-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_7299941-7464574

-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_46285-T1
Valid prediction for Augustus_model.g30728.t1
Valid prediction for snap_scaffold_20-snap.1612-T1
Valid prediction for GlimmerHMM_glimmerT_46271-T1
Valid prediction for GlimmerHMM_glimmerT_46273-T1
Valid prediction for snap_scaffold_20-snap.1605-T1
Valid prediction for snap_scaffold_20-snap.1613-T1
Valid prediction for GlimmerHMM_glimmerT_46289-T1
Valid prediction for Augustus_model.g30736.t1
Valid prediction for snap_scaffold_20-snap.1600-T1
Valid prediction for GlimmerHMM_glimmerT_46284-T1
Valid prediction for snap_scaffold_20-snap.1599-T1
Valid prediction for snap_scaffold_20-snap.1592-T1
Valid prediction for GlimmerHMM_glimmerT_46291-T1
Valid prediction for GlimmerHMM_glimmerT_46287-T1
Valid prediction for snap_scaffold_20-snap.1603-T1
Valid prediction for snap_scaffold_20-snap.1579-T1
Valid prediction for snap_scaffold_20-snap.1594-T1
Valid prediction for Augustus_model.g30730.t1
Valid prediction for snap_scaffold_20-snap.1583-T1
Valid prediction for snap_scaffold_20-snap.1586-T1
Valid prediction for Augustus_model.g30732.t1
Valid prediction for snap_scaffold_20-snap.1608-T1
Valid prediction for snap_scaffold_20-snap.1588-T1
Valid prediction for snap_scaffold_20-snap.1610-T1
Valid prediction for snap_scaffold_20-snap.1581-T1
Valid prediction for GlimmerHMM_glimmerT_46281-T1
Valid prediction for snap_scaffold_20-snap.1601-T1
Valid prediction for GlimmerHMM_glimmerT_46276-T1
Valid prediction for Augustus_model.g30737.t1
Valid prediction for GlimmerHMM_glimmerT_46277-T1
Valid prediction for GlimmerHMM_glimmerT_46293-T1
Valid prediction for GlimmerHMM_glimmerT_46274-T1
Valid prediction for snap_scaffold_20-snap.1593-T1
Valid prediction for GlimmerHMM_glimmerT_46295-T1
Valid prediction for snap_scaffold_20-snap.1596-T1
Valid prediction for GlimmerHMM_glimmerT_46297-T1
Valid prediction for snap_scaffold_20-snap.1590-T1
Valid prediction for GlimmerHMM_glimmerT_46280-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_46278-T1
Valid prediction for GlimmerHMM_glimmerT_46292-T1
Valid prediction for GlimmerHMM_glimmerT_46290-T1
Valid prediction for snap_scaffold_20-snap.1580-T1
Valid prediction for snap_scaffold_20-snap.1587-T1
Valid prediction for snap_scaffold_20-snap.1611-T1
Valid prediction for snap_scaffold_20-snap.1606-T1
Valid prediction for Augustus_model.g30738.t1
Valid prediction for Augustus_model.g30733.t1
Valid prediction for Augustus_model.g30731.t1
Valid prediction for CodingQuarry_transcript_30553-T1
Valid prediction for snap_scaffold_20-snap.1595-T1
Valid prediction for Augustus_model.g30727.t1
Valid prediction for Augustus_model.g30723.t1
Couldn't classify 58287, 58403
Sorry, prediction pasa_asmbl_26253.p1 fails validation.
(CTG)	 GT	58287-58403	GT	CGG
(ATC)	 AG	60593-60688	GT	GGG
(GAG)	 AG	60813-60909	GT	AGG
(TGG)	 AG	62810-62861	GT	AGG
(GAC)	 AG	62994-63285	AC	AGA
-recovered pasa_asmbl_26253.p1, terminal, 62994, 63285
-recovered pasa_asmbl_26253.p1, internal, 60593, 60688
-recovered pasa_asmbl_26253.p1, internal, 60813, 60909
-recovered pasa_asmbl_26253.p1, internal, 62810, 62861
Valid prediction for snap_scaffold_20-snap.1582-T1
Valid prediction for GlimmerHMM_glimmerT_46288-T1
Valid prediction for Augustus_model.g30724.t1
Valid prediction for snap_scaffold_20-snap.1589-T1
Valid prediction for snap_scaffold_20-snap.1597-T1
Valid prediction for Augustus_model.g30734.t1
Valid prediction for GlimmerHMM_glimmerT_46282-T1
Valid prediction for snap_scaffold_20-snap.1604-T1
Valid prediction for Augustus_model.g30735.t1
Valid prediction for snap_scaffold_20-snap.1585-T1
Valid prediction for GlimmerHMM_glimmerT_46279-T1
Valid prediction for Augustus_model.g30726.t1
Valid prediction for GlimmerHMM_glimmerT_46286-T1
Valid prediction for snap_scaffold_20-snap.1591-T1
Valid prediction for Augustus_model.g30722.t1
Valid prediction for Augustus_model.g30725.t1
Valid prediction for GlimmerHMM_glimmerT_46270-T1
Valid prediction for snap_scaffold_20-snap.1584-T1
Valid prediction for Augustus_model.g30739.t1
Valid prediction for snap_scaffold_20-snap.1607-T1
Valid prediction for HiQ_model.g30740.t1
Valid prediction for pasa_asmbl_25902.p1
Valid prediction for snap_scaffold_20-snap.1598-T1
Valid prediction for GlimmerHMM_glimmerT_46294-T1
Couldn't classify 51844, 51967
Couldn't classify 54763, 54898
Sorry, prediction pasa_asmbl_25900.p1 fails validation.
(CCA)	 AC	51844-51967	GT	GGG
(GGC)	 AG	54184-54312	GT	CGG
(ATA)	 AG	54582-54663	GT	TGG
(CTG)	 AG	54763-54898	TG	ACT
-recovered pasa_asmbl_25900.p1, internal, 54184, 54312
-recovered pasa_asmbl_25900.p1, internal, 54582, 54663
Valid prediction for GlimmerHMM_glimmerT_46296-T1
Valid prediction for snap_scaffold_20-snap.1609-T1
Valid prediction for snap_scaffold_20-snap.1614-T1
Valid prediction for GlimmerHMM_glimmerT_46272-T1
Valid prediction for snap_scaffold_20-snap.1615-T1
Valid prediction for GlimmerHMM_glimmerT_46275-T1
Valid prediction for GlimmerHMM_glimmerT_46283-T1
Valid prediction for snap_scaffold_20-snap.1602-T1
Valid prediction for GlimmerHMM_glimmerT_46298-T1
Valid prediction for Augustus_model.g30729.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10605, rend_intergenic: 2857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13300, rend_intergenic: 11457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19883, rend_intergenic: 13441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23514, rend_intergenic: 19883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30371, rend_intergenic: 26248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36475, rend_intergenic: 33022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43379, rend_intergenic: 36627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45501, rend_intergenic: 43395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46970, rend_intergenic: 46191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54565, rend_intergenic: 49756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57334, rend_intergenic: 55178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63748, rend_intergenic: 59771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70901, rend_intergenic: 63806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80410, rend_intergenic: 72152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88559, rend_intergenic: 82895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99326, rend_intergenic: 89504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107640, rend_intergenic: 104798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112836, rend_intergenic: 107842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133067, rend_intergenic: 127918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134726, rend_intergenic: 133811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144426, rend_intergenic: 137980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150619, rend_intergenic: 146383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 164634
-exon list size: 337


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
2.9    
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3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 10605, rend_intergenic: 2857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13300, rend_intergenic: 11457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19883, rend_intergenic: 13441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23514, rend_intergenic: 19883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30371, rend_intergenic: 26248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36475, rend_intergenic: 33022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43379, rend_intergenic: 36627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45501, rend_intergenic: 43395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46970, rend_intergenic: 46191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54565, rend_intergenic: 49756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57334, rend_intergenic: 55178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63748, rend_intergenic: 59771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70901, rend_intergenic: 63806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80410, rend_intergenic: 72152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88559, rend_intergenic: 82895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99326, rend_intergenic: 89504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107640, rend_intergenic: 104798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112836, rend_intergenic: 107842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133067, rend_intergenic: 127918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134726, rend_intergenic: 133811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144426, rend_intergenic: 137980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150619, rend_intergenic: 146383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support