-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_14663789-14975599

-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 snap_scaffold_4-snap.2971-T1
Valid prediction for GlimmerHMM_glimmerT_10856-T1
Valid prediction for HiQ_model.g7186.t1
Valid prediction for snap_scaffold_4-snap.2970-T1
Valid prediction for Augustus_model.g7182.t1
Valid prediction for GeneMark_model.17618_t
Valid prediction for GeneMark_model.17639_t
Valid prediction for Augustus_model.g7175.t1
Valid prediction for GlimmerHMM_glimmerT_10859-T1
Valid prediction for Augustus_model.g7185.t1
Valid prediction for GlimmerHMM_glimmerT_10867-T1
Valid prediction for GlimmerHMM_glimmerT_10865-T1
Valid prediction for GeneMark_model.17637_t
Valid prediction for GlimmerHMM_glimmerT_10868-T1
Valid prediction for GeneMark_model.17628_t
Valid prediction for snap_scaffold_4-snap.2985-T1
Valid prediction for pasa_asmbl_43244.p1
Couldn't classify 269109, 269462
Sorry, prediction pasa_asmbl_43239.p1 fails validation.
(ATG)	 GA	269109-269462	AG	TGA
Valid prediction for GlimmerHMM_glimmerT_10855-T1
Valid prediction for GeneMark_model.17631_t
Valid prediction for GeneMark_model.17636_t
Valid prediction for GeneMark_model.17625_t
Valid prediction for GlimmerHMM_glimmerT_10863-T1
Valid prediction for snap_scaffold_4-snap.2987-T1
Valid prediction for GeneMark_model.17634_t
Valid prediction for pasa_asmbl_43240.p1
Valid prediction for CodingQuarry_transcript_49139-T1
Valid prediction for GeneMark_model.17610_t
Valid prediction for snap_scaffold_4-snap.2986-T1
Valid prediction for snap_scaffold_4-snap.2968-T1
Valid prediction for snap_scaffold_4-snap.2982-T1
Valid prediction for Augustus_model.g7184.t1
Valid prediction for GeneMark_model.17609_t
Valid prediction for GeneMark_model.17611_t
Valid prediction for GeneMark_model.17640_t
Valid prediction for snap_scaffold_4-snap.2969-T1
Valid prediction for GeneMark_model.17630_t
Valid prediction for snap_scaffold_4-snap.2980-T1
Valid prediction for snap_scaffold_4-snap.2983-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 Augustus_model.g7176.t1
Valid prediction for snap_scaffold_4-snap.2984-T1
Valid prediction for GlimmerHMM_glimmerT_10851-T1
Valid prediction for GeneMark_model.17619_t
Valid prediction for snap_scaffold_4-snap.2979-T1
Valid prediction for GeneMark_model.17627_t
Valid prediction for Augustus_model.g7174.t1
Valid prediction for Augustus_model.g7181.t1
Valid prediction for Augustus_model.g7179.t1
Valid prediction for GeneMark_model.17632_t
Valid prediction for GeneMark_model.17608_t
Valid prediction for GlimmerHMM_glimmerT_10853-T1
Valid prediction for Augustus_model.g7177.t1
Valid prediction for GlimmerHMM_glimmerT_10850-T1
Valid prediction for GlimmerHMM_glimmerT_10860-T1
Valid prediction for CodingQuarry_transcript_49137-T1
Valid prediction for GeneMark_model.17616_t
Valid prediction for Augustus_model.g7173.t1
Valid prediction for snap_scaffold_4-snap.2963-T1
Valid prediction for snap_scaffold_4-snap.2965-T1
Valid prediction for GeneMark_model.17635_t
Valid prediction for GlimmerHMM_glimmerT_10858-T1
Valid prediction for GlimmerHMM_glimmerT_10861-T1
Valid prediction for GlimmerHMM_glimmerT_10852-T1
Valid prediction for HiQ_model.g7171.t1
Valid prediction for snap_scaffold_4-snap.2981-T1
Couldn't classify 289832, 289871
Sorry, prediction pasa_asmbl_41829.p1 fails validation.
(GAA)	 GC	289832-289871	GT	GGG
(CAC)	 AG	290158-290240	GC	AGG
(CCG)	 AG	290389-290596	GT	AGG
(CTC)	 AG	290787-290975	GT	ACG
(AGG)	 AG	291130-291231	GT	GGG
(CAC)	 AG	291492-291638	GT	AGG
(TTG)	 AG	291734-291877	GT	AGG
(ATG)	 AG	291993-292089	GT	AGG
(GCT)	 AG	292178-292259	GT	AGG
(GAT)	 AG	292354-292902	CC	GAC
add_exon() Sorry, pasa_asmbl_41829.p1 291993-292089-initial-1 is invalid.
-recovered pasa_asmbl_41829.p1, initial, 291993, 292089
add_exon() Sorry, pasa_asmbl_41829.p1 291734-291877-terminal-1 is invalid.
-recovered pasa_asmbl_41829.p1, terminal, 291734, 291877
-recovered pasa_asmbl_41829.p1, terminal, 292354, 292902
-recovered pasa_asmbl_41829.p1, internal, 290158, 290240
-recovered pasa_asmbl_41829.p1, internal, 290389, 290596
-recovered pasa_asmbl_41829.p1, internal, 290787, 290975
-recovered pasa_asmbl_41829.p1, internal, 291130, 291231
-recovered pasa_asmbl_41829.p1, internal, 291492, 291638
-recovered pasa_asmbl_41829.p1, internal, 291734, 291877
-recovered pasa_asmbl_41829.p1, internal, 291993, 292089
-recovered pasa_asmbl_41829.p1, internal, 292178, 292259
Valid prediction for snap_scaffold_4-snap.2973-T1
Valid prediction for GeneMark_model.17620_t
Valid prediction for GeneMark_model.17626_t
Valid prediction for snap_scaffold_4-snap.2975-T1
Valid prediction for pasa_asmbl_41824.p1
Valid prediction for snap_scaffold_4-snap.2977-T1
Valid prediction for snap_scaffold_4-snap.2974-T1
Valid prediction for GlimmerHMM_glimmerT_10866-T1
Valid prediction for GlimmerHMM_glimmerT_10862-T1
Valid prediction for GlimmerHMM_glimmerT_10864-T1
Valid prediction for GeneMark_model.17629_t
Valid prediction for GeneMark_model.17623_t
Valid prediction for GeneMark_model.17617_t
Couldn't classify 311519, 311572
Sorry, prediction pasa_asmbl_41819.p1 fails validation.
(ATG)	 TC	306918-306923	GT	AAG
(AGC)	 AG	308616-308742	GT	CGG
(GGC)	 AG	309249-309334	GT	AGG
(ATC)	 AG	309827-309973	GT	AGG
(GAT)	 AG	310707-310931	GT	AGG
(AAA)	 AG	311519-311572	TA	GGT
-recovered pasa_asmbl_41819.p1, initial, 306918, 306923
-recovered pasa_asmbl_41819.p1, internal, 308616, 308742
-recovered pasa_asmbl_41819.p1, internal, 309249, 309334
-recovered pasa_asmbl_41819.p1, internal, 309827, 309973
-recovered pasa_asmbl_41819.p1, internal, 310707, 310931
Valid prediction for GeneMark_model.17613_t
Valid prediction for Augustus_model.g7183.t1
Valid prediction for GeneMark_model.17633_t
Valid prediction for GlimmerHMM_glimmerT_10857-T1
Valid prediction for snap_scaffold_4-snap.2972-T1
Valid prediction for GeneMark_model.17615_t
Valid prediction for Augustus_model.g7172.t1
Valid prediction for GeneMark_model.17638_t
Valid prediction for snap_scaffold_4-snap.2964-T1
Valid prediction for GlimmerHMM_glimmerT_10869-T1
Valid prediction for Augustus_model.g7178.t1
Valid prediction for snap_scaffold_4-snap.2978-T1
Valid prediction for Augustus_model.g7180.t1
Valid prediction for GeneMark_model.17614_t
Valid prediction for snap_scaffold_4-snap.2976-T1
Valid prediction for GeneMark_model.17621_t
Valid prediction for GeneMark_model.17624_t
Valid prediction for snap_scaffold_4-snap.2966-T1
Valid prediction for GlimmerHMM_glimmerT_10854-T1
Valid prediction for snap_scaffold_4-snap.2967-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 131832, rend_intergenic: 131829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 311811
-exon list size: 351


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.3    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 19 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 131832, rend_intergenic: 131829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support