-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_7823370-7972666

-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.g33090.t1
Valid prediction for GeneMark_model.85407_t
Valid prediction for GeneMark_model.85435_t
Valid prediction for GeneMark_model.85406_t
Valid prediction for GeneMark_model.85423_t
Valid prediction for GeneMark_model.85432_t
Valid prediction for GeneMark_model.85412_t
Valid prediction for snap_scaffold_21-snap.1684-T1
Valid prediction for GlimmerHMM_glimmerT_49326-T1
Valid prediction for Augustus_model.g33080.t1
Valid prediction for GeneMark_model.85402_t
Valid prediction for snap_scaffold_21-snap.1674-T1
Valid prediction for snap_scaffold_21-snap.1666-T1
Valid prediction for GeneMark_model.85438_t
Valid prediction for snap_scaffold_21-snap.1660-T1
Valid prediction for GlimmerHMM_glimmerT_49322-T1
Valid prediction for GeneMark_model.85419_t
Valid prediction for GlimmerHMM_glimmerT_49328-T1
Valid prediction for GlimmerHMM_glimmerT_49330-T1
Valid prediction for GlimmerHMM_glimmerT_49339-T1
Valid prediction for GlimmerHMM_glimmerT_49337-T1
Valid prediction for snap_scaffold_21-snap.1671-T1
Valid prediction for GeneMark_model.85416_t
Valid prediction for GeneMark_model.85418_t
Valid prediction for snap_scaffold_21-snap.1682-T1
Valid prediction for GeneMark_model.85411_t
Valid prediction for GeneMark_model.85400_t
Valid prediction for snap_scaffold_21-snap.1668-T1
Valid prediction for GeneMark_model.85431_t
Valid prediction for GeneMark_model.85413_t
Valid prediction for GlimmerHMM_glimmerT_49325-T1
Valid prediction for GeneMark_model.85404_t
Valid prediction for GlimmerHMM_glimmerT_49329-T1
Valid prediction for HiQ_model.g33088.t1
Valid prediction for pasa_asmbl_28786.p1
Valid prediction for snap_scaffold_21-snap.1662-T1
Valid prediction for GeneMark_model.85409_t
Valid prediction for GeneMark_model.85434_t
Valid prediction for snap_scaffold_21-snap.1680-T1
Valid prediction for Augustus_model.g33078.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 GeneMark_model.85422_t
Valid prediction for GeneMark_model.85410_t
Valid prediction for HiQ_model.g33085.t1
Valid prediction for GeneMark_model.85430_t
Valid prediction for GlimmerHMM_glimmerT_49341-T1
Valid prediction for GlimmerHMM_glimmerT_49342-T1
Valid prediction for snap_scaffold_21-snap.1679-T1
Valid prediction for snap_scaffold_21-snap.1686-T1
Valid prediction for GeneMark_model.85405_t
Couldn't classify 33559, 33675
Sorry, prediction pasa_asmbl_27887.p1 fails validation.
(AGT)	 AC	33559-33675	GT	AGG
(GTG)	 AG	34622-34712	GT	AGG
(GAT)	 AG	35020-35116	GT	AGG
(GTA)	 AG	35620-35734	CA	GAC
-recovered pasa_asmbl_27887.p1, terminal, 35620, 35734
-recovered pasa_asmbl_27887.p1, internal, 34622, 34712
-recovered pasa_asmbl_27887.p1, internal, 35020, 35116
Valid prediction for GeneMark_model.85399_t
Valid prediction for GlimmerHMM_glimmerT_49323-T1
Valid prediction for GlimmerHMM_glimmerT_49331-T1
Valid prediction for snap_scaffold_21-snap.1667-T1
Valid prediction for snap_scaffold_21-snap.1677-T1
Valid prediction for Augustus_model.g33092.t1
Valid prediction for snap_scaffold_21-snap.1669-T1
Valid prediction for snap_scaffold_21-snap.1678-T1
Valid prediction for HiQ_model.g33086.t1
Valid prediction for GeneMark_model.85433_t
Valid prediction for snap_scaffold_21-snap.1683-T1
Valid prediction for Augustus_model.g33094.t1
Valid prediction for GlimmerHMM_glimmerT_49324-T1
Valid prediction for snap_scaffold_21-snap.1685-T1
Valid prediction for snap_scaffold_21-snap.1672-T1
Valid prediction for Augustus_model.g33091.t1
Valid prediction for GlimmerHMM_glimmerT_49332-T1
Valid prediction for snap_scaffold_21-snap.1689-T1
Valid prediction for GeneMark_model.85429_t
Valid prediction for GeneMark_model.85408_t
Valid prediction for Augustus_model.g33087.t1
Valid prediction for GlimmerHMM_glimmerT_49335-T1
Valid prediction for Augustus_model.g33082.t1
Valid prediction for GeneMark_model.85420_t
Couldn't classify 84961, 85149
Sorry, prediction pasa_asmbl_28258.p1 fails validation.
(ATG)	 TC	79185-79278	GT	CGG
(CAA)	 AG	79433-79504	GT	AGG
(CCT)	 AG	79653-79720	GT	AGG
(GTG)	 AG	80044-80194	GT	GGG
(ACT)	 AG	80416-80531	GT	AGG
(CTG)	 AG	80655-80762	GT	AGG
(AAA)	 AG	80955-81035	GT	AGG
(TCT)	 AG	81298-81401	GT	AAG
(GCG)	 AG	82645-82795	GT	AGG
(GGT)	 AG	82997-83158	GT	AGG
(GGT)	 AG	83323-83448	GT	AGG
(GAC)	 AG	83815-83948	GT	AGG
(AAT)	 AG	84197-84290	GT	AGG
(TAC)	 AG	84600-84770	GT	AGG
(AAT)	 AG	84961-85149	CT	TCC
-recovered pasa_asmbl_28258.p1, initial, 79185, 79278
-recovered pasa_asmbl_28258.p1, internal, 79433, 79504
-recovered pasa_asmbl_28258.p1, internal, 79653, 79720
-recovered pasa_asmbl_28258.p1, internal, 80044, 80194
-recovered pasa_asmbl_28258.p1, internal, 80416, 80531
-recovered pasa_asmbl_28258.p1, internal, 80655, 80762
-recovered pasa_asmbl_28258.p1, internal, 80955, 81035
-recovered pasa_asmbl_28258.p1, internal, 81298, 81401
-recovered pasa_asmbl_28258.p1, internal, 82645, 82795
-recovered pasa_asmbl_28258.p1, internal, 82997, 83158
-recovered pasa_asmbl_28258.p1, internal, 83323, 83448
-recovered pasa_asmbl_28258.p1, internal, 83815, 83948
-recovered pasa_asmbl_28258.p1, internal, 84197, 84290
-recovered pasa_asmbl_28258.p1, internal, 84600, 84770
Valid prediction for GlimmerHMM_glimmerT_49334-T1
Valid prediction for Augustus_model.g33081.t1
Valid prediction for GlimmerHMM_glimmerT_49338-T1
Valid prediction for snap_scaffold_21-snap.1663-T1
Valid prediction for Augustus_model.g33083.t1
Valid prediction for CodingQuarry_transcript_32588-T1
Valid prediction for GlimmerHMM_glimmerT_49340-T1
Valid prediction for Augustus_model.g33084.t1
Valid prediction for CodingQuarry_transcript_32587-T1
Valid prediction for GeneMark_model.85425_t
Valid prediction for HiQ_model.g33093.t1
Valid prediction for snap_scaffold_21-snap.1675-T1
Valid prediction for GeneMark_model.85417_t
Valid prediction for GeneMark_model.85436_t
Valid prediction for snap_scaffold_21-snap.1665-T1
Valid prediction for snap_scaffold_21-snap.1688-T1
Valid prediction for snap_scaffold_21-snap.1673-T1
Valid prediction for GeneMark_model.85427_t
Valid prediction for GeneMark_model.85401_t
Valid prediction for snap_scaffold_21-snap.1687-T1
Valid prediction for pasa_asmbl_27894.p2
Valid prediction for snap_scaffold_21-snap.1661-T1
Valid prediction for Augustus_model.g33089.t1
Valid prediction for snap_scaffold_21-snap.1670-T1
Valid prediction for GeneMark_model.85424_t
Valid prediction for snap_scaffold_21-snap.1681-T1
Valid prediction for snap_scaffold_21-snap.1676-T1
Valid prediction for pasa_asmbl_27883.p1
Valid prediction for Augustus_model.g33079.t1
Valid prediction for snap_scaffold_21-snap.1664-T1
Valid prediction for GeneMark_model.85439_t
Valid prediction for GeneMark_model.85414_t
Valid prediction for GlimmerHMM_glimmerT_49333-T1
Valid prediction for GlimmerHMM_glimmerT_49327-T1
Valid prediction for GeneMark_model.85426_t
Valid prediction for GlimmerHMM_glimmerT_49336-T1
Valid prediction for GeneMark_model.85428_t
Valid prediction for GeneMark_model.85415_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31680, rend_intergenic: 18725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44299, rend_intergenic: 42703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50658, rend_intergenic: 45092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54040, rend_intergenic: 51728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60539, rend_intergenic: 59177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70113, rend_intergenic: 67528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107443, rend_intergenic: 104789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119173, rend_intergenic: 113618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 149297
-exon list size: 507


building trellis

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5.9    
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8.8    
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25.9    
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27.5    
27.7    
27.9    
28.1    
28.3    
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28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
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34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
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40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
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44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
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51.1    
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54.2    
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54.6    
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55.0    
55.2    
55.4    
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56.8    
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57.8    
58.0    
58.2    
58.3    
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58.9    
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62.3    
62.5    
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62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.0    
64.2    
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65.0    
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66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
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67.6    
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68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
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69.9    
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72.1    
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72.9    
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73.3    
73.5    
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73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
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77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 31680, rend_intergenic: 18725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44299, rend_intergenic: 42703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50658, rend_intergenic: 45092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54040, rend_intergenic: 51728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60539, rend_intergenic: 59177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70113, rend_intergenic: 67528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107443, rend_intergenic: 104789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119173, rend_intergenic: 113618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12209
-exon list size: 31


building trellis

3.0    
6.1    
9.1    
12.1    
15.2    
18.2    
21.2    
24.2    
27.3    
30.3    
33.3    
36.4    
39.4    
42.4    
45.5    
48.5    
51.5    
54.5    
57.6    
60.6    
63.6    
66.7    
69.7    
72.7    
75.8    
78.8    
81.8    
84.8    
87.9    
90.9    
93.9    
97.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 11253
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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