-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_5510789-5701795

-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_22179-T1
Valid prediction for snap_scaffold_9-snap.1166-T1
Valid prediction for snap_scaffold_9-snap.1153-T1
Valid prediction for snap_scaffold_9-snap.1186-T1
Valid prediction for Augustus_model.g14737.t1
Valid prediction for snap_scaffold_9-snap.1173-T1
Valid prediction for CodingQuarry_transcript_62184-T1
Valid prediction for HiQ_model.g14752.t1
Valid prediction for snap_scaffold_9-snap.1176-T1
Valid prediction for GlimmerHMM_glimmerT_22194-T1
Valid prediction for snap_scaffold_9-snap.1169-T1
Valid prediction for snap_scaffold_9-snap.1167-T1
Valid prediction for snap_scaffold_9-snap.1161-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_22192-T1
Valid prediction for Augustus_model.g14741.t1
Valid prediction for GlimmerHMM_glimmerT_22188-T1
Valid prediction for snap_scaffold_9-snap.1152-T1
Valid prediction for snap_scaffold_9-snap.1160-T1
Valid prediction for GlimmerHMM_glimmerT_22189-T1
Valid prediction for HiQ_model.g14736.t1
Valid prediction for HiQ_model.g14753.t1
Valid prediction for pasa_asmbl_54062.p1
Valid prediction for snap_scaffold_9-snap.1180-T1
Valid prediction for snap_scaffold_9-snap.1183-T1
Valid prediction for pasa_asmbl_54064.p1
Valid prediction for snap_scaffold_9-snap.1177-T1
Valid prediction for Augustus_model.g14748.t1
Valid prediction for snap_scaffold_9-snap.1179-T1
Valid prediction for snap_scaffold_9-snap.1163-T1
Valid prediction for snap_scaffold_9-snap.1158-T1
Valid prediction for pasa_asmbl_54058.p1
Valid prediction for snap_scaffold_9-snap.1154-T1
Valid prediction for snap_scaffold_9-snap.1159-T1
Valid prediction for HiQ_model.g14751.t1
Couldn't classify 16247, 16329
Sorry, prediction pasa_asmbl_54049.p1 fails validation.
(TGG)	 CC	16247-16329	GT	GGG
(ACC)	 AG	18179-18366	GT	AGG
(GGT)	 AG	18463-18527	GT	CTG
(CTG)	 AG	18634-18727	GT	AGG
(GCC)	 AG	19845-19916	GT	AGG
(GAT)	 AG	20300-20452	GT	CGG
(AGG)	 AG	20675-20790	GT	AGG
(AGT)	 AG	21880-21891	CT	AAC
-recovered pasa_asmbl_54049.p1, terminal, 21880, 21891
-recovered pasa_asmbl_54049.p1, internal, 18179, 18366
-recovered pasa_asmbl_54049.p1, internal, 18463, 18527
-recovered pasa_asmbl_54049.p1, internal, 18634, 18727
-recovered pasa_asmbl_54049.p1, internal, 19845, 19916
-recovered pasa_asmbl_54049.p1, internal, 20300, 20452
-recovered pasa_asmbl_54049.p1, internal, 20675, 20790
Valid prediction for snap_scaffold_9-snap.1190-T1
Valid prediction for snap_scaffold_9-snap.1184-T1
Valid prediction for pasa_asmbl_54053.p1
Valid prediction for snap_scaffold_9-snap.1188-T1
Valid prediction for GlimmerHMM_glimmerT_22183-T1
Valid prediction for snap_scaffold_9-snap.1182-T1
Valid prediction for GlimmerHMM_glimmerT_22174-T1
Valid prediction for GlimmerHMM_glimmerT_22195-T1
Valid prediction for CodingQuarry_transcript_62183-T1
Valid prediction for snap_scaffold_9-snap.1151-T1
Valid prediction for GlimmerHMM_glimmerT_22177-T1
Valid prediction for CodingQuarry_transcript_62185-T1
Couldn't classify 78214, 78335
Couldn't classify 79601, 79665
Sorry, prediction pasa_asmbl_54788.p2 fails validation.
(CAC)	 CC	78214-78335	GT	AGG
(GTT)	 AG	79227-79390	GT	AGG
(ACA)	 AG	79601-79665	GC	GGG
-recovered pasa_asmbl_54788.p2, internal, 79227, 79390
-recovered pasa_asmbl_54788.p2, internal, 79601, 79665
Valid prediction for Augustus_model.g14744.t1
Valid prediction for GlimmerHMM_glimmerT_22191-T1
Valid prediction for snap_scaffold_9-snap.1148-T1
Valid prediction for snap_scaffold_9-snap.1150-T1
Valid prediction for GlimmerHMM_glimmerT_22181-T1
Valid prediction for snap_scaffold_9-snap.1164-T1
Valid prediction for snap_scaffold_9-snap.1171-T1
Valid prediction for snap_scaffold_9-snap.1187-T1
Valid prediction for CodingQuarry_transcript_62187-T1
Valid prediction for Augustus_model.g14756.t1
Valid prediction for GlimmerHMM_glimmerT_22186-T1
Valid prediction for snap_scaffold_9-snap.1168-T1
Valid prediction for GlimmerHMM_glimmerT_22185-T1
Valid prediction for Augustus_model.g14746.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_22196-T1
Valid prediction for GlimmerHMM_glimmerT_22190-T1
Valid prediction for Augustus_model.g14755.t1
Valid prediction for snap_scaffold_9-snap.1156-T1
Valid prediction for GlimmerHMM_glimmerT_22178-T1
Valid prediction for Augustus_model.g14749.t1
Couldn't classify 135501, 135569
Sorry, prediction pasa_asmbl_55016.p2 fails validation.
(GTG)	 AG	135501-135569	GT	AGG
(CAA)	 AG	135996-136147	GT	AAG
(GTG)	 AG	136568-136734	GT	AGG
(GGA)	 AG	136901-137097	CG	GAC
-recovered pasa_asmbl_55016.p2, terminal, 136901, 137097
-recovered pasa_asmbl_55016.p2, internal, 135501, 135569
-recovered pasa_asmbl_55016.p2, internal, 135996, 136147
-recovered pasa_asmbl_55016.p2, internal, 136568, 136734
Valid prediction for GlimmerHMM_glimmerT_22173-T1
Valid prediction for snap_scaffold_9-snap.1170-T1
Valid prediction for Augustus_model.g14743.t1
Valid prediction for GlimmerHMM_glimmerT_22184-T1
Valid prediction for Augustus_model.g14739.t1
Valid prediction for GlimmerHMM_glimmerT_22182-T1
Valid prediction for GlimmerHMM_glimmerT_22175-T1
Valid prediction for GlimmerHMM_glimmerT_22172-T1
Valid prediction for snap_scaffold_9-snap.1157-T1
Valid prediction for snap_scaffold_9-snap.1162-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1172-T1
Valid prediction for Augustus_model.g14738.t1
Valid prediction for Augustus_model.g14750.t1
Valid prediction for snap_scaffold_9-snap.1149-T1
Valid prediction for Augustus_model.g14757.t1
Couldn't classify 11127, 11237
Sorry, prediction pasa_asmbl_55020.p1 fails validation.
(ATG)	 AC	5615-6164	GT	AGG
(GCT)	 AG	7510-7673	GT	AGG
(GAG)	 AG	8439-8492	GT	AGG
(GTC)	 AG	8617-8713	GT	GGG
(GCG)	 AG	9394-9542	GT	CGG
(CCT)	 AG	11127-11237	GT	AGG
-recovered pasa_asmbl_55020.p1, initial, 5615, 6164
-recovered pasa_asmbl_55020.p1, internal, 7510, 7673
-recovered pasa_asmbl_55020.p1, internal, 8439, 8492
-recovered pasa_asmbl_55020.p1, internal, 8617, 8713
-recovered pasa_asmbl_55020.p1, internal, 9394, 9542
-recovered pasa_asmbl_55020.p1, internal, 11127, 11237
Valid prediction for Augustus_model.g14742.t1
Valid prediction for Augustus_model.g14745.t1
Valid prediction for CodingQuarry_transcript_62186-T1
Valid prediction for Augustus_model.g14740.t1
Valid prediction for Augustus_model.g14754.t1
Valid prediction for snap_scaffold_9-snap.1175-T1
Couldn't classify 145505, 145634
Sorry, prediction pasa_asmbl_55011.p1 fails validation.
(GCC)	 CA	145505-145634	GT	AGG
(GTT)	 AG	148264-148362	GT	GCG
(AAT)	 AG	149048-149235	GT	GGG
(ATC)	 AG	149391-149441	GT	AGG
(AGA)	 AG	152414-152500	GT	ATG
(CCC)	 AG	152833-153000	GG	AGG
-recovered pasa_asmbl_55011.p1, terminal, 152833, 153000
-recovered pasa_asmbl_55011.p1, internal, 148264, 148362
-recovered pasa_asmbl_55011.p1, internal, 149048, 149235
-recovered pasa_asmbl_55011.p1, internal, 149391, 149441
-recovered pasa_asmbl_55011.p1, internal, 152414, 152500
Couldn't classify 683, 1138
Sorry, prediction pasa_asmbl_55023.p1 fails validation.
(GGG)	 GC	683-1138	GG	CAG
Valid prediction for snap_scaffold_9-snap.1189-T1
Valid prediction for snap_scaffold_9-snap.1181-T1
Valid prediction for GlimmerHMM_glimmerT_22187-T1
Valid prediction for GlimmerHMM_glimmerT_22176-T1
Valid prediction for snap_scaffold_9-snap.1165-T1
Valid prediction for snap_scaffold_9-snap.1174-T1
Valid prediction for snap_scaffold_9-snap.1185-T1
Valid prediction for Augustus_model.g14747.t1
Valid prediction for snap_scaffold_9-snap.1178-T1
Valid prediction for snap_scaffold_9-snap.1155-T1
Valid prediction for GlimmerHMM_glimmerT_22180-T1
Valid prediction for GlimmerHMM_glimmerT_22193-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36785, rend_intergenic: 33620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49439, rend_intergenic: 43663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58529, rend_intergenic: 53911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62046, rend_intergenic: 58668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65184, rend_intergenic: 62151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97957, rend_intergenic: 96516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107119, rend_intergenic: 102738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110109, rend_intergenic: 108998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123375, rend_intergenic: 120430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158920, rend_intergenic: 158441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164858, rend_intergenic: 158993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185393, rend_intergenic: 178533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191007
-exon list size: 386


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.1    
2.3    
2.6    
2.8    
3.1    
3.4    
3.6    
3.9    
4.1    
4.4    
4.6    
4.9    
5.2    
5.4    
5.7    
5.9    
6.2    
6.4    
6.7    
7.0    
7.2    
7.5    
7.7    
8.0    
8.2    
8.5    
8.8    
9.0    
9.3    
9.5    
9.8    
10.1    
10.3    
10.6    
10.8    
11.1    
11.3    
11.6    
11.9    
12.1    
12.4    
12.6    
12.9    
13.1    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.5    
15.7    
16.0    
16.2    
16.5    
16.8    
17.0    
17.3    
17.5    
17.8    
18.0    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.2    
22.4    
22.7    
22.9    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.2    
30.4    
30.7    
30.9    
31.2    
31.4    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.6    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.1    
54.4    
54.6    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.9    
62.1    
62.4    
62.6    
62.9    
63.1    
63.4    
63.7    
63.9    
64.2    
64.4    
64.7    
64.9    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.0    
68.3    
68.6    
68.8    
69.1    
69.3    
69.6    
69.8    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.2    
72.4    
72.7    
72.9    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.1    
77.3    
77.6    
77.8    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.5    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.9    
87.1    
87.4    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 36785, rend_intergenic: 33620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49439, rend_intergenic: 43663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58529, rend_intergenic: 53911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62046, rend_intergenic: 58668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65184, rend_intergenic: 62151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97957, rend_intergenic: 96516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107119, rend_intergenic: 102738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110109, rend_intergenic: 108998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123375, rend_intergenic: 120430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158920, rend_intergenic: 158441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164858, rend_intergenic: 158993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185393, rend_intergenic: 178533  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