-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_1378420-1616429

-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.g36516.t1
Valid prediction for Augustus_model.g36518.t1
Valid prediction for snap_scaffold_26-snap.317-T1
Couldn't classify 118115, 118282
Sorry, prediction pasa_asmbl_34722.p1 fails validation.
(CCA)	 CT	118115-118282	GT	AGG
(ATG)	 AG	118485-118787	GC	AGG
add_exon() Sorry, pasa_asmbl_34722.p1 118485-118787-initial-1 is invalid.
-recovered pasa_asmbl_34722.p1, initial, 118485, 118787
-recovered pasa_asmbl_34722.p1, terminal, 118485, 118787
-recovered pasa_asmbl_34722.p1, internal, 118485, 118787
Valid prediction for GlimmerHMM_glimmerT_55094-T1
Valid prediction for snap_scaffold_26-snap.324-T1
Couldn't classify 14624, 14665
Couldn't classify 18085, 18219
Sorry, prediction pasa_asmbl_34717.p1 fails validation.
(AGC)	 CC	14624-14665	GT	AGG
(ACC)	 AG	14818-14904	GT	TGG
(TTT)	 AG	15273-15493	GT	AGG
(GAT)	 AG	16225-16327	GT	AGG
(ATC)	 AG	16748-16846	GT	GGG
(TCT)	 AG	17006-17152	GT	TGG
(GAC)	 AG	18085-18219	GT	AGG
-recovered pasa_asmbl_34717.p1, internal, 14818, 14904
-recovered pasa_asmbl_34717.p1, internal, 15273, 15493
-recovered pasa_asmbl_34717.p1, internal, 16225, 16327
-recovered pasa_asmbl_34717.p1, internal, 16748, 16846
-recovered pasa_asmbl_34717.p1, internal, 17006, 17152
-recovered pasa_asmbl_34717.p1, internal, 18085, 18219
Valid prediction for snap_scaffold_26-snap.307-T1
Valid prediction for GlimmerHMM_glimmerT_55091-T1
Valid prediction for GlimmerHMM_glimmerT_55087-T1
Valid prediction for snap_scaffold_26-snap.290-T1
Valid prediction for Augustus_model.g36514.t1
Valid prediction for Augustus_model.g36515.t1
Valid prediction for Augustus_model.g36522.t1
Valid prediction for snap_scaffold_26-snap.320-T1
Valid prediction for GlimmerHMM_glimmerT_55084-T1
Valid prediction for GlimmerHMM_glimmerT_55083-T1
Valid prediction for snap_scaffold_26-snap.312-T1
Valid prediction for snap_scaffold_26-snap.325-T1
Valid prediction for GlimmerHMM_glimmerT_55079-T1
Valid prediction for GlimmerHMM_glimmerT_55085-T1
Valid prediction for GlimmerHMM_glimmerT_55092-T1
Couldn't classify 20529, 20690
Sorry, prediction pasa_asmbl_34718.p1 fails validation.
(TGT)	 TG	20529-20690	GT	AGG
(CAG)	 AG	20955-21051	GT	AGG
(GGT)	 AG	21369-21550	CC	GAC
add_exon() Sorry, pasa_asmbl_34718.p1 20955-21051-terminal-3 is invalid.
-recovered pasa_asmbl_34718.p1, terminal, 20955, 21051
-recovered pasa_asmbl_34718.p1, terminal, 21369, 21550
-recovered pasa_asmbl_34718.p1, internal, 20955, 21051
Valid prediction for snap_scaffold_26-snap.318-T1
Valid prediction for snap_scaffold_26-snap.291-T1
Valid prediction for snap_scaffold_26-snap.302-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.310-T1
Valid prediction for GlimmerHMM_glimmerT_55080-T1
Valid prediction for GlimmerHMM_glimmerT_55098-T1
Valid prediction for Augustus_model.g36517.t1
Valid prediction for snap_scaffold_26-snap.287-T1
Valid prediction for snap_scaffold_26-snap.298-T1
Valid prediction for snap_scaffold_26-snap.329-T1
Valid prediction for snap_scaffold_26-snap.322-T1
Valid prediction for GlimmerHMM_glimmerT_55093-T1
Valid prediction for snap_scaffold_26-snap.295-T1
Valid prediction for snap_scaffold_26-snap.314-T1
Valid prediction for snap_scaffold_26-snap.284-T1
Valid prediction for Augustus_model.g36519.t1
Valid prediction for snap_scaffold_26-snap.293-T1
Valid prediction for snap_scaffold_26-snap.288-T1
Valid prediction for snap_scaffold_26-snap.308-T1
Valid prediction for GlimmerHMM_glimmerT_55097-T1
Valid prediction for snap_scaffold_26-snap.316-T1
Valid prediction for snap_scaffold_26-snap.306-T1
Valid prediction for GlimmerHMM_glimmerT_55090-T1
Valid prediction for Augustus_model.g36513.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_26-snap.309-T1
Valid prediction for snap_scaffold_26-snap.292-T1
Valid prediction for Augustus_model.g36523.t1
Valid prediction for GlimmerHMM_glimmerT_55096-T1
Valid prediction for snap_scaffold_26-snap.299-T1
Couldn't classify 65790, 66001
Couldn't classify 69849, 69964
Sorry, prediction pasa_asmbl_35404.p1 fails validation.
(GGT)	 CA	65790-66001	GT	AGG
(GGG)	 AG	67405-67585	GT	GGG
(GAA)	 AG	68947-69067	GT	GGG
(ACT)	 AG	69849-69964	GT	CGG
-recovered pasa_asmbl_35404.p1, internal, 67405, 67585
-recovered pasa_asmbl_35404.p1, internal, 68947, 69067
-recovered pasa_asmbl_35404.p1, internal, 69849, 69964
Valid prediction for snap_scaffold_26-snap.303-T1
Valid prediction for snap_scaffold_26-snap.286-T1
Valid prediction for Augustus_model.g36521.t1
Valid prediction for snap_scaffold_26-snap.297-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_55089-T1
Valid prediction for snap_scaffold_26-snap.313-T1
Valid prediction for GlimmerHMM_glimmerT_55099-T1
Valid prediction for snap_scaffold_26-snap.285-T1
Valid prediction for snap_scaffold_26-snap.300-T1
Valid prediction for snap_scaffold_26-snap.296-T1
Valid prediction for GlimmerHMM_glimmerT_55081-T1
Valid prediction for snap_scaffold_26-snap.321-T1
Valid prediction for GlimmerHMM_glimmerT_55095-T1
Valid prediction for snap_scaffold_26-snap.327-T1
Valid prediction for GlimmerHMM_glimmerT_55086-T1
Valid prediction for snap_scaffold_26-snap.323-T1
Valid prediction for snap_scaffold_26-snap.294-T1
Valid prediction for snap_scaffold_26-snap.301-T1
Valid prediction for snap_scaffold_26-snap.311-T1
Valid prediction for snap_scaffold_26-snap.289-T1
Valid prediction for GlimmerHMM_glimmerT_55088-T1
Valid prediction for snap_scaffold_26-snap.319-T1
Valid prediction for GlimmerHMM_glimmerT_55082-T1
Valid prediction for snap_scaffold_26-snap.315-T1
Valid prediction for snap_scaffold_26-snap.305-T1
Valid prediction for snap_scaffold_26-snap.326-T1
Valid prediction for Augustus_model.g36520.t1
Valid prediction for snap_scaffold_26-snap.304-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21981, rend_intergenic: 7148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38698, rend_intergenic: 32001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46855, rend_intergenic: 39372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52903, rend_intergenic: 50990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57984, rend_intergenic: 56213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73382, rend_intergenic: 58597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78417, rend_intergenic: 73436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80129, rend_intergenic: 78870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93775, rend_intergenic: 90996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104519, rend_intergenic: 94246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116261, rend_intergenic: 105805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134416, rend_intergenic: 125527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135048, rend_intergenic: 134428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146322, rend_intergenic: 135571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160915, rend_intergenic: 146707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163411, rend_intergenic: 161635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175230, rend_intergenic: 166748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179652, rend_intergenic: 179535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191502, rend_intergenic: 179727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191818, rend_intergenic: 191521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208477, rend_intergenic: 192024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210307, rend_intergenic: 208596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221511, rend_intergenic: 214671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 238010
-exon list size: 366


building trellis

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10.9    
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11.7    
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17.1    
17.4    
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17.9    
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18.5    
18.8    
19.0    
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19.6    
19.8    
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20.7    
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22.0    
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22.6    
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27.7    
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28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.1    
35.3    
35.6    
35.9    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.1    
64.4    
64.7    
64.9    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.4    
70.7    
70.9    
71.2    
71.5    
71.7    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.5    
78.8    
79.1    
79.3    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.3    
82.6    
82.9    
83.2    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.7    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 21981, rend_intergenic: 7148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38698, rend_intergenic: 32001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46855, rend_intergenic: 39372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52903, rend_intergenic: 50990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57984, rend_intergenic: 56213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73382, rend_intergenic: 58597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78417, rend_intergenic: 73436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80129, rend_intergenic: 78870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93775, rend_intergenic: 90996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104519, rend_intergenic: 94246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116261, rend_intergenic: 105805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134416, rend_intergenic: 125527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135048, rend_intergenic: 134428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146322, rend_intergenic: 135571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160915, rend_intergenic: 146707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163411, rend_intergenic: 161635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175230, rend_intergenic: 166748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179652, rend_intergenic: 179535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191502, rend_intergenic: 179727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191818, rend_intergenic: 191521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208477, rend_intergenic: 192024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210307, rend_intergenic: 208596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221511, rend_intergenic: 214671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 224402 - 238010
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal

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