-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_11823670-11986696

-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_13-snap.2212-T1
Couldn't classify 129767, 130216
Sorry, prediction pasa_asmbl_10115.p1 fails validation.
(GGG)	 GA	129767-130216	TT	AAT
Valid prediction for snap_scaffold_13-snap.2236-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g21686.t1
Valid prediction for GlimmerHMM_glimmerT_32444-T1
Valid prediction for GlimmerHMM_glimmerT_32454-T1
Valid prediction for snap_scaffold_13-snap.2208-T1
Valid prediction for snap_scaffold_13-snap.2206-T1
Valid prediction for GlimmerHMM_glimmerT_32467-T1
Valid prediction for GlimmerHMM_glimmerT_32446-T1
Valid prediction for snap_scaffold_13-snap.2238-T1
Valid prediction for CodingQuarry_transcript_13258-T1
Valid prediction for snap_scaffold_13-snap.2211-T1
Valid prediction for Augustus_model.g21680.t1
Valid prediction for GlimmerHMM_glimmerT_32460-T1
Valid prediction for snap_scaffold_13-snap.2229-T1
Valid prediction for Augustus_model.g21681.t1
Valid prediction for snap_scaffold_13-snap.2216-T1
Valid prediction for GlimmerHMM_glimmerT_32457-T1
Valid prediction for GlimmerHMM_glimmerT_32451-T1
Valid prediction for GlimmerHMM_glimmerT_32453-T1
Valid prediction for snap_scaffold_13-snap.2207-T1
Valid prediction for snap_scaffold_13-snap.2228-T1
Valid prediction for pasa_asmbl_11311.p1
Valid prediction for snap_scaffold_13-snap.2203-T1
Valid prediction for GlimmerHMM_glimmerT_32465-T1
Valid prediction for CodingQuarry_transcript_13259-T1
Valid prediction for snap_scaffold_13-snap.2224-T1
Valid prediction for GlimmerHMM_glimmerT_32461-T1
Valid prediction for snap_scaffold_13-snap.2205-T1
Valid prediction for Augustus_model.g21671.t1
Valid prediction for snap_scaffold_13-snap.2222-T1
Valid prediction for snap_scaffold_13-snap.2231-T1
Valid prediction for snap_scaffold_13-snap.2225-T1
Valid prediction for Augustus_model.g21682.t1
Couldn't classify 112329, 112651
Sorry, prediction pasa_asmbl_11606.p1 fails validation.
(ATG)	 TC	108092-108127	GT	AGG
(GAG)	 AG	109886-109994	GT	CGG
(CTT)	 AG	110713-110818	GT	AGG
(ACT)	 AG	111034-111241	GT	GTG
(GAT)	 AG	111428-111523	GT	AGG
(GTC)	 AG	111835-111895	GT	GGG
(TAA)	 AG	112045-112164	GT	GGG
(CTC)	 AG	112329-112651	CG	AGC
-recovered pasa_asmbl_11606.p1, initial, 108092, 108127
-recovered pasa_asmbl_11606.p1, internal, 109886, 109994
-recovered pasa_asmbl_11606.p1, internal, 110713, 110818
-recovered pasa_asmbl_11606.p1, internal, 111034, 111241
-recovered pasa_asmbl_11606.p1, internal, 111428, 111523
-recovered pasa_asmbl_11606.p1, internal, 111835, 111895
-recovered pasa_asmbl_11606.p1, internal, 112045, 112164
Valid prediction for GlimmerHMM_glimmerT_32459-T1
Valid prediction for Augustus_model.g21673.t1
Valid prediction for GlimmerHMM_glimmerT_32456-T1
Valid prediction for GlimmerHMM_glimmerT_32449-T1
Valid prediction for snap_scaffold_13-snap.2221-T1
Valid prediction for snap_scaffold_13-snap.2234-T1
Valid prediction for CodingQuarry_transcript_13261-T1
Valid prediction for Augustus_model.g21684.t1
Valid prediction for snap_scaffold_13-snap.2233-T1
Valid prediction for snap_scaffold_13-snap.2213-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 GlimmerHMM_glimmerT_32455-T1
Valid prediction for snap_scaffold_13-snap.2237-T1
Valid prediction for snap_scaffold_13-snap.2227-T1
Valid prediction for Augustus_model.g21687.t1
Valid prediction for GlimmerHMM_glimmerT_32462-T1
Valid prediction for snap_scaffold_13-snap.2215-T1
Valid prediction for GlimmerHMM_glimmerT_32452-T1
Valid prediction for pasa_asmbl_10113.p1
Valid prediction for pasa_asmbl_10106.p1
Valid prediction for snap_scaffold_13-snap.2209-T1
Valid prediction for Augustus_model.g21676.t1
Valid prediction for CodingQuarry_transcript_13265-T1
Valid prediction for snap_scaffold_13-snap.2235-T1
Valid prediction for Augustus_model.g21685.t1
Valid prediction for snap_scaffold_13-snap.2223-T1
Valid prediction for pasa_asmbl_10110.p1
Valid prediction for snap_scaffold_13-snap.2214-T1
Valid prediction for snap_scaffold_13-snap.2218-T1
Valid prediction for CodingQuarry_transcript_13264-T1
Valid prediction for snap_scaffold_13-snap.2232-T1
Valid prediction for GlimmerHMM_glimmerT_32445-T1
Valid prediction for GlimmerHMM_glimmerT_32464-T1
Valid prediction for Augustus_model.g21678.t1
Valid prediction for GlimmerHMM_glimmerT_32466-T1
Valid prediction for GlimmerHMM_glimmerT_32448-T1
Valid prediction for HiQ_model.g21683.t1
Valid prediction for Augustus_model.g21674.t1
Valid prediction for Augustus_model.g21679.t1
Valid prediction for CodingQuarry_transcript_13262-T1
Valid prediction for GlimmerHMM_glimmerT_32463-T1
Couldn't classify 150153, 151720
Couldn't classify 151887, 151938
Sorry, prediction CodingQuarry_transcript_13257-T1 fails validation.
(ATG)	 GC	149509-149925	GT	CGG
(GAG)	 AG	150153-151720	CT	GAC
(GAG)	 GA	151887-151938	AG	GAA
-recovered CodingQuarry_transcript_13257-T1, initial, 149509, 149925
Valid prediction for pasa_asmbl_10109.p1
Valid prediction for Augustus_model.g21675.t1
Valid prediction for GlimmerHMM_glimmerT_32450-T1
Valid prediction for snap_scaffold_13-snap.2230-T1
Valid prediction for GlimmerHMM_glimmerT_32447-T1
Valid prediction for snap_scaffold_13-snap.2219-T1
Valid prediction for snap_scaffold_13-snap.2210-T1
Valid prediction for CodingQuarry_transcript_13263-T1
Valid prediction for snap_scaffold_13-snap.2226-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for HiQ_model.g21672.t1
Valid prediction for Augustus_model.g21677.t1
Valid prediction for GlimmerHMM_glimmerT_32458-T1
Valid prediction for snap_scaffold_13-snap.2204-T1
Valid prediction for snap_scaffold_13-snap.2217-T1
Valid prediction for snap_scaffold_13-snap.2220-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26777, rend_intergenic: 9872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48814, rend_intergenic: 40127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97648, rend_intergenic: 93682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107497, rend_intergenic: 105772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112780, rend_intergenic: 110066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123283, rend_intergenic: 118432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133857, rend_intergenic: 132011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144826, rend_intergenic: 133935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146024, rend_intergenic: 144884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148576, rend_intergenic: 146043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151073, rend_intergenic: 149201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155453, rend_intergenic: 151599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163027
-exon list size: 342


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 26777, rend_intergenic: 9872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48814, rend_intergenic: 40127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97648, rend_intergenic: 93682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107497, rend_intergenic: 105772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112780, rend_intergenic: 110066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123283, rend_intergenic: 118432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133857, rend_intergenic: 132011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144826, rend_intergenic: 133935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146024, rend_intergenic: 144884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148576, rend_intergenic: 146043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151073, rend_intergenic: 149201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155453, rend_intergenic: 151599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support