-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_5116365-5312904

-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_11-snap.1240-T1
Valid prediction for pasa_asmbl_5556.p1
Valid prediction for Augustus_model.g17925.t1
Valid prediction for snap_scaffold_11-snap.1267-T1
Valid prediction for Augustus_model.g17919.t1
Valid prediction for snap_scaffold_11-snap.1243-T1
Valid prediction for GlimmerHMM_glimmerT_27087-T1
Valid prediction for GlimmerHMM_glimmerT_27093-T1
Valid prediction for GlimmerHMM_glimmerT_27082-T1
Valid prediction for snap_scaffold_11-snap.1247-T1
Valid prediction for Augustus_model.g17920.t1
Valid prediction for snap_scaffold_11-snap.1256-T1
Valid prediction for CodingQuarry_transcript_8068-T1
Valid prediction for Augustus_model.g17923.t1
Valid prediction for GlimmerHMM_glimmerT_27081-T1
Valid prediction for Augustus_model.g17928.t1
Valid prediction for GlimmerHMM_glimmerT_27097-T1
Valid prediction for HiQ_model.g17918.t1
Valid prediction for snap_scaffold_11-snap.1249-T1
Valid prediction for Augustus_model.g17924.t1
Couldn't classify 10799, 10972
Sorry, prediction pasa_asmbl_6355.p1 fails validation.
(GGC)	 CC	10799-10972	GT	AGG
(ACG)	 AG	11216-11363	GT	AGG
(TGA)	 AG	11581-11615	GT	CGG
(AGT)	 AG	11726-11816	GT	CAG
(ACA)	 AG	12100-12139	GT	TGG
(CAT)	 AG	12270-12360	GT	AGG
(GTG)	 AG	12486-12579	GT	AGG
(GGG)	 AG	12679-12764	GT	CTG
(GTA)	 AG	12892-13012	GT	GGG
(GAG)	 AG	13149-13231	GT	AGG
(GCT)	 AG	13381-13443	TT	GAT
-recovered pasa_asmbl_6355.p1, terminal, 13381, 13443
-recovered pasa_asmbl_6355.p1, internal, 11216, 11363
-recovered pasa_asmbl_6355.p1, internal, 11581, 11615
-recovered pasa_asmbl_6355.p1, internal, 11726, 11816
-recovered pasa_asmbl_6355.p1, internal, 12100, 12139
-recovered pasa_asmbl_6355.p1, internal, 12270, 12360
-recovered pasa_asmbl_6355.p1, internal, 12486, 12579
-recovered pasa_asmbl_6355.p1, internal, 12679, 12764
-recovered pasa_asmbl_6355.p1, internal, 12892, 13012
-recovered pasa_asmbl_6355.p1, internal, 13149, 13231
Valid prediction for GlimmerHMM_glimmerT_27090-T1
Valid prediction for snap_scaffold_11-snap.1265-T1
Valid prediction for GlimmerHMM_glimmerT_27104-T1
Valid prediction for snap_scaffold_11-snap.1235-T1
Valid prediction for GlimmerHMM_glimmerT_27100-T1
Valid prediction for GlimmerHMM_glimmerT_27080-T1
Valid prediction for snap_scaffold_11-snap.1245-T1
Couldn't classify 126348, 126653
Sorry, prediction pasa_asmbl_5555.p1 fails validation.
(CTG)	 CT	126348-126653	GG	GAG
Valid prediction for Augustus_model.g17930.t1
Couldn't classify 44075, 44178
Sorry, prediction pasa_asmbl_5548.p1 fails validation.
(ATC)	 AA	44075-44178	GT	AGG
(GGT)	 AG	44466-44784	AC	AGA
-recovered pasa_asmbl_5548.p1, terminal, 44466, 44784
Valid prediction for snap_scaffold_11-snap.1270-T1
Valid prediction for GlimmerHMM_glimmerT_27095-T1
Valid prediction for snap_scaffold_11-snap.1272-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.1268-T1
Valid prediction for Augustus_model.g17929.t1
Couldn't classify 27506, 28909
Couldn't classify 30090, 30245
Sorry, prediction pasa_asmbl_5547.p1 fails validation.
(GAC)	 AG	27506-28909	GT	AGG
(CCA)	 AG	30090-30245	AG	GTA
-recovered pasa_asmbl_5547.p1, internal, 27506, 28909
Valid prediction for GlimmerHMM_glimmerT_27098-T1
Valid prediction for snap_scaffold_11-snap.1273-T1
Valid prediction for snap_scaffold_11-snap.1239-T1
Couldn't classify 67732, 67983
Couldn't classify 69808, 69921
Sorry, prediction pasa_asmbl_5551.p1 fails validation.
(GAC)	 AG	67732-67983	GT	AGG
(ACC)	 AG	68408-69547	GT	GGG
(AAG)	 AG	69808-69921	AC	ACA
-recovered pasa_asmbl_5551.p1, internal, 67732, 67983
-recovered pasa_asmbl_5551.p1, internal, 68408, 69547
Valid prediction for snap_scaffold_11-snap.1252-T1
Valid prediction for Augustus_model.g17922.t1
Valid prediction for Augustus_model.g17927.t1
Valid prediction for snap_scaffold_11-snap.1260-T1
Valid prediction for GlimmerHMM_glimmerT_27102-T1
Couldn't classify 70042, 70281
Couldn't classify 73145, 73267
Sorry, prediction pasa_asmbl_5552.p1 fails validation.
(AGC)	 CC	70042-70281	GT	AGG
(GGG)	 AG	73145-73267	GT	TGG
-recovered pasa_asmbl_5552.p1, internal, 73145, 73267
Valid prediction for snap_scaffold_11-snap.1254-T1
Valid prediction for Augustus_model.g17915.t1
Valid prediction for GlimmerHMM_glimmerT_27083-T1
Valid prediction for Augustus_model.g17921.t1
Valid prediction for GlimmerHMM_glimmerT_27091-T1
Couldn't classify 25673, 27448
Sorry, prediction pasa_asmbl_5546.p1 fails validation.
(CTG)	 TG	25673-27448	GT	GGG
Valid prediction for snap_scaffold_11-snap.1238-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_11-snap.1274-T1
Valid prediction for HiQ_model.g17917.t1
Valid prediction for CodingQuarry_transcript_8063-T1
Valid prediction for snap_scaffold_11-snap.1269-T1
Valid prediction for GlimmerHMM_glimmerT_27094-T1
Valid prediction for snap_scaffold_11-snap.1261-T1
Valid prediction for GlimmerHMM_glimmerT_27103-T1
Valid prediction for Augustus_model.g17931.t1
Valid prediction for GlimmerHMM_glimmerT_27086-T1
Valid prediction for snap_scaffold_11-snap.1246-T1
Valid prediction for snap_scaffold_11-snap.1236-T1
Valid prediction for snap_scaffold_11-snap.1241-T1
Valid prediction for snap_scaffold_11-snap.1242-T1
Valid prediction for GlimmerHMM_glimmerT_27096-T1
Valid prediction for snap_scaffold_11-snap.1244-T1
Valid prediction for GlimmerHMM_glimmerT_27084-T1
Couldn't classify 191247, 191448
Couldn't classify 191564, 191597
Sorry, prediction CodingQuarry_transcript_8064-T1 fails validation.
(ATG)	 AG	189010-189122	GT	AGG
(ACC)	 AG	189571-189645	GT	AGG
(ACG)	 AG	189750-189821	GT	AGG
(GCT)	 AG	189964-190039	GT	AGG
(CCA)	 AG	190122-190216	GT	AGG
(AAA)	 AG	190401-190476	GT	AGG
(CAA)	 AG	190586-190741	GT	TGG
(CAA)	 AG	190950-191088	GT	TGG
(TGG)	 AG	191247-191448	GG	ATG
(AGG)	 AT	191564-191597	CT	AGC
-recovered CodingQuarry_transcript_8064-T1, initial, 189010, 189122
-recovered CodingQuarry_transcript_8064-T1, internal, 189010, 189122
-recovered CodingQuarry_transcript_8064-T1, internal, 189571, 189645
-recovered CodingQuarry_transcript_8064-T1, internal, 189750, 189821
-recovered CodingQuarry_transcript_8064-T1, internal, 189964, 190039
-recovered CodingQuarry_transcript_8064-T1, internal, 190122, 190216
-recovered CodingQuarry_transcript_8064-T1, internal, 190401, 190476
-recovered CodingQuarry_transcript_8064-T1, internal, 190586, 190741
-recovered CodingQuarry_transcript_8064-T1, internal, 190950, 191088
Valid prediction for snap_scaffold_11-snap.1266-T1
Valid prediction for GlimmerHMM_glimmerT_27099-T1
Valid prediction for GlimmerHMM_glimmerT_27085-T1
Valid prediction for GlimmerHMM_glimmerT_27079-T1
Valid prediction for snap_scaffold_11-snap.1253-T1
Valid prediction for snap_scaffold_11-snap.1259-T1
Valid prediction for GlimmerHMM_glimmerT_27088-T1
Valid prediction for GlimmerHMM_glimmerT_27092-T1
Valid prediction for CodingQuarry_transcript_8066-T1
Valid prediction for snap_scaffold_11-snap.1255-T1
Valid prediction for Augustus_model.g17932.t1
Valid prediction for HiQ_model.g17916.t1
Valid prediction for CodingQuarry_transcript_8067-T1
Valid prediction for snap_scaffold_11-snap.1248-T1
Valid prediction for snap_scaffold_11-snap.1271-T1
Valid prediction for snap_scaffold_11-snap.1250-T1
Valid prediction for snap_scaffold_11-snap.1264-T1
Valid prediction for pasa_asmbl_6654.p1
Valid prediction for snap_scaffold_11-snap.1257-T1
Valid prediction for snap_scaffold_11-snap.1262-T1
Valid prediction for snap_scaffold_11-snap.1237-T1
Valid prediction for snap_scaffold_11-snap.1258-T1
Valid prediction for GlimmerHMM_glimmerT_27101-T1
Valid prediction for snap_scaffold_11-snap.1263-T1
Valid prediction for CodingQuarry_transcript_8065-T1
Valid prediction for snap_scaffold_11-snap.1251-T1
Valid prediction for GlimmerHMM_glimmerT_27089-T1
Valid prediction for pasa_asmbl_6653.p1
Valid prediction for Augustus_model.g17926.t1
Valid prediction for snap_scaffold_11-snap.1275-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 33587, rend_intergenic: 30332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39857, rend_intergenic: 33710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44784, rend_intergenic: 40569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50336, rend_intergenic: 48144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58576, rend_intergenic: 52424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79233, rend_intergenic: 68363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80429, rend_intergenic: 79409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82954, rend_intergenic: 80585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88348, rend_intergenic: 83125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104146, rend_intergenic: 93135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121813, rend_intergenic: 104269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144054, rend_intergenic: 122892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157419, rend_intergenic: 154489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166632, rend_intergenic: 163452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171836, rend_intergenic: 167230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176737, rend_intergenic: 173525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185379, rend_intergenic: 180112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191190, rend_intergenic: 187295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196540
-exon list size: 368


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.2    
3.5    
3.8    
4.1    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
5.9    
6.2    
6.5    
6.8    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.5    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.4    
12.7    
13.0    
13.2    
13.5    
13.8    
14.1    
14.3    
14.6    
14.9    
15.1    
15.4    
15.7    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.1    
21.4    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.4    
28.6    
28.9    
29.2    
29.5    
29.7    
30.0    
30.3    
30.5    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.4    
42.7    
43.0    
43.2    
43.5    
43.8    
44.1    
44.3    
44.6    
44.9    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.8    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.2    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.1    
55.4    
55.7    
55.9    
56.2    
56.5    
56.8    
57.0    
57.3    
57.6    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.2    
69.5    
69.7    
70.0    
70.3    
70.5    
70.8    
71.1    
71.4    
71.6    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.6    
78.9    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.3    
84.6    
84.9    
85.1    
85.4    
85.7    
85.9    
86.2    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.5    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 33587, rend_intergenic: 30332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39857, rend_intergenic: 33710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44784, rend_intergenic: 40569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50336, rend_intergenic: 48144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58576, rend_intergenic: 52424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79233, rend_intergenic: 68363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80429, rend_intergenic: 79409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82954, rend_intergenic: 80585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88348, rend_intergenic: 83125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104146, rend_intergenic: 93135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121813, rend_intergenic: 104269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144054, rend_intergenic: 122892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157419, rend_intergenic: 154489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166632, rend_intergenic: 163452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171836, rend_intergenic: 167230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176737, rend_intergenic: 173525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185379, rend_intergenic: 180112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191190, rend_intergenic: 187295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 185735 - 196540
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 185946 - 196540
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support