-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_6225313-6473345

-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_8-snap.1262-T1
Valid prediction for snap_scaffold_8-snap.1241-T1
Valid prediction for snap_scaffold_8-snap.1269-T1
Valid prediction for Augustus_model.g13227.t1
Valid prediction for GlimmerHMM_glimmerT_19885-T1
Valid prediction for CodingQuarry_transcript_59678-T1
Valid prediction for Augustus_model.g13241.t1
Valid prediction for snap_scaffold_8-snap.1233-T1
Valid prediction for snap_scaffold_8-snap.1258-T1
Valid prediction for snap_scaffold_8-snap.1230-T1
Valid prediction for Augustus_model.g13229.t1
Valid prediction for GlimmerHMM_glimmerT_19882-T1
Valid prediction for GlimmerHMM_glimmerT_19879-T1
Valid prediction for Augustus_model.g13226.t1
Valid prediction for snap_scaffold_8-snap.1232-T1
Valid prediction for Augustus_model.g13234.t1
Valid prediction for snap_scaffold_8-snap.1234-T1
Couldn't classify 26485, 27575
Couldn't classify 30575, 30734
Sorry, prediction pasa_asmbl_52949.p1 fails validation.
(ATC)	 AC	26485-27575	GT	AGG
(GAC)	 AG	30575-30734	AA	TCA
Valid prediction for GlimmerHMM_glimmerT_19875-T1
Valid prediction for Augustus_model.g13246.t1
Valid prediction for GlimmerHMM_glimmerT_19884-T1
Couldn't classify 45763, 45819
Sorry, prediction pasa_asmbl_52955.p1 fails validation.
(GAT)	 TA	45763-45819	GT	GAG
(TCA)	 AG	45956-46082	GT	AGG
(TCC)	 AG	47805-48925	AT	AAA
-recovered pasa_asmbl_52955.p1, terminal, 47805, 48925
-recovered pasa_asmbl_52955.p1, internal, 45956, 46082
Valid prediction for pasa_asmbl_52959.p1
Valid prediction for snap_scaffold_8-snap.1267-T1
Couldn't classify 83769, 84039
Sorry, prediction pasa_asmbl_52960.p1 fails validation.
(GGA)	 GT	83769-84039	GT	TGG
(GAT)	 AG	84141-84244	GT	TGG
(GCC)	 AG	84417-84551	GT	AGG
(CCT)	 AG	84676-84866	GT	AGG
(GAG)	 AG	84982-85132	GA	GAG
-recovered pasa_asmbl_52960.p1, terminal, 84982, 85132
-recovered pasa_asmbl_52960.p1, internal, 84141, 84244
-recovered pasa_asmbl_52960.p1, internal, 84417, 84551
-recovered pasa_asmbl_52960.p1, internal, 84676, 84866
Valid prediction for snap_scaffold_8-snap.1255-T1
Valid prediction for GlimmerHMM_glimmerT_19901-T1
Valid prediction for GlimmerHMM_glimmerT_19876-T1
Valid prediction for GlimmerHMM_glimmerT_19890-T1
Valid prediction for snap_scaffold_8-snap.1245-T1
Valid prediction for Augustus_model.g13225.t1
Valid prediction for snap_scaffold_8-snap.1256-T1
Couldn't classify 40504, 40715
Sorry, prediction pasa_asmbl_52952.p1 fails validation.
(GTA)	 CT	40504-40715	GT	AGG
(CAT)	 AG	41214-41386	GT	CTG
(CTC)	 AG	41491-41660	GT	AAG
-recovered pasa_asmbl_52952.p1, terminal, 41491, 41660
-recovered pasa_asmbl_52952.p1, internal, 41214, 41386
-recovered pasa_asmbl_52952.p1, internal, 41491, 41660
Valid prediction for Augustus_model.g13242.t1
Valid prediction for snap_scaffold_8-snap.1225-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for HiQ_model.g13233.t1
Valid prediction for snap_scaffold_8-snap.1228-T1
Valid prediction for snap_scaffold_8-snap.1268-T1
Valid prediction for snap_scaffold_8-snap.1244-T1
Valid prediction for GlimmerHMM_glimmerT_19886-T1
Valid prediction for snap_scaffold_8-snap.1240-T1
Valid prediction for snap_scaffold_8-snap.1237-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.g13237.t1
Valid prediction for snap_scaffold_8-snap.1264-T1
Valid prediction for GlimmerHMM_glimmerT_19896-T1
Valid prediction for snap_scaffold_8-snap.1260-T1
Valid prediction for pasa_asmbl_51878.p1
Couldn't classify 86107, 86496
Sorry, prediction pasa_asmbl_51884.p1 fails validation.
(AAG)	 CA	86107-86496	GT	TGG
(CAC)	 AG	86812-87038	GT	AGG
(GAT)	 AG	87742-87890	GT	TGG
(AGC)	 AG	88555-88683	GT	AGG
(TGG)	 AG	88873-89046	GT	GTG
(TGC)	 AG	89523-89696	GT	TGG
(CCA)	 AG	90817-90990	GT	AGG
(GAT)	 AG	91118-91273	GT	TGG
(GTG)	 AG	91375-91501	GT	AGG
(GTT)	 AG	94029-94165	GT	AGG
(GCA)	 AG	94794-94953	GT	AGG
(GTA)	 AG	95164-95273	GT	AGG
(ATT)	 AG	95996-96099	GC	AAG
add_exon() Sorry, pasa_asmbl_51884.p1 95164-95273-terminal-2 is invalid.
-recovered pasa_asmbl_51884.p1, terminal, 95164, 95273
-recovered pasa_asmbl_51884.p1, terminal, 95996, 96099
-recovered pasa_asmbl_51884.p1, internal, 86812, 87038
-recovered pasa_asmbl_51884.p1, internal, 87742, 87890
-recovered pasa_asmbl_51884.p1, internal, 88555, 88683
-recovered pasa_asmbl_51884.p1, internal, 88873, 89046
-recovered pasa_asmbl_51884.p1, internal, 89523, 89696
-recovered pasa_asmbl_51884.p1, internal, 90817, 90990
-recovered pasa_asmbl_51884.p1, internal, 91118, 91273
-recovered pasa_asmbl_51884.p1, internal, 91375, 91501
-recovered pasa_asmbl_51884.p1, internal, 94029, 94165
-recovered pasa_asmbl_51884.p1, internal, 94794, 94953
-recovered pasa_asmbl_51884.p1, internal, 95164, 95273
-recovered pasa_asmbl_51884.p1, internal, 95996, 96099
Valid prediction for snap_scaffold_8-snap.1224-T1
Valid prediction for snap_scaffold_8-snap.1239-T1
Valid prediction for snap_scaffold_8-snap.1253-T1
Valid prediction for Augustus_model.g13231.t1
Valid prediction for GlimmerHMM_glimmerT_19898-T1
Valid prediction for Augustus_model.g13245.t1
Valid prediction for snap_scaffold_8-snap.1227-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_8-snap.1238-T1
Couldn't classify 210183, 210581
Sorry, prediction pasa_asmbl_52951.p1 fails validation.
(GAG)	 AA	210183-210581	AA	GAA
Valid prediction for GlimmerHMM_glimmerT_19883-T1
Valid prediction for GlimmerHMM_glimmerT_19887-T1
Valid prediction for GlimmerHMM_glimmerT_19881-T1
Valid prediction for Augustus_model.g13236.t1
Valid prediction for Augustus_model.g13243.t1
Couldn't classify 123028, 123105
Sorry, prediction pasa_asmbl_51881.p2 fails validation.
(ATT)	 AT	123028-123105	GT	TGG
(TTT)	 AG	124192-124359	GT	AGG
(AGG)	 AG	125017-125088	GT	CGG
(CTC)	 AG	125244-125267	CA	GAC
-recovered pasa_asmbl_51881.p2, terminal, 125244, 125267
-recovered pasa_asmbl_51881.p2, internal, 124192, 124359
-recovered pasa_asmbl_51881.p2, internal, 125017, 125088
Valid prediction for GlimmerHMM_glimmerT_19892-T1
Valid prediction for snap_scaffold_8-snap.1249-T1
Valid prediction for snap_scaffold_8-snap.1263-T1
Valid prediction for HiQ_model.g13238.t1
Valid prediction for snap_scaffold_8-snap.1248-T1
Couldn't classify 170001, 170528
Sorry, prediction pasa_asmbl_51874.p1 fails validation.
(TCT)	 CA	170001-170528	AC	AGA
Valid prediction for HiQ_model.g13235.t1
Valid prediction for snap_scaffold_8-snap.1251-T1
Valid prediction for GlimmerHMM_glimmerT_19902-T1
Valid prediction for snap_scaffold_8-snap.1229-T1
Valid prediction for GlimmerHMM_glimmerT_19893-T1
Valid prediction for snap_scaffold_8-snap.1266-T1
Valid prediction for GlimmerHMM_glimmerT_19899-T1
Valid prediction for snap_scaffold_8-snap.1259-T1
Valid prediction for snap_scaffold_8-snap.1254-T1
Valid prediction for Augustus_model.g13247.t1
Valid prediction for snap_scaffold_8-snap.1226-T1
Valid prediction for snap_scaffold_8-snap.1250-T1
Valid prediction for CodingQuarry_transcript_59679-T1
Valid prediction for snap_scaffold_8-snap.1243-T1
Valid prediction for GlimmerHMM_glimmerT_19897-T1
Valid prediction for Augustus_model.g13232.t1
Valid prediction for snap_scaffold_8-snap.1246-T1
Valid prediction for snap_scaffold_8-snap.1235-T1
Valid prediction for snap_scaffold_8-snap.1257-T1
Valid prediction for GlimmerHMM_glimmerT_19894-T1
Valid prediction for snap_scaffold_8-snap.1231-T1
Valid prediction for Augustus_model.g13224.t1
Valid prediction for GlimmerHMM_glimmerT_19895-T1
Valid prediction for snap_scaffold_8-snap.1252-T1
Valid prediction for GlimmerHMM_glimmerT_19900-T1
Valid prediction for snap_scaffold_8-snap.1270-T1
Valid prediction for GlimmerHMM_glimmerT_19891-T1
Valid prediction for snap_scaffold_8-snap.1247-T1
Valid prediction for CodingQuarry_transcript_59680-T1
Valid prediction for snap_scaffold_8-snap.1242-T1
Valid prediction for Augustus_model.g13230.t1
Valid prediction for GlimmerHMM_glimmerT_19878-T1
Valid prediction for GlimmerHMM_glimmerT_19877-T1
Valid prediction for snap_scaffold_8-snap.1265-T1
Valid prediction for GlimmerHMM_glimmerT_19888-T1
Valid prediction for GlimmerHMM_glimmerT_19874-T1
Valid prediction for Augustus_model.g13244.t1
Valid prediction for HiQ_model.g13239.t1
Valid prediction for GlimmerHMM_glimmerT_19880-T1
Valid prediction for snap_scaffold_8-snap.1236-T1
Valid prediction for GlimmerHMM_glimmerT_19903-T1
Valid prediction for Augustus_model.g13240.t1
Valid prediction for snap_scaffold_8-snap.1261-T1
Valid prediction for GlimmerHMM_glimmerT_19889-T1
Valid prediction for pasa_asmbl_51882.p1
Valid prediction for Augustus_model.g13228.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25134, rend_intergenic: 17873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27206, rend_intergenic: 25628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28809, rend_intergenic: 27231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32862, rend_intergenic: 29577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39873, rend_intergenic: 32865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53105, rend_intergenic: 50506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190675, rend_intergenic: 189568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194879, rend_intergenic: 192873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232320, rend_intergenic: 229415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248033
-exon list size: 409


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
1.9    
2.2    
2.4    
2.7    
2.9    
3.2    
3.4    
3.6    
3.9    
4.1    
4.4    
4.6    
4.9    
5.1    
5.4    
5.6    
5.8    
6.1    
6.3    
6.6    
6.8    
7.1    
7.3    
7.5    
7.8    
8.0    
8.3    
8.5    
8.8    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.5    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
12.9    
13.1    
13.4    
13.6    
13.9    
14.1    
14.4    
14.6    
14.8    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.5    
16.8    
17.0    
17.3    
17.5    
17.8    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.4    
23.6    
23.8    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
28.2    
28.5    
28.7    
29.0    
29.2    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.8    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.2    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.8    
71.0    
71.3    
71.5    
71.8    
72.0    
72.3    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.4    
76.6    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 25134, rend_intergenic: 17873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27206, rend_intergenic: 25628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28809, rend_intergenic: 27231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32862, rend_intergenic: 29577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39873, rend_intergenic: 32865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53105, rend_intergenic: 50506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190675, rend_intergenic: 189568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194879, rend_intergenic: 192873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232320, rend_intergenic: 229415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support