-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_8032801-8222812

-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 GeneMark_model.43670_t
Valid prediction for GeneMark_model.43675_t
Valid prediction for GlimmerHMM_glimmerT_25549-T1
Valid prediction for snap_scaffold_10-snap.1600-T1
Valid prediction for GeneMark_model.43695_t
Valid prediction for GeneMark_model.43693_t
Valid prediction for GlimmerHMM_glimmerT_25553-T1
Valid prediction for snap_scaffold_10-snap.1608-T1
Valid prediction for GeneMark_model.43689_t
Valid prediction for GeneMark_model.43684_t
Valid prediction for GeneMark_model.43681_t
Valid prediction for GeneMark_model.43669_t
Valid prediction for GeneMark_model.43699_t
Valid prediction for snap_scaffold_10-snap.1620-T1
Valid prediction for snap_scaffold_10-snap.1604-T1
Valid prediction for GlimmerHMM_glimmerT_25559-T1
Valid prediction for GeneMark_model.43697_t
Valid prediction for GeneMark_model.43701_t
Couldn't classify 106240, 106332
Couldn't classify 108762, 108961
Sorry, prediction pasa_asmbl_4589.p1 fails validation.
(GTG)	 AG	106240-106332	GT	AGG
(GTG)	 AG	107689-107845	GT	AGG
(AGA)	 AG	108762-108961	GG	CAG
-recovered pasa_asmbl_4589.p1, internal, 106240, 106332
-recovered pasa_asmbl_4589.p1, internal, 107689, 107845
Valid prediction for Augustus_model.g17156.t1
Valid prediction for GlimmerHMM_glimmerT_25557-T1
Valid prediction for GlimmerHMM_glimmerT_25545-T1
Couldn't classify 127543, 127683
Sorry, prediction pasa_asmbl_4590.p1 fails validation.
(TGT)	 TG	127543-127683	GT	GGG
(TTG)	 AG	129986-130273	AA	AGA
-recovered pasa_asmbl_4590.p1, terminal, 129986, 130273
Valid prediction for snap_scaffold_10-snap.1612-T1
Valid prediction for snap_scaffold_10-snap.1619-T1
Valid prediction for snap_scaffold_10-snap.1615-T1
Valid prediction for HiQ_model.g17158.t1
Valid prediction for snap_scaffold_10-snap.1602-T1
Valid prediction for GlimmerHMM_glimmerT_25556-T1
Valid prediction for GeneMark_model.43691_t
Valid prediction for snap_scaffold_10-snap.1596-T1
Valid prediction for snap_scaffold_10-snap.1621-T1
Valid prediction for Augustus_model.g17157.t1
Valid prediction for Augustus_model.g17159.t1
Valid prediction for GlimmerHMM_glimmerT_25560-T1
Valid prediction for GlimmerHMM_glimmerT_25563-T1
Valid prediction for snap_scaffold_10-snap.1613-T1
Valid prediction for GeneMark_model.43672_t
Valid prediction for snap_scaffold_10-snap.1594-T1
Valid prediction for GlimmerHMM_glimmerT_25561-T1
Valid prediction for GeneMark_model.43667_t
Valid prediction for GlimmerHMM_glimmerT_25547-T1
Valid prediction for GeneMark_model.43686_t
Valid prediction for snap_scaffold_10-snap.1610-T1
Valid prediction for snap_scaffold_10-snap.1622-T1
Valid prediction for snap_scaffold_10-snap.1606-T1
Valid prediction for snap_scaffold_10-snap.1617-T1
Valid prediction for snap_scaffold_10-snap.1616-T1
Valid prediction for GeneMark_model.43677_t
Valid prediction for snap_scaffold_10-snap.1598-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.43682_t
Valid prediction for GeneMark_model.43696_t
Valid prediction for Augustus_model.g17155.t1
Valid prediction for GeneMark_model.43683_t
Valid prediction for snap_scaffold_10-snap.1599-T1
Valid prediction for GeneMark_model.43678_t
Valid prediction for GlimmerHMM_glimmerT_25551-T1
Valid prediction for GeneMark_model.43680_t
Valid prediction for GeneMark_model.43698_t
Valid prediction for GlimmerHMM_glimmerT_25546-T1
Valid prediction for snap_scaffold_10-snap.1611-T1
Valid prediction for snap_scaffold_10-snap.1614-T1
Valid prediction for snap_scaffold_10-snap.1603-T1
Valid prediction for GlimmerHMM_glimmerT_25565-T1
Valid prediction for GeneMark_model.43692_t
Valid prediction for GlimmerHMM_glimmerT_25554-T1
Valid prediction for snap_scaffold_10-snap.1624-T1
Valid prediction for snap_scaffold_10-snap.1618-T1
Valid prediction for snap_scaffold_10-snap.1609-T1
Couldn't classify 140335, 141231
Sorry, prediction pasa_asmbl_3484.p1 fails validation.
(GAG)	 CA	140335-141231	GG	ACG
Valid prediction for GlimmerHMM_glimmerT_25562-T1
Valid prediction for GeneMark_model.43666_t
Valid prediction for GlimmerHMM_glimmerT_25555-T1
Valid prediction for GlimmerHMM_glimmerT_25552-T1
Valid prediction for snap_scaffold_10-snap.1597-T1
Valid prediction for snap_scaffold_10-snap.1605-T1
Valid prediction for GeneMark_model.43685_t
Valid prediction for snap_scaffold_10-snap.1601-T1
Valid prediction for GlimmerHMM_glimmerT_25564-T1
Valid prediction for GeneMark_model.43690_t
Valid prediction for snap_scaffold_10-snap.1595-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.43679_t
Valid prediction for GeneMark_model.43671_t
Valid prediction for GeneMark_model.43676_t
Valid prediction for GlimmerHMM_glimmerT_25548-T1
Valid prediction for GlimmerHMM_glimmerT_25558-T1
Valid prediction for GeneMark_model.43700_t
Valid prediction for GeneMark_model.43687_t
Valid prediction for snap_scaffold_10-snap.1607-T1
Valid prediction for GeneMark_model.43674_t
Valid prediction for GlimmerHMM_glimmerT_25566-T1
Valid prediction for GeneMark_model.43668_t
Valid prediction for GlimmerHMM_glimmerT_25550-T1
Valid prediction for GeneMark_model.43688_t
Valid prediction for GeneMark_model.43673_t
Valid prediction for snap_scaffold_10-snap.1623-T1
Valid prediction for GeneMark_model.43694_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9116, rend_intergenic: 5980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11330, rend_intergenic: 9118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18269, rend_intergenic: 11879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36908, rend_intergenic: 31722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38387, rend_intergenic: 37216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44265, rend_intergenic: 40862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49228, rend_intergenic: 48734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50224, rend_intergenic: 50021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65286, rend_intergenic: 63640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67084, rend_intergenic: 66533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73377, rend_intergenic: 68329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89051, rend_intergenic: 84545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190012
-exon list size: 408


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
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10.5    
10.7    
11.0    
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11.5    
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12.2    
12.4    
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13.4    
13.7    
13.9    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.1    
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17.6    
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18.0    
18.3    
18.5    
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19.3    
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20.5    
20.7    
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23.9    
24.1    
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24.6    
24.9    
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25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.0    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.3    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.5    
69.8    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.7    
72.0    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 9116, rend_intergenic: 5980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11330, rend_intergenic: 9118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18269, rend_intergenic: 11879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36908, rend_intergenic: 31722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38387, rend_intergenic: 37216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44265, rend_intergenic: 40862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49228, rend_intergenic: 48734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50224, rend_intergenic: 50021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65286, rend_intergenic: 63640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67084, rend_intergenic: 66533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73377, rend_intergenic: 68329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89051, rend_intergenic: 84545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 7 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 179172 - 190012
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal

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