-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_6315415-6488869

-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.90829_t
Valid prediction for GlimmerHMM_glimmerT_52392-T1
Valid prediction for GeneMark_model.90798_t
Valid prediction for GlimmerHMM_glimmerT_52387-T1
Valid prediction for Augustus_model.g35238.t1
Couldn't classify 27905, 28113
Couldn't classify 28135, 28378
Sorry, prediction CodingQuarry_transcript_35620-T1 fails validation.
(ATG)	 CC	27905-28113	GA	GAG
(CTC)	 AT	28135-28378	AC	AGA
Valid prediction for GeneMark_model.90809_t
Valid prediction for GlimmerHMM_glimmerT_52397-T1
Valid prediction for snap_scaffold_23-snap.1166-T1
Valid prediction for snap_scaffold_23-snap.1165-T1
Valid prediction for GeneMark_model.90815_t
Valid prediction for GeneMark_model.90802_t
Couldn't classify 28806, 28814
Sorry, prediction pasa_asmbl_30916.p1 fails validation.
(GCT)	 AT	28806-28814	GT	AGG
(ACT)	 AG	29217-29271	GT	AGG
(CAG)	 AG	29805-29958	GT	AGG
(TGC)	 AG	30116-30306	GT	AGG
(CAG)	 AG	30609-30954	GT	AGG
(ACC)	 AG	31174-31642	GT	AGG
(GTG)	 AG	31800-31907	CA	GAC
-recovered pasa_asmbl_30916.p1, terminal, 31800, 31907
-recovered pasa_asmbl_30916.p1, internal, 29217, 29271
-recovered pasa_asmbl_30916.p1, internal, 29805, 29958
-recovered pasa_asmbl_30916.p1, internal, 30116, 30306
-recovered pasa_asmbl_30916.p1, internal, 30609, 30954
-recovered pasa_asmbl_30916.p1, internal, 31174, 31642
Valid prediction for snap_scaffold_23-snap.1160-T1
Valid prediction for CodingQuarry_transcript_35619-T1
Valid prediction for CodingQuarry_transcript_35618-T1
Couldn't classify 17609, 18246
Couldn't classify 18412, 18597
Sorry, prediction CodingQuarry_transcript_35616-T1 fails validation.
(ATG)	 CC	13355-13502	GT	AGG
(CAC)	 AG	13767-13906	GT	AGG
(GGC)	 AG	14128-14226	GT	GAG
(GTG)	 AG	14403-14534	GT	AGG
(GCC)	 AG	14634-14717	GT	AGG
(GGT)	 AG	14983-15009	GT	AGG
(AAT)	 AG	15092-15139	GT	AAG
(CCG)	 AG	15465-15527	GT	CAG
(GAG)	 AG	16146-16760	GT	AGG
(TCT)	 AG	17386-17512	GC	AGG
(GCA)	 AG	17609-18246	AA	ACA
(GAC)	 AA	18412-18597	GT	TGG
(GCT)	 AG	18705-18776	AT	AAA
-recovered CodingQuarry_transcript_35616-T1, initial, 13355, 13502
add_exon() Sorry, CodingQuarry_transcript_35616-T1 17386-17512-terminal-3 is invalid.
-recovered CodingQuarry_transcript_35616-T1, terminal, 17386, 17512
-recovered CodingQuarry_transcript_35616-T1, terminal, 18705, 18776
-recovered CodingQuarry_transcript_35616-T1, internal, 13767, 13906
-recovered CodingQuarry_transcript_35616-T1, internal, 14128, 14226
-recovered CodingQuarry_transcript_35616-T1, internal, 14403, 14534
-recovered CodingQuarry_transcript_35616-T1, internal, 14634, 14717
-recovered CodingQuarry_transcript_35616-T1, internal, 14983, 15009
-recovered CodingQuarry_transcript_35616-T1, internal, 15092, 15139
-recovered CodingQuarry_transcript_35616-T1, internal, 15465, 15527
-recovered CodingQuarry_transcript_35616-T1, internal, 16146, 16760
-recovered CodingQuarry_transcript_35616-T1, internal, 17386, 17512
Couldn't classify 26099, 26146
Couldn't classify 26609, 27348
Sorry, prediction pasa_asmbl_30915.p1 fails validation.
(GGG)	 GG	26099-26146	GT	TTG
(GAT)	 AG	26292-26328	GT	GGG
(AGA)	 AG	26423-26506	GT	AGG
(AAA)	 AG	26609-27348	GA	CTG
-recovered pasa_asmbl_30915.p1, internal, 26292, 26328
-recovered pasa_asmbl_30915.p1, internal, 26423, 26506
Couldn't classify 24555, 24616
Couldn't classify 25314, 25656
Sorry, prediction pasa_asmbl_30914.p1 fails validation.
(GAG)	 AT	24555-24616	GT	AGG
(CTC)	 AG	24713-24917	GT	AGG
(GAG)	 AG	25048-25175	GT	CGG
(GTA)	 AG	25314-25656	AG	ACA
-recovered pasa_asmbl_30914.p1, internal, 24713, 24917
-recovered pasa_asmbl_30914.p1, internal, 25048, 25175
Valid prediction for pasa_asmbl_30911.p1
Valid prediction for Augustus_model.g35236.t1
Valid prediction for Augustus_model.g35235.t1
Valid prediction for CodingQuarry_transcript_35622-T1
Valid prediction for GeneMark_model.90812_t
Valid prediction for snap_scaffold_23-snap.1151-T1
Valid prediction for snap_scaffold_23-snap.1144-T1
Valid prediction for snap_scaffold_23-snap.1161-T1
Valid prediction for snap_scaffold_23-snap.1158-T1
Valid prediction for snap_scaffold_23-snap.1142-T1
Valid prediction for GeneMark_model.90804_t
Valid prediction for GeneMark_model.90801_t
Valid prediction for GlimmerHMM_glimmerT_52402-T1
Valid prediction for snap_scaffold_23-snap.1159-T1
Valid prediction for snap_scaffold_23-snap.1143-T1
Valid prediction for snap_scaffold_23-snap.1157-T1
Valid prediction for snap_scaffold_23-snap.1153-T1
Couldn't classify 22547, 22638
Couldn't classify 24553, 24569
Sorry, prediction pasa_asmbl_30912.p1 fails validation.
(GAC)	 AA	22547-22638	GT	AGG
(TCT)	 AG	23193-23326	GT	AGG
(AGA)	 AG	23599-23693	GT	AGG
(AAC)	 AG	23794-23848	GT	CAG
(GAG)	 AG	23933-24079	GT	AGG
(CCA)	 AG	24237-24446	GT	AGG
(ATG)	 AG	24553-24569	GA	CTG
-recovered pasa_asmbl_30912.p1, internal, 23193, 23326
-recovered pasa_asmbl_30912.p1, internal, 23599, 23693
-recovered pasa_asmbl_30912.p1, internal, 23794, 23848
-recovered pasa_asmbl_30912.p1, internal, 23933, 24079
-recovered pasa_asmbl_30912.p1, internal, 24237, 24446
Valid prediction for CodingQuarry_transcript_35621-T1
Valid prediction for Augustus_model.g35234.t1
Valid prediction for snap_scaffold_23-snap.1156-T1
Valid prediction for GlimmerHMM_glimmerT_52395-T1
Valid prediction for snap_scaffold_23-snap.1163-T1
Valid prediction for snap_scaffold_23-snap.1152-T1
Couldn't classify 17609, 18246
Couldn't classify 18412, 18597
Sorry, prediction CodingQuarry_transcript_35617-T1 fails validation.
(ATG)	 CC	13355-13502	GT	AGG
(CAC)	 AG	13767-13906	GT	AGG
(GGC)	 AG	14128-14226	GT	GAG
(GTG)	 AG	14403-14534	GT	AGG
(GCC)	 AG	14634-14717	GT	AGG
(GGT)	 AG	14983-15009	GT	AGG
(AAT)	 AG	15092-15139	GT	AAG
(CCG)	 AG	15465-15527	GT	CAG
(TCT)	 AG	17386-17512	GC	AGG
(GCA)	 AG	17609-18246	AA	ACA
(GAC)	 AA	18412-18597	GT	TGG
(GCT)	 AG	18705-18776	AT	AAA
-recovered CodingQuarry_transcript_35617-T1, initial, 13355, 13502
add_exon() Sorry, CodingQuarry_transcript_35617-T1 17386-17512-terminal-3 is invalid.
-recovered CodingQuarry_transcript_35617-T1, terminal, 17386, 17512
-recovered CodingQuarry_transcript_35617-T1, terminal, 18705, 18776
-recovered CodingQuarry_transcript_35617-T1, internal, 13767, 13906
-recovered CodingQuarry_transcript_35617-T1, internal, 14128, 14226
-recovered CodingQuarry_transcript_35617-T1, internal, 14403, 14534
-recovered CodingQuarry_transcript_35617-T1, internal, 14634, 14717
-recovered CodingQuarry_transcript_35617-T1, internal, 14983, 15009
-recovered CodingQuarry_transcript_35617-T1, internal, 15092, 15139
-recovered CodingQuarry_transcript_35617-T1, internal, 15465, 15527
-recovered CodingQuarry_transcript_35617-T1, internal, 17386, 17512
Valid prediction for GeneMark_model.90799_t
Valid prediction for Augustus_model.g35242.t1
Valid prediction for GeneMark_model.90826_t
Valid prediction for GeneMark_model.90805_t
Valid prediction for GeneMark_model.90807_t
Valid prediction for GlimmerHMM_glimmerT_52384-T1
Valid prediction for pasa_asmbl_30907.p1
Valid prediction for GlimmerHMM_glimmerT_52383-T1
Valid prediction for snap_scaffold_23-snap.1147-T1
Valid prediction for GlimmerHMM_glimmerT_52400-T1
Valid prediction for GeneMark_model.90822_t

-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 Augustus_model.g35239.t1
Valid prediction for GeneMark_model.90800_t
Valid prediction for GeneMark_model.90830_t
Valid prediction for GeneMark_model.90821_t
Valid prediction for Augustus_model.g35240.t1
Valid prediction for GeneMark_model.90820_t
Valid prediction for GlimmerHMM_glimmerT_52398-T1
Valid prediction for GlimmerHMM_glimmerT_52393-T1
Valid prediction for GeneMark_model.90814_t
Valid prediction for GlimmerHMM_glimmerT_52390-T1
Valid prediction for GeneMark_model.90813_t
Valid prediction for GeneMark_model.90825_t
Valid prediction for GeneMark_model.90803_t
Valid prediction for GlimmerHMM_glimmerT_52401-T1
Valid prediction for GeneMark_model.90828_t
Valid prediction for GlimmerHMM_glimmerT_52386-T1
Valid prediction for snap_scaffold_23-snap.1148-T1
Valid prediction for GeneMark_model.90819_t
Valid prediction for GeneMark_model.90827_t
Valid prediction for snap_scaffold_23-snap.1150-T1
Couldn't classify 111592, 111758
Couldn't classify 111983, 112160
Sorry, prediction pasa_asmbl_31699.p1 fails validation.
(TAT)	 CC	111592-111758	GT	ACG
(AGC)	 AG	111983-112160	GA	AGG
Valid prediction for snap_scaffold_23-snap.1164-T1
Valid prediction for snap_scaffold_23-snap.1149-T1
Valid prediction for snap_scaffold_23-snap.1162-T1
Valid prediction for GeneMark_model.90823_t
Valid prediction for Augustus_model.g35237.t1
Valid prediction for snap_scaffold_23-snap.1155-T1
Valid prediction for GeneMark_model.90818_t
Valid prediction for GeneMark_model.90816_t
Valid prediction for snap_scaffold_23-snap.1154-T1
Valid prediction for GeneMark_model.90817_t
Valid prediction for GlimmerHMM_glimmerT_52399-T1
Valid prediction for snap_scaffold_23-snap.1146-T1
Valid prediction for GeneMark_model.90824_t
Valid prediction for snap_scaffold_23-snap.1145-T1
Valid prediction for GlimmerHMM_glimmerT_52385-T1
Valid prediction for GeneMark_model.90811_t
Valid prediction for snap_scaffold_23-snap.1167-T1
Valid prediction for GeneMark_model.90806_t
Valid prediction for GlimmerHMM_glimmerT_52394-T1
Valid prediction for GeneMark_model.90810_t
Valid prediction for GlimmerHMM_glimmerT_52396-T1
Valid prediction for Augustus_model.g35241.t1
Valid prediction for GlimmerHMM_glimmerT_52391-T1
Valid prediction for GlimmerHMM_glimmerT_52389-T1
Valid prediction for GeneMark_model.90808_t
Valid prediction for GlimmerHMM_glimmerT_52388-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 38187, rend_intergenic: 34449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168026, rend_intergenic: 159802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171613, rend_intergenic: 168176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173455
-exon list size: 445


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.6    
1.8    
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2.2    
2.5    
2.7    
2.9    
3.1    
3.4    
3.6    
3.8    
4.0    
4.3    
4.5    
4.7    
4.9    
5.1    
5.4    
5.6    
5.8    
6.0    
6.3    
6.5    
6.7    
6.9    
7.2    
7.4    
7.6    
7.8    
8.1    
8.3    
8.5    
8.7    
8.9    
9.2    
9.4    
9.6    
9.8    
10.1    
10.3    
10.5    
10.7    
11.0    
11.2    
11.4    
11.6    
11.9    
12.1    
12.3    
12.5    
12.8    
13.0    
13.2    
13.4    
13.6    
13.9    
14.1    
14.3    
14.5    
14.8    
15.0    
15.2    
15.4    
15.7    
15.9    
16.1    
16.3    
16.6    
16.8    
17.0    
17.2    
17.4    
17.7    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.2    
19.5    
19.7    
19.9    
20.1    
20.4    
20.6    
20.8    
21.0    
21.3    
21.5    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.0    
23.3    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
26.0    
26.2    
26.4    
26.6    
26.8    
27.1    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.5    
29.8    
30.0    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.5    
31.8    
32.0    
32.2    
32.4    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.5    
36.7    
36.9    
37.1    
37.4    
37.6    
37.8    
38.0    
38.3    
38.5    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.8    
42.1    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.8    
47.0    
47.2    
47.4    
47.7    
47.9    
48.1    
48.3    
48.5    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.5    
51.7    
51.9    
52.1    
52.3    
52.6    
52.8    
53.0    
53.2    
53.5    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
57.9    
58.2    
58.4    
58.6    
58.8    
59.1    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.9    
61.1    
61.3    
61.5    
61.7    
62.0    
62.2    
62.4    
62.6    
62.9    
63.1    
63.3    
63.5    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.3    
65.5    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.3    
67.6    
67.8    
68.0    
68.2    
68.5    
68.7    
68.9    
69.1    
69.4    
69.6    
69.8    
70.0    
70.2    
70.5    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.0    
72.3    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.8    
74.0    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.5    
78.7    
79.0    
79.2    
79.4    
79.6    
79.9    
80.1    
80.3    
80.5    
80.8    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.3    
82.6    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.3    
84.6    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.4    
86.6    
86.8    
87.0    
87.2    
87.5    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
89.9    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.8    
93.1    
93.3    
93.5    
93.7    
94.0    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 38187, rend_intergenic: 34449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168026, rend_intergenic: 159802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171613, rend_intergenic: 168176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13354
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 12408
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 11493
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 462 - 11493