-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_6896251-7109394

-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 HiQ_model.g15309.t1
Valid prediction for HiQ_model.g15302.t1
Valid prediction for pasa_asmbl_54102.p1
Valid prediction for GeneMark_model.39249_t
Valid prediction for GlimmerHMM_glimmerT_22861-T1
Valid prediction for Augustus_model.g15303.t1
Valid prediction for GlimmerHMM_glimmerT_22876-T1
Valid prediction for snap_scaffold_9-snap.1457-T1
Valid prediction for GeneMark_model.39238_t
Valid prediction for Augustus_model.g15308.t1
Valid prediction for snap_scaffold_9-snap.1470-T1
Valid prediction for snap_scaffold_9-snap.1469-T1
Valid prediction for GeneMark_model.39242_t
Valid prediction for snap_scaffold_9-snap.1458-T1
Valid prediction for snap_scaffold_9-snap.1460-T1
Valid prediction for snap_scaffold_9-snap.1448-T1
Valid prediction for snap_scaffold_9-snap.1451-T1
Valid prediction for Augustus_model.g15305.t1
Valid prediction for Augustus_model.g15297.t1
Valid prediction for GeneMark_model.39255_t
Valid prediction for GlimmerHMM_glimmerT_22879-T1
Valid prediction for GeneMark_model.39260_t
Valid prediction for snap_scaffold_9-snap.1468-T1
Valid prediction for snap_scaffold_9-snap.1461-T1
Valid prediction for GlimmerHMM_glimmerT_22882-T1
Valid prediction for GlimmerHMM_glimmerT_22868-T1
Valid prediction for snap_scaffold_9-snap.1452-T1
Valid prediction for snap_scaffold_9-snap.1445-T1
Valid prediction for GeneMark_model.39262_t
Valid prediction for GlimmerHMM_glimmerT_22869-T1
Couldn't classify 126460, 126624
Sorry, prediction pasa_asmbl_54110.p1 fails validation.
(GAC)	 GG	126460-126624	GT	AGG
(TTG)	 AG	127322-127417	GT	AGG
(GAT)	 AG	127500-127596	GT	AGG
(AGA)	 AG	127885-127968	GT	ACG
(GTA)	 AG	128198-128283	GT	AGG
(TTG)	 AG	128383-128492	GT	AGG
(GAT)	 AG	128725-128852	GT	CAG
(ACT)	 AG	128961-129082	GT	TGG
(ATT)	 AG	129288-129387	GT	AGG
(CCC)	 AG	129516-129646	GT	AGG
(GTG)	 AG	129728-129877	AA	GAA
-recovered pasa_asmbl_54110.p1, terminal, 129728, 129877
-recovered pasa_asmbl_54110.p1, internal, 127322, 127417
-recovered pasa_asmbl_54110.p1, internal, 127500, 127596
-recovered pasa_asmbl_54110.p1, internal, 127885, 127968
-recovered pasa_asmbl_54110.p1, internal, 128198, 128283
-recovered pasa_asmbl_54110.p1, internal, 128383, 128492
-recovered pasa_asmbl_54110.p1, internal, 128725, 128852
-recovered pasa_asmbl_54110.p1, internal, 128961, 129082
-recovered pasa_asmbl_54110.p1, internal, 129288, 129387
-recovered pasa_asmbl_54110.p1, internal, 129516, 129646
Valid prediction for GlimmerHMM_glimmerT_22884-T1
Valid prediction for GlimmerHMM_glimmerT_22872-T1
Valid prediction for GeneMark_model.39251_t
Valid prediction for GeneMark_model.39245_t
Valid prediction for snap_scaffold_9-snap.1459-T1
Valid prediction for GlimmerHMM_glimmerT_22874-T1
Valid prediction for GlimmerHMM_glimmerT_22880-T1
Valid prediction for GlimmerHMM_glimmerT_22875-T1
Couldn't classify 44980, 45122
Sorry, prediction pasa_asmbl_54099.p1 fails validation.
(CCA)	 CA	44980-45122	GT	AGG
(GAA)	 AG	45241-45370	GT	AGG
(CAG)	 AG	45512-45637	GT	AAG
(GCT)	 AG	45762-45872	GT	AGG
(GTT)	 AG	46104-46200	GT	AGG
(GAG)	 AG	46924-47126	GC	GAG
-recovered pasa_asmbl_54099.p1, terminal, 46924, 47126
-recovered pasa_asmbl_54099.p1, internal, 45241, 45370
-recovered pasa_asmbl_54099.p1, internal, 45512, 45637
-recovered pasa_asmbl_54099.p1, internal, 45762, 45872
-recovered pasa_asmbl_54099.p1, internal, 46104, 46200
-recovered pasa_asmbl_54099.p1, internal, 46924, 47126
Valid prediction for snap_scaffold_9-snap.1449-T1
Valid prediction for snap_scaffold_9-snap.1453-T1
Valid prediction for GeneMark_model.39258_t
Valid prediction for GeneMark_model.39241_t
Couldn't classify 62168, 62512
Sorry, prediction pasa_asmbl_54101.p1 fails validation.
(GTG)	 GT	62168-62512	GG	TAG
Valid prediction for snap_scaffold_9-snap.1463-T1
Valid prediction for GlimmerHMM_glimmerT_22873-T1
Valid prediction for snap_scaffold_9-snap.1473-T1
Valid prediction for GeneMark_model.39253_t
Valid prediction for GeneMark_model.39261_t
Valid prediction for snap_scaffold_9-snap.1472-T1
Valid prediction for GeneMark_model.39244_t
Valid prediction for GeneMark_model.39250_t
Valid prediction for GeneMark_model.39246_t
Valid prediction for snap_scaffold_9-snap.1454-T1
Valid prediction for GlimmerHMM_glimmerT_22877-T1
Valid prediction for snap_scaffold_9-snap.1441-T1
Valid prediction for GeneMark_model.39239_t
Valid prediction for CodingQuarry_transcript_62068-T1
Valid prediction for GlimmerHMM_glimmerT_22871-T1
Valid prediction for CodingQuarry_transcript_62066-T1
Couldn't classify 92139, 92217
Sorry, prediction pasa_asmbl_54105.p1 fails validation.
(GTG)	 AC	92139-92217	GT	TGG
(TGC)	 AG	92552-92839	GT	TGG
(CCC)	 AG	92945-93256	GT	GGG
(AAG)	 AG	93407-93697	GT	TGG
(ACA)	 AG	93840-94002	GT	AGG
(GAG)	 AG	94706-94866	GT	TAG
(TGA)	 AG	94987-95062	GT	AGG
(CAG)	 AG	96305-96338	GT	AGG
(AAG)	 AG	96507-96656	CA	AGC
-recovered pasa_asmbl_54105.p1, terminal, 96507, 96656
-recovered pasa_asmbl_54105.p1, internal, 92552, 92839
-recovered pasa_asmbl_54105.p1, internal, 92945, 93256
-recovered pasa_asmbl_54105.p1, internal, 93407, 93697
-recovered pasa_asmbl_54105.p1, internal, 93840, 94002
-recovered pasa_asmbl_54105.p1, internal, 94706, 94866
-recovered pasa_asmbl_54105.p1, internal, 94987, 95062
-recovered pasa_asmbl_54105.p1, internal, 96305, 96338
Valid prediction for CodingQuarry_transcript_62065-T1
Valid prediction for GeneMark_model.39248_t
Valid prediction for CodingQuarry_transcript_62070-T1
Valid prediction for snap_scaffold_9-snap.1475-T1
Valid prediction for Augustus_model.g15306.t1
Valid prediction for pasa_asmbl_54112.p1
Valid prediction for CodingQuarry_transcript_62067-T1
Valid prediction for Augustus_model.g15304.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 CodingQuarry_transcript_62069-T1
Valid prediction for GeneMark_model.39234_t
Valid prediction for snap_scaffold_9-snap.1444-T1
Valid prediction for snap_scaffold_9-snap.1442-T1
Valid prediction for GeneMark_model.39257_t
Couldn't classify 183458, 183474
Sorry, prediction pasa_asmbl_55065.p1 fails validation.
(CTC)	 GA	183458-183474	GT	AGG
(GTT)	 AG	183794-183948	GT	AGG
(CCC)	 AG	184116-184339	GT	AGG
(GTA)	 AG	185666-185815	GT	AGG
(ACG)	 AG	185919-185970	GT	CGG
(ATC)	 AG	186329-186492	GT	AGG
(CCT)	 AG	186786-186962	GT	GGG
(TTA)	 AG	188227-188291	GT	AGG
(TGC)	 AG	188668-188827	GT	CAG
(TCA)	 AG	188945-189007	GT	ATG
(CTC)	 AG	189234-189302	GT	AGG
(AAT)	 AG	189745-189841	GT	GGG
(TGG)	 AG	190430-190500	AG	GAA
-recovered pasa_asmbl_55065.p1, terminal, 190430, 190500
-recovered pasa_asmbl_55065.p1, internal, 183794, 183948
-recovered pasa_asmbl_55065.p1, internal, 184116, 184339
-recovered pasa_asmbl_55065.p1, internal, 185666, 185815
-recovered pasa_asmbl_55065.p1, internal, 185919, 185970
-recovered pasa_asmbl_55065.p1, internal, 186329, 186492
-recovered pasa_asmbl_55065.p1, internal, 186786, 186962
-recovered pasa_asmbl_55065.p1, internal, 188227, 188291
-recovered pasa_asmbl_55065.p1, internal, 188668, 188827
-recovered pasa_asmbl_55065.p1, internal, 188945, 189007
-recovered pasa_asmbl_55065.p1, internal, 189234, 189302
-recovered pasa_asmbl_55065.p1, internal, 189745, 189841
Valid prediction for GeneMark_model.39252_t
Valid prediction for Augustus_model.g15312.t1
Valid prediction for GlimmerHMM_glimmerT_22883-T1
Valid prediction for GlimmerHMM_glimmerT_22870-T1
Valid prediction for CodingQuarry_transcript_62063-T1
Valid prediction for GeneMark_model.39235_t
Valid prediction for Augustus_model.g15301.t1
Valid prediction for snap_scaffold_9-snap.1446-T1
Valid prediction for GeneMark_model.39240_t
Valid prediction for pasa_asmbl_55070.p1
Valid prediction for GeneMark_model.39256_t
Valid prediction for GlimmerHMM_glimmerT_22881-T1
Valid prediction for GlimmerHMM_glimmerT_22885-T1
Valid prediction for GeneMark_model.39254_t
Valid prediction for snap_scaffold_9-snap.1467-T1
Valid prediction for GeneMark_model.39237_t
Valid prediction for HiQ_model.g15300.t1
Valid prediction for GlimmerHMM_glimmerT_22863-T1
Valid prediction for GlimmerHMM_glimmerT_22886-T1
Valid prediction for snap_scaffold_9-snap.1447-T1
Valid prediction for snap_scaffold_9-snap.1474-T1
Valid prediction for Augustus_model.g15311.t1
Valid prediction for snap_scaffold_9-snap.1464-T1
Valid prediction for GeneMark_model.39247_t
Valid prediction for GeneMark_model.39259_t
Valid prediction for GlimmerHMM_glimmerT_22865-T1
Valid prediction for snap_scaffold_9-snap.1465-T1
Valid prediction for snap_scaffold_9-snap.1462-T1
Valid prediction for GlimmerHMM_glimmerT_22867-T1
Valid prediction for pasa_asmbl_55049.p1
Valid prediction for snap_scaffold_9-snap.1456-T1
Valid prediction for snap_scaffold_9-snap.1443-T1
Valid prediction for GlimmerHMM_glimmerT_22878-T1
Valid prediction for snap_scaffold_9-snap.1471-T1
Valid prediction for GlimmerHMM_glimmerT_22864-T1
Valid prediction for GlimmerHMM_glimmerT_22866-T1
Valid prediction for Augustus_model.g15310.t1
Valid prediction for HiQ_model.g15298.t1
Valid prediction for snap_scaffold_9-snap.1450-T1
Valid prediction for GlimmerHMM_glimmerT_22862-T1
Valid prediction for GeneMark_model.39243_t
Valid prediction for snap_scaffold_9-snap.1466-T1
Valid prediction for pasa_asmbl_55060.p1
Valid prediction for snap_scaffold_9-snap.1455-T1
Valid prediction for Augustus_model.g15299.t1
Valid prediction for Augustus_model.g15307.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 116771, rend_intergenic: 98693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191467, rend_intergenic: 188991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206902, rend_intergenic: 204964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213144
-exon list size: 551


building trellis

0.2    
0.4    
0.5    
0.7    
0.9    
1.1    
1.3    
1.4    
1.6    
1.8    
2.0    
2.2    
2.4    
2.5    
2.7    
2.9    
3.1    
3.3    
3.4    
3.6    
3.8    
4.0    
4.2    
4.3    
4.5    
4.7    
4.9    
5.1    
5.2    
5.4    
5.6    
5.8    
6.0    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
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7.6    
7.8    
8.0    
8.1    
8.3    
8.5    
8.7    
8.9    
9.0    
9.2    
9.4    
9.6    
9.8    
9.9    
10.1    
10.3    
10.5    
10.7    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
11.9    
12.1    
12.3    
12.5    
12.7    
12.8    
13.0    
13.2    
13.4    
13.6    
13.7    
13.9    
14.1    
14.3    
14.5    
14.6    
14.8    
15.0    
15.2    
15.4    
15.6    
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15.9    
16.1    
16.3    
16.5    
16.6    
16.8    
17.0    
17.2    
17.4    
17.5    
17.7    
17.9    
18.1    
18.3    
18.4    
18.6    
18.8    
19.0    
19.2    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.4    
20.6    
20.8    
21.0    
21.2    
21.3    
21.5    
21.7    
21.9    
22.1    
22.2    
22.4    
22.6    
22.8    
23.0    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.0    
26.2    
26.4    
26.6    
26.8    
26.9    
27.1    
27.3    
27.5    
27.7    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
28.9    
29.1    
29.3    
29.5    
29.7    
29.8    
30.0    
30.2    
30.4    
30.6    
30.7    
30.9    
31.1    
31.3    
31.5    
31.6    
31.8    
32.0    
32.2    
32.4    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.4    
34.5    
34.7    
34.9    
35.1    
35.3    
35.4    
35.6    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.4    
37.6    
37.8    
38.0    
38.2    
38.3    
38.5    
38.7    
38.9    
39.1    
39.2    
39.4    
39.6    
39.8    
40.0    
40.1    
40.3    
40.5    
40.7    
40.9    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.1    
42.3    
42.5    
42.7    
42.9    
43.0    
43.2    
43.4    
43.6    
43.8    
43.9    
44.1    
44.3    
44.5    
44.7    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
45.9    
46.1    
46.3    
46.5    
46.7    
46.8    
47.0    
47.2    
47.4    
47.6    
47.7    
47.9    
48.1    
48.3    
48.5    
48.6    
48.8    
49.0    
49.2    
49.4    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.6    
50.8    
51.0    
51.2    
51.4    
51.5    
51.7    
51.9    
52.1    
52.3    
52.4    
52.6    
52.8    
53.0    
53.2    
53.3    
53.5    
53.7    
53.9    
54.1    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.3    
55.5    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.8    
57.0    
57.1    
57.3    
57.5    
57.7    
57.9    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.1    
59.3    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.6    
60.8    
60.9    
61.1    
61.3    
61.5    
61.7    
61.8    
62.0    
62.2    
62.4    
62.6    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.4    
64.6    
64.7    
64.9    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.6    
67.8    
68.0    
68.2    
68.4    
68.5    
68.7    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
70.0    
70.2    
70.3    
70.5    
70.7    
70.9    
71.1    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.9    
73.1    
73.2    
73.4    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.8    
81.0    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 116771, rend_intergenic: 98693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191467, rend_intergenic: 188991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206902, rend_intergenic: 204964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 192921 - 213144
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-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 192921 - 206597
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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