-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_2043958-2281563

-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_55186-T1
Valid prediction for snap_scaffold_26-snap.418-T1
Valid prediction for GlimmerHMM_glimmerT_55183-T1
Valid prediction for snap_scaffold_26-snap.407-T1
Valid prediction for Augustus_model.g36548.t1
Valid prediction for Augustus_model.g36549.t1
Valid prediction for snap_scaffold_26-snap.434-T1
Couldn't classify 118093, 118578
Sorry, prediction pasa_asmbl_34732.p1 fails validation.
(CCC)	 AG	118093-118578	AA	ACA
Couldn't classify 222467, 222726
Sorry, prediction pasa_asmbl_34742.p1 fails validation.
(ATG)	 CA	220925-221468	GT	AGG
(GCA)	 AG	222467-222726	AA	GGA
-recovered pasa_asmbl_34742.p1, initial, 220925, 221468
Valid prediction for GlimmerHMM_glimmerT_55161-T1
Valid prediction for pasa_asmbl_34740.p2
Valid prediction for Augustus_model.g36550.t1
Valid prediction for snap_scaffold_26-snap.446-T1
Couldn't classify 185163, 185243
Sorry, prediction pasa_asmbl_35318.p1 fails validation.
(ATG)	 CG	184761-184851	GT	GGG
(ATG)	 AG	184928-185067	GT	GGG
(CAC)	 AG	185163-185243	GT	AGG
-recovered pasa_asmbl_35318.p1, initial, 184761, 184851
add_exon() Sorry, pasa_asmbl_35318.p1 184928-185067-initial-1 is invalid.
-recovered pasa_asmbl_35318.p1, initial, 184928, 185067
-recovered pasa_asmbl_35318.p1, internal, 184928, 185067
-recovered pasa_asmbl_35318.p1, internal, 185163, 185243
Valid prediction for snap_scaffold_26-snap.438-T1
Valid prediction for snap_scaffold_26-snap.437-T1
Valid prediction for snap_scaffold_26-snap.449-T1
Valid prediction for GlimmerHMM_glimmerT_55171-T1
Valid prediction for snap_scaffold_26-snap.421-T1
Valid prediction for pasa_asmbl_34743.p1
Valid prediction for snap_scaffold_26-snap.447-T1
Valid prediction for snap_scaffold_26-snap.433-T1
Valid prediction for snap_scaffold_26-snap.429-T1
Valid prediction for snap_scaffold_26-snap.427-T1
Valid prediction for GlimmerHMM_glimmerT_55185-T1
Valid prediction for Augustus_model.g36558.t1
Valid prediction for GlimmerHMM_glimmerT_55179-T1
Valid prediction for Augustus_model.g36551.t1
Valid prediction for snap_scaffold_26-snap.454-T1
Valid prediction for snap_scaffold_26-snap.414-T1
Valid prediction for GlimmerHMM_glimmerT_55166-T1
Valid prediction for GlimmerHMM_glimmerT_55173-T1
Valid prediction for snap_scaffold_26-snap.431-T1
Valid prediction for snap_scaffold_26-snap.420-T1
Valid prediction for snap_scaffold_26-snap.423-T1
Valid prediction for Augustus_model.g36559.t1
Valid prediction for GlimmerHMM_glimmerT_55170-T1
Valid prediction for GlimmerHMM_glimmerT_55169-T1
Valid prediction for snap_scaffold_26-snap.428-T1
Valid prediction for snap_scaffold_26-snap.453-T1
Valid prediction for CodingQuarry_transcript_40259-T1
Valid prediction for snap_scaffold_26-snap.435-T1
Valid prediction for GlimmerHMM_glimmerT_55174-T1
Valid prediction for pasa_asmbl_34734.p1
Valid prediction for snap_scaffold_26-snap.409-T1
Valid prediction for GlimmerHMM_glimmerT_55188-T1
Valid prediction for GlimmerHMM_glimmerT_55187-T1
Valid prediction for Augustus_model.g36552.t1
Valid prediction for snap_scaffold_26-snap.445-T1
Couldn't classify 206480, 206481
Sorry, prediction CodingQuarry_transcript_40258-T1 fails validation.
(ATG)	 AA	206480-206481	GT	ATG
(GTA)	 AG	207016-207093	GT	AGG
(CAG)	 AG	208708-208865	GT	TGG
(ACT)	 AG	209609-209778	GT	TTG
(GAA)	 AG	211310-211339	GG	GAG
-recovered CodingQuarry_transcript_40258-T1, terminal, 211310, 211339
-recovered CodingQuarry_transcript_40258-T1, internal, 207016, 207093
-recovered CodingQuarry_transcript_40258-T1, internal, 208708, 208865
-recovered CodingQuarry_transcript_40258-T1, internal, 209609, 209778
Valid prediction for CodingQuarry_transcript_40257-T1
Valid prediction for snap_scaffold_26-snap.456-T1
Valid prediction for snap_scaffold_26-snap.452-T1
Valid prediction for GlimmerHMM_glimmerT_55163-T1
Valid prediction for GlimmerHMM_glimmerT_55176-T1
Valid prediction for HiQ_model.g36557.t1
Valid prediction for snap_scaffold_26-snap.417-T1
Couldn't classify 232237, 232324
Couldn't classify 232648, 232870
Sorry, prediction pasa_asmbl_34746.p1 fails validation.
(GTC)	 TG	232237-232324	GT	ATG
(TGA)	 AG	232436-232511	GT	CGG
(GTA)	 AG	232648-232870	GG	GGG
-recovered pasa_asmbl_34746.p1, internal, 232436, 232511
Valid prediction for snap_scaffold_26-snap.441-T1
Valid prediction for snap_scaffold_26-snap.440-T1
Valid prediction for GlimmerHMM_glimmerT_55165-T1
Valid prediction for GlimmerHMM_glimmerT_55175-T1
Valid prediction for Augustus_model.g36554.t1
Valid prediction for GlimmerHMM_glimmerT_55177-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.g36547.t1
Valid prediction for snap_scaffold_26-snap.411-T1
Valid prediction for Augustus_model.g36555.t1
Valid prediction for GlimmerHMM_glimmerT_55164-T1
Valid prediction for snap_scaffold_26-snap.457-T1
Valid prediction for GlimmerHMM_glimmerT_55184-T1
Valid prediction for GlimmerHMM_glimmerT_55182-T1
Valid prediction for GlimmerHMM_glimmerT_55181-T1
Valid prediction for snap_scaffold_26-snap.426-T1
Valid prediction for snap_scaffold_26-snap.443-T1
Couldn't classify 49320, 49440
Couldn't classify 49783, 49919
Sorry, prediction pasa_asmbl_35893.p1 fails validation.
(CTG)	 TG	49320-49440	GT	ATG
(ATC)	 AG	49543-49650	GT	CAG
(GGT)	 AG	49783-49919	GG	GAG
-recovered pasa_asmbl_35893.p1, internal, 49543, 49650
Valid prediction for GlimmerHMM_glimmerT_55168-T1
Valid prediction for GlimmerHMM_glimmerT_55159-T1
Valid prediction for GlimmerHMM_glimmerT_55167-T1
Valid prediction for GlimmerHMM_glimmerT_55178-T1
Valid prediction for Augustus_model.g36553.t1
Couldn't classify 57207, 57317
Sorry, prediction pasa_asmbl_35437.p1 fails validation.
(ATG)	 CT	56053-56081	GT	AGG
(CAT)	 AG	56324-56414	GT	TGG
(GGT)	 AG	56535-56645	GT	AGG
(GCG)	 AG	56729-56884	GT	AGG
(CTG)	 AG	57207-57317	GT	AGG
-recovered pasa_asmbl_35437.p1, initial, 56053, 56081
-recovered pasa_asmbl_35437.p1, internal, 56324, 56414
-recovered pasa_asmbl_35437.p1, internal, 56535, 56645
-recovered pasa_asmbl_35437.p1, internal, 56729, 56884
-recovered pasa_asmbl_35437.p1, internal, 57207, 57317
Valid prediction for pasa_asmbl_35442.p1
Valid prediction for snap_scaffold_26-snap.451-T1
Valid prediction for CodingQuarry_transcript_40255-T1
Valid prediction for GlimmerHMM_glimmerT_55172-T1
Valid prediction for snap_scaffold_26-snap.416-T1
Valid prediction for GlimmerHMM_glimmerT_55162-T1
Valid prediction for snap_scaffold_26-snap.436-T1
Valid prediction for snap_scaffold_26-snap.425-T1
Valid prediction for snap_scaffold_26-snap.442-T1
Valid prediction for snap_scaffold_26-snap.455-T1
Valid prediction for snap_scaffold_26-snap.444-T1
Valid prediction for snap_scaffold_26-snap.439-T1
Valid prediction for snap_scaffold_26-snap.419-T1
Valid prediction for snap_scaffold_26-snap.415-T1
Valid prediction for GlimmerHMM_glimmerT_55155-T1
Valid prediction for snap_scaffold_26-snap.448-T1
Valid prediction for snap_scaffold_26-snap.410-T1
Valid prediction for snap_scaffold_26-snap.408-T1
Valid prediction for snap_scaffold_26-snap.450-T1
Valid prediction for snap_scaffold_26-snap.432-T1
Valid prediction for snap_scaffold_26-snap.422-T1
Valid prediction for GlimmerHMM_glimmerT_55157-T1
Valid prediction for snap_scaffold_26-snap.412-T1
Valid prediction for snap_scaffold_26-snap.406-T1
Valid prediction for GlimmerHMM_glimmerT_55158-T1
Valid prediction for HiQ_model.g36556.t1
Valid prediction for GlimmerHMM_glimmerT_55180-T1
Valid prediction for snap_scaffold_26-snap.430-T1
Valid prediction for CodingQuarry_transcript_40256-T1
Valid prediction for GlimmerHMM_glimmerT_55160-T1
Valid prediction for snap_scaffold_26-snap.424-T1
Valid prediction for snap_scaffold_26-snap.413-T1
Valid prediction for GlimmerHMM_glimmerT_55156-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24348, rend_intergenic: 17152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44024, rend_intergenic: 25418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47986, rend_intergenic: 44769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53952, rend_intergenic: 48793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64890, rend_intergenic: 54054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72108, rend_intergenic: 68852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80766, rend_intergenic: 72859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86075, rend_intergenic: 80882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94233, rend_intergenic: 93830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99948, rend_intergenic: 94372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109306, rend_intergenic: 102124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110865, rend_intergenic: 109667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158235, rend_intergenic: 128461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162767, rend_intergenic: 158897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181554, rend_intergenic: 174631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189108, rend_intergenic: 186925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209860, rend_intergenic: 208748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235310, rend_intergenic: 232577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 237606
-exon list size: 371


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.0    
8.3    
8.6    
8.8    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.1    
13.4    
13.7    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.4    
16.6    
16.9    
17.2    
17.4    
17.7    
18.0    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.3    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.3    
27.6    
27.9    
28.2    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.0    
30.3    
30.6    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.2    
69.4    
69.7    
70.0    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.8    
72.1    
72.4    
72.7    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.7    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.0    
82.3    
82.6    
82.8    
83.1    
83.4    
83.6    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.3    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 24348, rend_intergenic: 17152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44024, rend_intergenic: 25418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47986, rend_intergenic: 44769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53952, rend_intergenic: 48793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64890, rend_intergenic: 54054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72108, rend_intergenic: 68852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80766, rend_intergenic: 72859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86075, rend_intergenic: 80882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94233, rend_intergenic: 93830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99948, rend_intergenic: 94372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109306, rend_intergenic: 102124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110865, rend_intergenic: 109667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158235, rend_intergenic: 128461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162767, rend_intergenic: 158897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181554, rend_intergenic: 174631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189108, rend_intergenic: 186925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209860, rend_intergenic: 208748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235310, rend_intergenic: 232577  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

-building DP trellis

-building trellis in range 1 - 34475
-exon list size: 28


building trellis

3.3    
6.7    
10.0    
13.3    
16.7    
20.0    
23.3    
26.7    
30.0    
33.3    
36.7    
40.0    
43.3    
46.7    
50.0    
53.3    
56.7    
60.0    
63.3    
66.7    
70.0    
73.3    
76.7    
80.0    
83.3    
86.7    
90.0    
93.3    
96.7    
-found 2 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 - 17151
-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 - 14958
-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 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13817
-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