-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_12016868-12251332

-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 HiQ_model.g4976.t1
Valid prediction for snap_scaffold_3-snap.2404-T1
Valid prediction for GeneMark_model.12574_t
Valid prediction for snap_scaffold_3-snap.2392-T1
Valid prediction for GlimmerHMM_glimmerT_7591-T1
Valid prediction for GlimmerHMM_glimmerT_7598-T1
Valid prediction for GeneMark_model.12561_t
Valid prediction for Augustus_model.g4973.t1
Valid prediction for GlimmerHMM_glimmerT_7596-T1
Valid prediction for GeneMark_model.12568_t
Valid prediction for Augustus_model.g4977.t1
Valid prediction for GeneMark_model.12569_t
Valid prediction for Augustus_model.g4987.t1
Valid prediction for GlimmerHMM_glimmerT_7604-T1
Valid prediction for GeneMark_model.12563_t
Valid prediction for GeneMark_model.12583_t
Valid prediction for GeneMark_model.12567_t
Valid prediction for GeneMark_model.12581_t
Valid prediction for snap_scaffold_3-snap.2389-T1
Valid prediction for GeneMark_model.12587_t
Valid prediction for GeneMark_model.12560_t
Valid prediction for snap_scaffold_3-snap.2410-T1
Valid prediction for GlimmerHMM_glimmerT_7586-T1
Valid prediction for snap_scaffold_3-snap.2383-T1
Valid prediction for CodingQuarry_transcript_46188-T1
Valid prediction for snap_scaffold_3-snap.2391-T1
Valid prediction for pasa_asmbl_40346.p1
Valid prediction for snap_scaffold_3-snap.2401-T1
Valid prediction for Augustus_model.g4982.t1
Valid prediction for snap_scaffold_3-snap.2388-T1
Valid prediction for GlimmerHMM_glimmerT_7587-T1
Valid prediction for snap_scaffold_3-snap.2393-T1
Valid prediction for GlimmerHMM_glimmerT_7590-T1
Valid prediction for GeneMark_model.12571_t
Valid prediction for snap_scaffold_3-snap.2395-T1
Valid prediction for snap_scaffold_3-snap.2413-T1
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 191150, 192166
Sorry, prediction pasa_asmbl_40350.p1 fails validation.
(ATG)	 GC	191150-192166	TG	GGT

-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 snap_scaffold_3-snap.2412-T1
Valid prediction for GeneMark_model.12584_t
Valid prediction for GlimmerHMM_glimmerT_7589-T1
Valid prediction for snap_scaffold_3-snap.2411-T1
Sorry, intron length (6) is less than minimum required (10)
Couldn't classify 106038, 106775
Sorry, prediction pasa_asmbl_39161.p1 fails validation.
(GTT)	 AG	106038-106775	AA	GCA
Valid prediction for snap_scaffold_3-snap.2408-T1
Valid prediction for GlimmerHMM_glimmerT_7599-T1
Valid prediction for GeneMark_model.12564_t
Valid prediction for GeneMark_model.12575_t
Valid prediction for GeneMark_model.12570_t
Valid prediction for snap_scaffold_3-snap.2387-T1
Couldn't classify 207847, 207945
Couldn't classify 216237, 216370
Sorry, prediction pasa_asmbl_39154.p1 fails validation.
(ATA)	 AG	207847-207945	GT	TGG
(TCT)	 AG	208245-208398	GT	CCG
(TTC)	 AG	210131-210253	GT	AGG
(ATC)	 AG	212149-212247	GT	AGG
(GCT)	 AG	214140-214217	GT	AGG
(AGG)	 AG	216237-216370	AG	TCA
-recovered pasa_asmbl_39154.p1, internal, 207847, 207945
-recovered pasa_asmbl_39154.p1, internal, 208245, 208398
-recovered pasa_asmbl_39154.p1, internal, 210131, 210253
-recovered pasa_asmbl_39154.p1, internal, 212149, 212247
-recovered pasa_asmbl_39154.p1, internal, 214140, 214217
Valid prediction for snap_scaffold_3-snap.2386-T1
Valid prediction for GlimmerHMM_glimmerT_7600-T1
Valid prediction for Augustus_model.g4972.t1
Valid prediction for Augustus_model.g4985.t1
Valid prediction for GeneMark_model.12578_t
Valid prediction for snap_scaffold_3-snap.2407-T1
Valid prediction for GeneMark_model.12572_t
Valid prediction for Augustus_model.g4978.t1
Valid prediction for GeneMark_model.12577_t
Valid prediction for snap_scaffold_3-snap.2398-T1
Valid prediction for Augustus_model.g4986.t1
Valid prediction for GlimmerHMM_glimmerT_7602-T1
Valid prediction for GlimmerHMM_glimmerT_7593-T1
Valid prediction for snap_scaffold_3-snap.2394-T1
Valid prediction for GlimmerHMM_glimmerT_7601-T1
Valid prediction for GlimmerHMM_glimmerT_7597-T1
Valid prediction for snap_scaffold_3-snap.2409-T1
Valid prediction for GeneMark_model.12573_t
Valid prediction for snap_scaffold_3-snap.2399-T1
Valid prediction for Augustus_model.g4980.t1
Valid prediction for GlimmerHMM_glimmerT_7595-T1
Valid prediction for GeneMark_model.12579_t
Valid prediction for GlimmerHMM_glimmerT_7585-T1
Valid prediction for snap_scaffold_3-snap.2403-T1
Couldn't classify 199013, 199087
Sorry, prediction pasa_asmbl_39158.p1 fails validation.
(ATG)	 GA	193407-193420	GT	AGG
(AAT)	 AG	194586-194760	GT	CTG
(ATT)	 AG	196812-196877	GT	CTG
(GGG)	 AG	197125-197274	GT	TGG
(AAA)	 AG	199013-199087	AA	GGA
-recovered pasa_asmbl_39158.p1, initial, 193407, 193420
-recovered pasa_asmbl_39158.p1, internal, 194586, 194760
-recovered pasa_asmbl_39158.p1, internal, 196812, 196877
-recovered pasa_asmbl_39158.p1, internal, 197125, 197274
Valid prediction for snap_scaffold_3-snap.2397-T1
Valid prediction for Augustus_model.g4979.t1
Valid prediction for snap_scaffold_3-snap.2406-T1
Valid prediction for snap_scaffold_3-snap.2402-T1
Valid prediction for pasa_asmbl_39160.p1
Valid prediction for snap_scaffold_3-snap.2381-T1
Valid prediction for GlimmerHMM_glimmerT_7592-T1
Valid prediction for GeneMark_model.12580_t
Valid prediction for snap_scaffold_3-snap.2385-T1
Valid prediction for snap_scaffold_3-snap.2396-T1
Valid prediction for GeneMark_model.12582_t
Valid prediction for snap_scaffold_3-snap.2382-T1
Valid prediction for snap_scaffold_3-snap.2405-T1
Valid prediction for snap_scaffold_3-snap.2390-T1
Valid prediction for Augustus_model.g4981.t1
Valid prediction for GeneMark_model.12566_t
Valid prediction for GeneMark_model.12585_t
Valid prediction for GlimmerHMM_glimmerT_7603-T1
Valid prediction for snap_scaffold_3-snap.2400-T1
Valid prediction for GlimmerHMM_glimmerT_7584-T1
Valid prediction for GlimmerHMM_glimmerT_7594-T1
Valid prediction for CodingQuarry_transcript_46190-T1
Valid prediction for Augustus_model.g4971.t1
Valid prediction for GlimmerHMM_glimmerT_7588-T1
Valid prediction for Augustus_model.g4983.t1
Valid prediction for GeneMark_model.12586_t
Valid prediction for Augustus_model.g4984.t1
Valid prediction for snap_scaffold_3-snap.2384-T1
Valid prediction for Augustus_model.g4974.t1
Valid prediction for GeneMark_model.12565_t
Valid prediction for GeneMark_model.12562_t
Valid prediction for Augustus_model.g4975.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10087, rend_intergenic: 8979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102003, rend_intergenic: 98819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196014, rend_intergenic: 193329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 234465
-exon list size: 356


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.2    
2.5    
2.8    
3.1    
3.4    
3.6    
3.9    
4.2    
4.5    
4.7    
5.0    
5.3    
5.6    
5.9    
6.1    
6.4    
6.7    
7.0    
7.3    
7.5    
7.8    
8.1    
8.4    
8.7    
8.9    
9.2    
9.5    
9.8    
10.1    
10.3    
10.6    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
12.8    
13.1    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.4    
15.6    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.9    
18.2    
18.4    
18.7    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.7    
20.9    
21.2    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.2    
23.5    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.4    
27.7    
27.9    
28.2    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.3    
31.6    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.6    
34.9    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.1    
41.3    
41.6    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.6    
43.9    
44.1    
44.4    
44.7    
45.0    
45.3    
45.5    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.5    
54.7    
55.0    
55.3    
55.6    
55.9    
56.1    
56.4    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.4    
58.7    
58.9    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.1    
65.4    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.4    
68.7    
69.0    
69.3    
69.6    
69.8    
70.1    
70.4    
70.7    
70.9    
71.2    
71.5    
71.8    
72.1    
72.3    
72.6    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.5    
76.8    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.8    
79.1    
79.3    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.3    
81.6    
81.8    
82.1    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.4    
84.6    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.8    
91.1    
91.3    
91.6    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.6    
93.9    
94.1    
94.4    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.4    
96.6    
96.9    
97.2    
97.5    
97.8    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 10087, rend_intergenic: 8979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102003, rend_intergenic: 98819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196014, rend_intergenic: 193329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support