-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_11343651-11581241

-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_10480-T1
Valid prediction for GeneMark_model.17072_t
Valid prediction for GlimmerHMM_glimmerT_10474-T1
Valid prediction for GeneMark_model.17075_t
Valid prediction for GeneMark_model.17085_t
Valid prediction for snap_scaffold_4-snap.2468-T1
Valid prediction for snap_scaffold_4-snap.2478-T1
Valid prediction for snap_scaffold_4-snap.2476-T1
Valid prediction for GlimmerHMM_glimmerT_10462-T1
Valid prediction for snap_scaffold_4-snap.2467-T1
Valid prediction for Augustus_model.g6870.t1
Valid prediction for GlimmerHMM_glimmerT_10470-T1
Valid prediction for GlimmerHMM_glimmerT_10463-T1
Valid prediction for snap_scaffold_4-snap.2465-T1
Valid prediction for Augustus_model.g6869.t1
Valid prediction for GeneMark_model.17078_t
Valid prediction for snap_scaffold_4-snap.2492-T1
Valid prediction for snap_scaffold_4-snap.2471-T1
Valid prediction for snap_scaffold_4-snap.2491-T1
Valid prediction for GlimmerHMM_glimmerT_10476-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.17081_t
Valid prediction for GeneMark_model.17069_t
Valid prediction for GeneMark_model.17093_t
Valid prediction for snap_scaffold_4-snap.2479-T1
Valid prediction for GlimmerHMM_glimmerT_10478-T1
Valid prediction for GlimmerHMM_glimmerT_10468-T1
Valid prediction for snap_scaffold_4-snap.2486-T1
Valid prediction for GlimmerHMM_glimmerT_10469-T1
Valid prediction for snap_scaffold_4-snap.2482-T1
Valid prediction for GeneMark_model.17090_t
Valid prediction for GeneMark_model.17083_t
Valid prediction for snap_scaffold_4-snap.2472-T1
Valid prediction for GlimmerHMM_glimmerT_10472-T1
Valid prediction for GeneMark_model.17097_t
Valid prediction for GlimmerHMM_glimmerT_10482-T1
Valid prediction for GeneMark_model.17087_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 GeneMark_model.17098_t
Valid prediction for CodingQuarry_transcript_49030-T1
Valid prediction for GlimmerHMM_glimmerT_10466-T1
Valid prediction for snap_scaffold_4-snap.2474-T1
Valid prediction for snap_scaffold_4-snap.2490-T1
Valid prediction for GeneMark_model.17068_t
Valid prediction for Augustus_model.g6871.t1
Valid prediction for GlimmerHMM_glimmerT_10471-T1
Valid prediction for GeneMark_model.17076_t
Valid prediction for Augustus_model.g6878.t1
Valid prediction for GeneMark_model.17084_t
Valid prediction for GeneMark_model.17099_t
Valid prediction for GeneMark_model.17074_t
Valid prediction for GeneMark_model.17067_t
Valid prediction for pasa_asmbl_41623.p1
Valid prediction for GeneMark_model.17101_t
Valid prediction for HiQ_model.g6881.t1
Valid prediction for GlimmerHMM_glimmerT_10473-T1
Valid prediction for GlimmerHMM_glimmerT_10475-T1
Valid prediction for GeneMark_model.17073_t
Valid prediction for GeneMark_model.17079_t
Valid prediction for GlimmerHMM_glimmerT_10465-T1
Valid prediction for Augustus_model.g6880.t1
Valid prediction for Augustus_model.g6873.t1
Valid prediction for snap_scaffold_4-snap.2469-T1
Valid prediction for GlimmerHMM_glimmerT_10479-T1
Valid prediction for snap_scaffold_4-snap.2484-T1
Valid prediction for snap_scaffold_4-snap.2487-T1
Valid prediction for snap_scaffold_4-snap.2462-T1
Valid prediction for Augustus_model.g6874.t1
Valid prediction for snap_scaffold_4-snap.2475-T1
Valid prediction for GeneMark_model.17096_t
Valid prediction for snap_scaffold_4-snap.2470-T1
Valid prediction for GlimmerHMM_glimmerT_10460-T1
Valid prediction for snap_scaffold_4-snap.2481-T1
Valid prediction for GeneMark_model.17088_t
Valid prediction for HiQ_model.g6867.t1
Valid prediction for HiQ_model.g6868.t1
Valid prediction for snap_scaffold_4-snap.2489-T1
Valid prediction for GlimmerHMM_glimmerT_10467-T1
Valid prediction for GlimmerHMM_glimmerT_10477-T1
Valid prediction for snap_scaffold_4-snap.2485-T1
Valid prediction for GlimmerHMM_glimmerT_10459-T1
Valid prediction for GeneMark_model.17091_t
Valid prediction for Augustus_model.g6876.t1
Valid prediction for snap_scaffold_4-snap.2477-T1
Valid prediction for GeneMark_model.17070_t
Valid prediction for GeneMark_model.17071_t
Couldn't classify 24070, 24225
Sorry, prediction pasa_asmbl_41629.p1 fails validation.
(ACC)	 CA	24070-24225	GT	TGG
(GGT)	 AG	25751-26744	GT	AGG
(ATC)	 AG	26957-27032	GT	AGG
(CAC)	 AG	28388-28445	TC	GAT
add_exon() Sorry, pasa_asmbl_41629.p1 25751-26744-terminal-3 is invalid.
-recovered pasa_asmbl_41629.p1, terminal, 25751, 26744
-recovered pasa_asmbl_41629.p1, terminal, 28388, 28445
-recovered pasa_asmbl_41629.p1, internal, 25751, 26744
-recovered pasa_asmbl_41629.p1, internal, 26957, 27032
Valid prediction for snap_scaffold_4-snap.2483-T1
Valid prediction for GeneMark_model.17089_t
Valid prediction for GeneMark_model.17092_t
Valid prediction for GeneMark_model.17094_t
Valid prediction for Augustus_model.g6872.t1
Valid prediction for GeneMark_model.17080_t
Valid prediction for GeneMark_model.17095_t
Valid prediction for snap_scaffold_4-snap.2466-T1
Valid prediction for Augustus_model.g6879.t1
Valid prediction for snap_scaffold_4-snap.2480-T1
Valid prediction for snap_scaffold_4-snap.2464-T1
Valid prediction for snap_scaffold_4-snap.2473-T1
Valid prediction for GlimmerHMM_glimmerT_10481-T1
Valid prediction for snap_scaffold_4-snap.2463-T1
Valid prediction for GeneMark_model.17077_t
Couldn't classify 168844, 168984
Sorry, prediction pasa_asmbl_41627.p1 fails validation.
(ACC)	 CG	168844-168984	GT	AGG
(GAC)	 AG	170211-170306	GT	TGG
(TGG)	 AG	171729-171877	GT	AGG
(ACC)	 AG	172047-172219	GT	TGG
(ATC)	 AG	172330-172460	GT	AGG
(AAA)	 AG	172646-172769	GT	CCG
(AGT)	 AG	172946-173190	GT	AGG
(ATT)	 AG	173466-173604	GT	AGG
(GCC)	 AG	174636-174762	GT	AGG
(ATG)	 AG	176629-176833	GT	AGG
(TGT)	 AG	177129-177323	GT	AGG
(TGC)	 AG	177516-177749	GT	AGG
(TGC)	 AG	178058-178205	GT	AGG
(ATA)	 AG	178299-178414	GT	AGG
-recovered pasa_asmbl_41627.p1, initial, 176629, 176833
-recovered pasa_asmbl_41627.p1, terminal, 178299, 178414
-recovered pasa_asmbl_41627.p1, internal, 170211, 170306
-recovered pasa_asmbl_41627.p1, internal, 171729, 171877
-recovered pasa_asmbl_41627.p1, internal, 172047, 172219
-recovered pasa_asmbl_41627.p1, internal, 172330, 172460
-recovered pasa_asmbl_41627.p1, internal, 172646, 172769
-recovered pasa_asmbl_41627.p1, internal, 172946, 173190
-recovered pasa_asmbl_41627.p1, internal, 173466, 173604
-recovered pasa_asmbl_41627.p1, internal, 174636, 174762
-recovered pasa_asmbl_41627.p1, internal, 176629, 176833
-recovered pasa_asmbl_41627.p1, internal, 177129, 177323
-recovered pasa_asmbl_41627.p1, internal, 177516, 177749
-recovered pasa_asmbl_41627.p1, internal, 178058, 178205
-recovered pasa_asmbl_41627.p1, internal, 178299, 178414
Valid prediction for GlimmerHMM_glimmerT_10461-T1
Valid prediction for GeneMark_model.17082_t
Valid prediction for CodingQuarry_transcript_49031-T1
Valid prediction for pasa_asmbl_42274.p1
Valid prediction for snap_scaffold_4-snap.2488-T1
Valid prediction for GeneMark_model.17100_t
Valid prediction for Augustus_model.g6875.t1
Valid prediction for Augustus_model.g6877.t1
Valid prediction for GeneMark_model.17086_t
Valid prediction for GlimmerHMM_glimmerT_10464-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 64177, rend_intergenic: 61872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 237591
-exon list size: 415


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.2    
2.4    
2.6    
2.9    
3.1    
3.4    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.0    
5.3    
5.5    
5.8    
6.0    
6.2    
6.5    
6.7    
7.0    
7.2    
7.4    
7.7    
7.9    
8.2    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.8    
10.1    
10.3    
10.6    
10.8    
11.0    
11.3    
11.5    
11.8    
12.0    
12.2    
12.5    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.1    
14.4    
14.6    
14.9    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.5    
16.8    
17.0    
17.3    
17.5    
17.7    
18.0    
18.2    
18.5    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.1    
26.4    
26.6    
26.9    
27.1    
27.3    
27.6    
27.8    
28.1    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
30.9    
31.2    
31.4    
31.7    
31.9    
32.1    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.9    
38.1    
38.4    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.0    
46.3    
46.5    
46.8    
47.0    
47.2    
47.5    
47.7    
48.0    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.6    
51.8    
52.0    
52.3    
52.5    
52.8    
53.0    
53.2    
53.5    
53.7    
54.0    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.6    
61.9    
62.1    
62.4    
62.6    
62.8    
63.1    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.9    
68.1    
68.3    
68.6    
68.8    
69.1    
69.3    
69.5    
69.8    
70.0    
70.3    
70.5    
70.7    
71.0    
71.2    
71.5    
71.7    
71.9    
72.2    
72.4    
72.7    
72.9    
73.1    
73.4    
73.6    
73.9    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.1    
85.4    
85.6    
85.9    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.5    
87.8    
88.0    
88.2    
88.5    
88.7    
89.0    
89.2    
89.4    
89.7    
89.9    
90.2    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.6    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 64177, rend_intergenic: 61872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support