.t1
Valid prediction for Augustus_model.g28485.t1
Valid prediction for snap_scaffold_18-snap.1667-T1
Valid prediction for GlimmerHMM_glimmerT_42684-T1
Valid prediction for GlimmerHMM_glimmerT_42683-T1
Valid prediction for HiQ_model.g28473.t1
Valid prediction for Augustus_model.g28470.t1
Valid prediction for GlimmerHMM_glimmerT_42703-T1
Valid prediction for pasa_asmbl_20800.p1
Valid prediction for GlimmerHMM_glimmerT_42693-T1
Valid prediction for GlimmerHMM_glimmerT_42679-T1
Valid prediction for GlimmerHMM_glimmerT_42677-T1
Valid prediction for snap_scaffold_18-snap.1644-T1
Valid prediction for CodingQuarry_transcript_23832-T1
Valid prediction for snap_scaffold_18-snap.1643-T1
Valid prediction for CodingQuarry_transcript_23834-T1
Valid prediction for Augustus_model.g28486.t1
Valid prediction for Augustus_model.g28490.t1
Valid prediction for Augustus_model.g28493.t1
Valid prediction for GlimmerHMM_glimmerT_42687-T1
Valid prediction for GlimmerHMM_glimmerT_42690-T1
Valid prediction for snap_scaffold_18-snap.1677-T1
Valid prediction for snap_scaffold_18-snap.1665-T1
Valid prediction for Augustus_model.g28488.t1
Valid prediction for snap_scaffold_18-snap.1647-T1
Valid prediction for snap_scaffold_18-snap.1666-T1
Valid prediction for Augustus_model.g28482.t1
Valid prediction for CodingQuarry_transcript_23831-T1
Valid prediction for Augustus_model.g28478.t1
Valid prediction for GlimmerHMM_glimmerT_42681-T1
Valid prediction for snap_scaffold_18-snap.1652-T1
Valid prediction for CodingQuarry_transcript_23833-T1
Valid prediction for Augustus_model.g28476.t1
Valid prediction for snap_scaffold_18-snap.1655-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for pasa_asmbl_20795.p1
Valid prediction for GlimmerHMM_glimmerT_42676-T1
Valid prediction for pasa_asmbl_20796.p1
Valid prediction for snap_scaffold_18-snap.1654-T1
Valid prediction for GlimmerHMM_glimmerT_42701-T1
Valid prediction for GlimmerHMM_glimmerT_42686-T1
Valid prediction for snap_scaffold_18-snap.1674-T1
Valid prediction for GlimmerHMM_glimmerT_42696-T1
Valid prediction for GlimmerHMM_glimmerT_42705-T1
Valid prediction for Augustus_model.g28479.t1
Valid prediction for snap_scaffold_18-snap.1650-T1
Valid prediction for Augustus_model.g28492.t1
Valid prediction for Augustus_model.g28477.t1
Valid prediction for snap_scaffold_18-snap.1668-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_18-snap.1663-T1
Valid prediction for GlimmerHMM_glimmerT_42691-T1
Valid prediction for snap_scaffold_18-snap.1675-T1
Valid prediction for snap_scaffold_18-snap.1659-T1
Valid prediction for GlimmerHMM_glimmerT_42688-T1
Valid prediction for snap_scaffold_18-snap.1673-T1
Valid prediction for Augustus_model.g28483.t1
Valid prediction for GlimmerHMM_glimmerT_42698-T1
Valid prediction for Augustus_model.g28487.t1
Valid prediction for snap_scaffold_18-snap.1676-T1
Valid prediction for snap_scaffold_18-snap.1656-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_42678-T1
Valid prediction for GlimmerHMM_glimmerT_42700-T1
Valid prediction for Augustus_model.g28489.t1
Valid prediction for snap_scaffold_18-snap.1657-T1
Valid prediction for CodingQuarry_transcript_23836-T1
Valid prediction for Augustus_model.g28481.t1
Valid prediction for Augustus_model.g28480.t1
Valid prediction for Augustus_model.g28491.t1
Valid prediction for pasa_asmbl_19991.p1
Valid prediction for snap_scaffold_18-snap.1651-T1
Valid prediction for snap_scaffold_18-snap.1653-T1
Valid prediction for snap_scaffold_18-snap.1640-T1
Valid prediction for GlimmerHMM_glimmerT_42680-T1
Valid prediction for snap_scaffold_18-snap.1648-T1
Valid prediction for Augustus_model.g28469.t1
Valid prediction for snap_scaffold_18-snap.1649-T1
Valid prediction for GlimmerHMM_glimmerT_42699-T1
Valid prediction for GlimmerHMM_glimmerT_42692-T1
Valid prediction for snap_scaffold_18-snap.1664-T1
Valid prediction for snap_scaffold_18-snap.1671-T1
Valid prediction for snap_scaffold_18-snap.1646-T1
Valid prediction for GlimmerHMM_glimmerT_42694-T1
Valid prediction for snap_scaffold_18-snap.1661-T1
Valid prediction for Augustus_model.g28475.t1
Valid prediction for snap_scaffold_18-snap.1645-T1
Valid prediction for GlimmerHMM_glimmerT_42702-T1
Valid prediction for GlimmerHMM_glimmerT_42674-T1
Valid prediction for GlimmerHMM_glimmerT_42697-T1
Valid prediction for Augustus_model.g28484.t1
Valid prediction for GlimmerHMM_glimmerT_42704-T1
Couldn't classify 124836, 124865
Sorry, prediction pasa_asmbl_19981.p2 fails validation.
(CAT)	 CG	124836-124865	GT	AGG
(ACT)	 AG	125271-125315	GT	ACG
(CGT)	 AG	125427-125543	GT	CGG
(GAG)	 AG	126957-127022	GT	AGG
(GCT)	 AG	127165-127266	TA	AAT
-recovered pasa_asmbl_19981.p2, terminal, 127165, 127266
-recovered pasa_asmbl_19981.p2, internal, 125271, 125315
-recovered pasa_asmbl_19981.p2, internal, 125427, 125543
-recovered pasa_asmbl_19981.p2, internal, 126957, 127022
Valid prediction for snap_scaffold_18-snap.1642-T1
Valid prediction for GlimmerHMM_glimmerT_42682-T1
Valid prediction for snap_scaffold_18-snap.1672-T1
Valid prediction for Augustus_model.g28474.t1
Valid prediction for snap_scaffold_18-snap.1662-T1
Valid prediction for HiQ_model.g28472.t1
Valid prediction for snap_scaffold_18-snap.1670-T1
Valid prediction for GlimmerHMM_glimmerT_42675-T1
Valid prediction for GlimmerHMM_glimmerT_42689-T1
Valid prediction for snap_scaffold_18-snap.1658-T1
Valid prediction for snap_scaffold_18-snap.1641-T1
Valid prediction for CodingQuarry_transcript_23830-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 52043, rend_intergenic: 37911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180093
-exon list size: 267


building trellis

0.4    
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2.6    
3.0    
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25.7    
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29.0    
29.4    
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30.1    
30.5    
30.9    
31.2    
31.6    
32.0    
32.3    
32.7    
33.1    
33.5    
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39.8    
40.1    
40.5    
40.9    
41.3    
41.6    
42.0    
42.4    
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44.6    
45.0    
45.4    
45.7    
46.1    
46.5    
46.8    
47.2    
47.6    
48.0    
48.3    
48.7    
49.1    
49.4    
49.8    
50.2    
50.6    
50.9    
51.3    
51.7    
52.0    
52.4    
52.8    
53.2    
53.5    
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54.3    
54.6    
55.0    
55.4    
55.8    
56.1    
56.5    
56.9    
57.2    
57.6    
58.0    
58.4    
58.7    
59.1    
59.5    
59.9    
60.2    
60.6    
61.0    
61.3    
61.7    
62.1    
62.5    
62.8    
63.2    
63.6    
63.9    
64.3    
64.7    
65.1    
65.4    
65.8    
66.2    
66.5    
66.9    
67.3    
67.7    
68.0    
68.4    
68.8    
69.1    
69.5    
69.9    
70.3    
70.6    
71.0    
71.4    
71.7    
72.1    
72.5    
72.9    
73.2    
73.6    
74.0    
74.3    
74.7    
75.1    
75.5    
75.8    
76.2    
76.6    
77.0    
77.3    
77.7    
78.1    
78.4    
78.8    
79.2    
79.6    
79.9    
80.3    
80.7    
81.0    
81.4    
81.8    
82.2    
82.5    
82.9    
83.3    
83.6    
84.0    
84.4    
84.8    
85.1    
85.5    
85.9    
86.2    
86.6    
87.0    
87.4    
87.7    
88.1    
88.5    
88.8    
89.2    
89.6    
90.0    
90.3    
90.7    
91.1    
91.4    
91.8    
92.2    
92.6    
92.9    
93.3    
93.7    
94.1    
94.4    
94.8    
95.2    
95.5    
95.9    
96.3    
96.7    
97.0    
97.4    
97.8    
98.1    
98.5    
98.9    
99.3    
99.6    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 52043, rend_intergenic: 37911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11280
-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 1 predictions persist after filtering for low support