-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_6361080-6537982

-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 Augustus_model.g33095.t1
Valid prediction for GlimmerHMM_glimmerT_49583-T1
Valid prediction for pasa_asmbl_30119.p1
Valid prediction for snap_scaffold_22-snap.1234-T1
Valid prediction for snap_scaffold_22-snap.1262-T1
Valid prediction for snap_scaffold_22-snap.1237-T1
Valid prediction for snap_scaffold_22-snap.1232-T1
Valid prediction for snap_scaffold_22-snap.1240-T1
Valid prediction for Augustus_model.g33082.t1
Valid prediction for GlimmerHMM_glimmerT_49598-T1
Valid prediction for Augustus_model.g33094.t1
Valid prediction for GlimmerHMM_glimmerT_49588-T1
Valid prediction for Augustus_model.g33089.t1
Valid prediction for snap_scaffold_22-snap.1251-T1
Valid prediction for GlimmerHMM_glimmerT_49591-T1
Valid prediction for snap_scaffold_22-snap.1265-T1
Valid prediction for Augustus_model.g33081.t1
Valid prediction for Augustus_model.g33071.t1
Valid prediction for GlimmerHMM_glimmerT_49616-T1
Valid prediction for snap_scaffold_22-snap.1258-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49615-T1
Valid prediction for GlimmerHMM_glimmerT_49613-T1
Valid prediction for snap_scaffold_22-snap.1250-T1
Valid prediction for Augustus_model.g33090.t1
Valid prediction for GlimmerHMM_glimmerT_49601-T1
Valid prediction for snap_scaffold_22-snap.1256-T1
Valid prediction for GlimmerHMM_glimmerT_49587-T1
Valid prediction for Augustus_model.g33078.t1
Valid prediction for Augustus_model.g33075.t1
Valid prediction for GlimmerHMM_glimmerT_49594-T1
Valid prediction for snap_scaffold_22-snap.1247-T1
Valid prediction for snap_scaffold_22-snap.1252-T1
Valid prediction for Augustus_model.g33083.t1
Valid prediction for GlimmerHMM_glimmerT_49585-T1
Valid prediction for snap_scaffold_22-snap.1253-T1
Valid prediction for GlimmerHMM_glimmerT_49595-T1
Valid prediction for Augustus_model.g33092.t1
Valid prediction for GlimmerHMM_glimmerT_49614-T1
Valid prediction for Augustus_model.g33072.t1
Valid prediction for GlimmerHMM_glimmerT_49605-T1
Valid prediction for GlimmerHMM_glimmerT_49603-T1
Valid prediction for snap_scaffold_22-snap.1246-T1
Valid prediction for snap_scaffold_22-snap.1227-T1
Valid prediction for Augustus_model.g33085.t1
Valid prediction for CodingQuarry_transcript_34189-T1
Valid prediction for Augustus_model.g33087.t1
Couldn't classify 151657, 151673
Couldn't classify 152548, 152622
Sorry, prediction pasa_asmbl_30115.p1 fails validation.
(TTC)	 TA	151657-151673	GT	AGG
(GTG)	 AG	151888-151988	GT	AGG
(GCG)	 AG	152086-152159	GT	AGG
(CTC)	 AG	152276-152413	GT	AGG
(TGC)	 AG	152548-152622	TC	GCT
-recovered pasa_asmbl_30115.p1, internal, 151888, 151988
-recovered pasa_asmbl_30115.p1, internal, 152086, 152159
-recovered pasa_asmbl_30115.p1, internal, 152276, 152413
Valid prediction for Augustus_model.g33073.t1
Valid prediction for snap_scaffold_22-snap.1261-T1
Valid prediction for snap_scaffold_22-snap.1249-T1
Valid prediction for Augustus_model.g33074.t1
Valid prediction for snap_scaffold_22-snap.1238-T1
Valid prediction for GlimmerHMM_glimmerT_49610-T1
Valid prediction for GlimmerHMM_glimmerT_49597-T1
Valid prediction for snap_scaffold_22-snap.1245-T1
Valid prediction for pasa_asmbl_30117.p1
Valid prediction for GlimmerHMM_glimmerT_49609-T1
Couldn't classify 147702, 147791
Couldn't classify 148966, 148987
Sorry, prediction pasa_asmbl_30523.p2 fails validation.
(GAG)	 CA	147702-147791	GT	AGG
(AGG)	 AG	148120-148234	GT	AGG
(GAC)	 AG	148714-148822	GT	AGG
(GGG)	 AG	148966-148987	GC	AGG
-recovered pasa_asmbl_30523.p2, internal, 148120, 148234
-recovered pasa_asmbl_30523.p2, internal, 148714, 148822
-recovered pasa_asmbl_30523.p2, internal, 148966, 148987
Valid prediction for GlimmerHMM_glimmerT_49607-T1
Couldn't classify 149069, 149180
Couldn't classify 150175, 150215
Sorry, prediction pasa_asmbl_30114.p2 fails validation.
(CGC)	 CT	149069-149180	GT	TGG
(ACG)	 AG	149334-149560	GT	AGG
(AAG)	 AG	149697-149850	GT	GGG
(AGA)	 AG	150175-150215	AA	GGA
-recovered pasa_asmbl_30114.p2, internal, 149334, 149560
-recovered pasa_asmbl_30114.p2, internal, 149697, 149850
Valid prediction for Augustus_model.g33093.t1
Valid prediction for GlimmerHMM_glimmerT_49604-T1
Valid prediction for CodingQuarry_transcript_34187-T1
Valid prediction for Augustus_model.g33079.t1
Valid prediction for GlimmerHMM_glimmerT_49596-T1
Valid prediction for CodingQuarry_transcript_34188-T1
Valid prediction for snap_scaffold_22-snap.1254-T1
Valid prediction for Augustus_model.g33091.t1
Valid prediction for snap_scaffold_22-snap.1241-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 snap_scaffold_22-snap.1255-T1
Valid prediction for snap_scaffold_22-snap.1244-T1
Valid prediction for snap_scaffold_22-snap.1248-T1
Valid prediction for GlimmerHMM_glimmerT_49586-T1
Valid prediction for GlimmerHMM_glimmerT_49606-T1
Valid prediction for Augustus_model.g33077.t1
Valid prediction for Augustus_model.g33088.t1
Valid prediction for snap_scaffold_22-snap.1228-T1
Valid prediction for GlimmerHMM_glimmerT_49602-T1
Valid prediction for snap_scaffold_22-snap.1229-T1
Valid prediction for GlimmerHMM_glimmerT_49612-T1
Valid prediction for GlimmerHMM_glimmerT_49589-T1
Valid prediction for GlimmerHMM_glimmerT_49608-T1
Valid prediction for GlimmerHMM_glimmerT_49590-T1
Valid prediction for snap_scaffold_22-snap.1233-T1
Valid prediction for snap_scaffold_22-snap.1239-T1
Valid prediction for snap_scaffold_22-snap.1235-T1
Valid prediction for GlimmerHMM_glimmerT_49611-T1
Valid prediction for snap_scaffold_22-snap.1264-T1
Valid prediction for snap_scaffold_22-snap.1259-T1
Valid prediction for snap_scaffold_22-snap.1242-T1
Valid prediction for snap_scaffold_22-snap.1257-T1
Valid prediction for Augustus_model.g33080.t1
Valid prediction for GlimmerHMM_glimmerT_49600-T1
Valid prediction for GlimmerHMM_glimmerT_49592-T1
Valid prediction for snap_scaffold_22-snap.1260-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49599-T1
Valid prediction for snap_scaffold_22-snap.1243-T1
Valid prediction for snap_scaffold_22-snap.1231-T1
Valid prediction for Augustus_model.g33086.t1
Valid prediction for snap_scaffold_22-snap.1236-T1
Valid prediction for snap_scaffold_22-snap.1230-T1
Valid prediction for snap_scaffold_22-snap.1266-T1
Valid prediction for GlimmerHMM_glimmerT_49584-T1
Valid prediction for Augustus_model.g33084.t1
Valid prediction for Augustus_model.g33076.t1
Valid prediction for GlimmerHMM_glimmerT_49593-T1
Valid prediction for snap_scaffold_22-snap.1263-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 53658, rend_intergenic: 53655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25346, rend_intergenic: 6064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35465, rend_intergenic: 27345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49420, rend_intergenic: 36619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61813, rend_intergenic: 51131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63685, rend_intergenic: 62565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68834, rend_intergenic: 67231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89902, rend_intergenic: 69044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94852, rend_intergenic: 93680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155611, rend_intergenic: 143842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168140, rend_intergenic: 163283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174222, rend_intergenic: 171020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176903
-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 37 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 53658, rend_intergenic: 53655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25346, rend_intergenic: 6064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35465, rend_intergenic: 27345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49420, rend_intergenic: 36619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61813, rend_intergenic: 51131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63685, rend_intergenic: 62565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68834, rend_intergenic: 67231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89902, rend_intergenic: 69044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94852, rend_intergenic: 93680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155611, rend_intergenic: 143842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168140, rend_intergenic: 163283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174222, rend_intergenic: 171020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support