-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_177447-405338

-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_31617-T1
Valid prediction for GlimmerHMM_glimmerT_31623-T1
Valid prediction for GlimmerHMM_glimmerT_31628-T1
Valid prediction for snap_scaffold_13-snap.61-T1
Valid prediction for HiQ_model.g21125.t1
Valid prediction for snap_scaffold_13-snap.39-T1
Valid prediction for GeneMark_model.54419_t
Valid prediction for GlimmerHMM_glimmerT_31612-T1
Valid prediction for snap_scaffold_13-snap.53-T1
Valid prediction for CodingQuarry_transcript_12788-T1
Valid prediction for GlimmerHMM_glimmerT_31624-T1
Valid prediction for snap_scaffold_13-snap.49-T1
Valid prediction for GeneMark_model.54420_t
Valid prediction for snap_scaffold_13-snap.66-T1
Valid prediction for GeneMark_model.54417_t
Valid prediction for snap_scaffold_13-snap.62-T1
Valid prediction for GlimmerHMM_glimmerT_31618-T1
Valid prediction for snap_scaffold_13-snap.65-T1
Valid prediction for snap_scaffold_13-snap.41-T1
Valid prediction for GlimmerHMM_glimmerT_31638-T1
Valid prediction for GeneMark_model.54418_t
Valid prediction for GlimmerHMM_glimmerT_31620-T1
Valid prediction for HiQ_model.g21129.t1
Valid prediction for pasa_asmbl_10444.p1
Valid prediction for GlimmerHMM_glimmerT_31613-T1
Valid prediction for GeneMark_model.54423_t
Valid prediction for snap_scaffold_13-snap.71-T1
Valid prediction for GeneMark_model.54426_t
Valid prediction for Augustus_model.g21126.t1
Valid prediction for GlimmerHMM_glimmerT_31634-T1
Valid prediction for GeneMark_model.54434_t
Valid prediction for GeneMark_model.54428_t
Valid prediction for snap_scaffold_13-snap.54-T1
Valid prediction for Augustus_model.g21133.t1
Valid prediction for GeneMark_model.54413_t
Valid prediction for CodingQuarry_transcript_12787-T1
Valid prediction for GlimmerHMM_glimmerT_31629-T1
Valid prediction for snap_scaffold_13-snap.42-T1
Valid prediction for Augustus_model.g21139.t1
Valid prediction for snap_scaffold_13-snap.50-T1
Valid prediction for GeneMark_model.54415_t
Valid prediction for GlimmerHMM_glimmerT_31619-T1
Valid prediction for pasa_asmbl_10439.p1
Valid prediction for Augustus_model.g21127.t1
Valid prediction for GlimmerHMM_glimmerT_31630-T1
Valid prediction for snap_scaffold_13-snap.51-T1
Valid prediction for snap_scaffold_13-snap.52-T1
Valid prediction for GeneMark_model.54440_t
Valid prediction for pasa_asmbl_10431.p1
Valid prediction for snap_scaffold_13-snap.57-T1
Valid prediction for GeneMark_model.54437_t
Valid prediction for snap_scaffold_13-snap.67-T1
Valid prediction for GeneMark_model.54436_t
Valid prediction for snap_scaffold_13-snap.82-T1
Valid prediction for GlimmerHMM_glimmerT_31621-T1
Valid prediction for Augustus_model.g21142.t1
Valid prediction for GeneMark_model.54432_t
Valid prediction for GeneMark_model.54422_t
Valid prediction for snap_scaffold_13-snap.45-T1
Valid prediction for snap_scaffold_13-snap.56-T1
Valid prediction for snap_scaffold_13-snap.47-T1
Valid prediction for snap_scaffold_13-snap.73-T1
Valid prediction for Augustus_model.g21128.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_13-snap.72-T1
Valid prediction for snap_scaffold_13-snap.68-T1
Valid prediction for Augustus_model.g21134.t1
Valid prediction for snap_scaffold_13-snap.43-T1
Couldn't classify 29671, 29897
Couldn't classify 34964, 35197
Sorry, prediction pasa_asmbl_9290.p1 fails validation.
(AAC)	 CA	29671-29897	GT	AGG
(CGG)	 AG	30247-30347	GT	AGG
(TGG)	 AG	31759-32023	GT	TGG
(GCA)	 AG	34651-34861	GT	AGG
(GTG)	 AG	34964-35197	TA	GGT
-recovered pasa_asmbl_9290.p1, internal, 30247, 30347
-recovered pasa_asmbl_9290.p1, internal, 31759, 32023
-recovered pasa_asmbl_9290.p1, internal, 34651, 34861
Valid prediction for GeneMark_model.54414_t
Valid prediction for GeneMark_model.54425_t
Valid prediction for GlimmerHMM_glimmerT_31639-T1
Valid prediction for snap_scaffold_13-snap.80-T1
Valid prediction for GlimmerHMM_glimmerT_31640-T1
Valid prediction for snap_scaffold_13-snap.44-T1
Valid prediction for HiQ_model.g21138.t1
Valid prediction for GeneMark_model.54444_t
Valid prediction for Augustus_model.g21124.t1
Valid prediction for GeneMark_model.54433_t
Valid prediction for GeneMark_model.54416_t
Valid prediction for pasa_asmbl_9297.p1
Valid prediction for snap_scaffold_13-snap.59-T1
Valid prediction for snap_scaffold_13-snap.40-T1
Valid prediction for GlimmerHMM_glimmerT_31625-T1
Valid prediction for snap_scaffold_13-snap.63-T1
Valid prediction for GlimmerHMM_glimmerT_31627-T1
Valid prediction for GeneMark_model.54412_t
Valid prediction for Augustus_model.g21136.t1
Valid prediction for GlimmerHMM_glimmerT_31614-T1
Valid prediction for GeneMark_model.54431_t
Valid prediction for pasa_asmbl_9271.p1
Valid prediction for GeneMark_model.54429_t
Valid prediction for snap_scaffold_13-snap.64-T1
Valid prediction for CodingQuarry_transcript_12797-T1
Valid prediction for snap_scaffold_13-snap.46-T1
Valid prediction for GlimmerHMM_glimmerT_31615-T1
Valid prediction for snap_scaffold_13-snap.70-T1
Valid prediction for HiQ_model.g21144.t1
Valid prediction for snap_scaffold_13-snap.83-T1
Valid prediction for pasa_asmbl_9276.p1
Valid prediction for GeneMark_model.54421_t
Valid prediction for GeneMark_model.54443_t
Valid prediction for Augustus_model.g21140.t1
Valid prediction for snap_scaffold_13-snap.60-T1
Valid prediction for Augustus_model.g21141.t1
Valid prediction for CodingQuarry_transcript_12795-T1
Valid prediction for snap_scaffold_13-snap.55-T1
Valid prediction for CodingQuarry_transcript_12799-T1
Valid prediction for Augustus_model.g21131.t1
Valid prediction for Augustus_model.g21132.t1
Valid prediction for pasa_asmbl_9300.p1
Valid prediction for snap_scaffold_13-snap.74-T1
Valid prediction for GlimmerHMM_glimmerT_31641-T1
Valid prediction for snap_scaffold_13-snap.75-T1
Valid prediction for snap_scaffold_13-snap.69-T1
Valid prediction for GlimmerHMM_glimmerT_31635-T1
Valid prediction for GeneMark_model.54439_t
Valid prediction for GeneMark_model.54442_t
Valid prediction for snap_scaffold_13-snap.81-T1
Valid prediction for GeneMark_model.54438_t
Valid prediction for GlimmerHMM_glimmerT_31631-T1
Valid prediction for Augustus_model.g21137.t1
Valid prediction for GlimmerHMM_glimmerT_31642-T1
Valid prediction for Augustus_model.g21130.t1
Valid prediction for Augustus_model.g21135.t1
Valid prediction for snap_scaffold_13-snap.76-T1
Valid prediction for GeneMark_model.54430_t
Couldn't classify 42366, 42711
Sorry, prediction pasa_asmbl_9284.p1 fails validation.
(CAT)	 GA	42366-42711	GT	CGG
(GTA)	 AG	42930-43121	GT	TGG
(GCG)	 AG	44460-44553	GT	ACG
(TCA)	 AG	44647-44758	GT	AGG
(CTC)	 AG	45080-45133	GT	AGG
(TTC)	 AG	45322-45576	AA	GAA
-recovered pasa_asmbl_9284.p1, terminal, 45322, 45576
-recovered pasa_asmbl_9284.p1, internal, 42930, 43121
-recovered pasa_asmbl_9284.p1, internal, 44460, 44553
-recovered pasa_asmbl_9284.p1, internal, 44647, 44758
-recovered pasa_asmbl_9284.p1, internal, 45080, 45133
Valid prediction for GeneMark_model.54441_t
Valid prediction for GeneMark_model.54427_t
Valid prediction for snap_scaffold_13-snap.58-T1
Valid prediction for GlimmerHMM_glimmerT_31616-T1
Valid prediction for snap_scaffold_13-snap.48-T1
Valid prediction for GlimmerHMM_glimmerT_31626-T1
Valid prediction for snap_scaffold_13-snap.77-T1
Valid prediction for GeneMark_model.54435_t
Valid prediction for snap_scaffold_13-snap.78-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.79-T1
Valid prediction for GlimmerHMM_glimmerT_31636-T1
Valid prediction for CodingQuarry_transcript_12792-T1
Valid prediction for CodingQuarry_transcript_12798-T1
Valid prediction for GlimmerHMM_glimmerT_31632-T1
Valid prediction for CodingQuarry_transcript_12794-T1
Valid prediction for GeneMark_model.54424_t
Valid prediction for GlimmerHMM_glimmerT_31637-T1
Valid prediction for GlimmerHMM_glimmerT_31633-T1
Couldn't classify 24487, 24617
Sorry, prediction pasa_asmbl_9291.p1 fails validation.
(ATG)	 GA	23268-23285	GT	AGG
(CGC)	 AG	23466-23621	GT	AGG
(AAT)	 AG	23797-23857	GT	TGG
(TGC)	 AG	24038-24244	GT	AGG
(ATG)	 AG	24487-24617	GT	CCG
-recovered pasa_asmbl_9291.p1, initial, 23268, 23285
add_exon() Sorry, pasa_asmbl_9291.p1 24487-24617-initial-1 is invalid.
-recovered pasa_asmbl_9291.p1, initial, 24487, 24617
-recovered pasa_asmbl_9291.p1, internal, 23466, 23621
-recovered pasa_asmbl_9291.p1, internal, 23797, 23857
-recovered pasa_asmbl_9291.p1, internal, 24038, 24244
-recovered pasa_asmbl_9291.p1, internal, 24487, 24617
Valid prediction for snap_scaffold_13-snap.84-T1
Valid prediction for CodingQuarry_transcript_12796-T1
Valid prediction for GlimmerHMM_glimmerT_31622-T1
Valid prediction for Augustus_model.g21143.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 43048, rend_intergenic: 38205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188123, rend_intergenic: 184764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220004, rend_intergenic: 215992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227892
-exon list size: 491


building trellis

0.2    
0.4    
0.6    
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2.8    
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3.4    
3.7    
3.9    
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8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.3    
10.5    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
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12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
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14.4    
14.6    
14.8    
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16.6    
16.8    
17.0    
17.2    
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17.6    
17.8    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
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19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
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    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.5    
46.7    
46.9    
47.1    
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    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
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    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
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    
96.6    
96.8    
97.0    
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 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 43048, rend_intergenic: 38205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188123, rend_intergenic: 184764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220004, rend_intergenic: 215992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14976
-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
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 - 14919
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-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 - 13603
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13336
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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

-building DP trellis

-building trellis in range 1 - 10496
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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