-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_6549800-6786854

-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.1575-T1
Valid prediction for GlimmerHMM_glimmerT_27275-T1
Valid prediction for GlimmerHMM_glimmerT_27291-T1
Valid prediction for snap_scaffold_11-snap.1552-T1
Valid prediction for snap_scaffold_11-snap.1558-T1
Valid prediction for GlimmerHMM_glimmerT_27296-T1
Valid prediction for GlimmerHMM_glimmerT_27294-T1
Valid prediction for snap_scaffold_11-snap.1576-T1
Valid prediction for snap_scaffold_11-snap.1534-T1
Valid prediction for GlimmerHMM_glimmerT_27274-T1
Valid prediction for snap_scaffold_11-snap.1537-T1
Valid prediction for snap_scaffold_11-snap.1544-T1
Valid prediction for snap_scaffold_11-snap.1565-T1
Valid prediction for snap_scaffold_11-snap.1556-T1
Valid prediction for Augustus_model.g18065.t1
Valid prediction for GlimmerHMM_glimmerT_27295-T1
Valid prediction for snap_scaffold_11-snap.1578-T1
Valid prediction for snap_scaffold_11-snap.1555-T1
Valid prediction for Augustus_model.g18071.t1
Valid prediction for Augustus_model.g18069.t1
Valid prediction for snap_scaffold_11-snap.1574-T1
Valid prediction for snap_scaffold_11-snap.1533-T1
Valid prediction for snap_scaffold_11-snap.1562-T1
Valid prediction for snap_scaffold_11-snap.1557-T1
Valid prediction for GlimmerHMM_glimmerT_27284-T1
Valid prediction for snap_scaffold_11-snap.1560-T1
Valid prediction for snap_scaffold_11-snap.1563-T1
Valid prediction for snap_scaffold_11-snap.1542-T1
Valid prediction for snap_scaffold_11-snap.1545-T1
Valid prediction for snap_scaffold_11-snap.1572-T1
Valid prediction for Augustus_model.g18063.t1
Valid prediction for GlimmerHMM_glimmerT_27286-T1
Valid prediction for GlimmerHMM_glimmerT_27297-T1
Valid prediction for GlimmerHMM_glimmerT_27293-T1
Valid prediction for Augustus_model.g18053.t1
Valid prediction for GlimmerHMM_glimmerT_27282-T1
Valid prediction for snap_scaffold_11-snap.1535-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.g18055.t1
Valid prediction for snap_scaffold_11-snap.1541-T1
Valid prediction for pasa_asmbl_6734.p1
Valid prediction for GlimmerHMM_glimmerT_27280-T1
Couldn't classify 71870, 71962
Sorry, prediction pasa_asmbl_6738.p1 fails validation.
(GCG)	 AT	71870-71962	GT	CAG
(CTT)	 AG	72517-72633	GT	AGG
(ACT)	 AG	72821-73042	GT	AGG
(ATT)	 AG	73638-73734	GT	GGG
(AGA)	 AG	74202-74267	GT	AGG
(TCA)	 AG	74465-74632	GT	AGG
(AAG)	 AG	74783-74880	GT	ACG
(AGT)	 AG	75319-75357	GT	AGG
(GGC)	 AG	75499-75606	TC	GAT
-recovered pasa_asmbl_6738.p1, terminal, 75499, 75606
-recovered pasa_asmbl_6738.p1, internal, 72517, 72633
-recovered pasa_asmbl_6738.p1, internal, 72821, 73042
-recovered pasa_asmbl_6738.p1, internal, 73638, 73734
-recovered pasa_asmbl_6738.p1, internal, 74202, 74267
-recovered pasa_asmbl_6738.p1, internal, 74465, 74632
-recovered pasa_asmbl_6738.p1, internal, 74783, 74880
-recovered pasa_asmbl_6738.p1, internal, 75319, 75357
Valid prediction for Augustus_model.g18060.t1
Valid prediction for pasa_asmbl_6722.p1
Valid prediction for HiQ_model.g18066.t1
Valid prediction for snap_scaffold_11-snap.1548-T1
Valid prediction for GlimmerHMM_glimmerT_27277-T1
Valid prediction for CodingQuarry_transcript_8101-T1
Couldn't classify 188872, 189165
Couldn't classify 189421, 189444
Sorry, prediction pasa_asmbl_6727.p1 fails validation.
(CAT)	 AC	188872-189165	GT	AGG
(GAT)	 AG	189421-189444	GA	GGG
Valid prediction for snap_scaffold_11-snap.1559-T1
Valid prediction for Augustus_model.g18061.t1
Valid prediction for CodingQuarry_transcript_8102-T1
Valid prediction for Augustus_model.g18068.t1
Valid prediction for snap_scaffold_11-snap.1567-T1
Valid prediction for snap_scaffold_11-snap.1561-T1
Valid prediction for snap_scaffold_11-snap.1568-T1
Valid prediction for Augustus_model.g18070.t1
Valid prediction for snap_scaffold_11-snap.1566-T1
Valid prediction for HiQ_model.g18062.t1
Valid prediction for snap_scaffold_11-snap.1553-T1
Valid prediction for Augustus_model.g18067.t1
Valid prediction for CodingQuarry_transcript_8103-T1
Valid prediction for GlimmerHMM_glimmerT_27281-T1
Valid prediction for GlimmerHMM_glimmerT_27278-T1
Valid prediction for snap_scaffold_11-snap.1547-T1
Couldn't classify 141593, 143095
Sorry, prediction pasa_asmbl_6731.p1 fails validation.
(GCT)	 CA	141593-143095	AA	AAA
Couldn't classify 189889, 189915
Sorry, prediction pasa_asmbl_6724.p1 fails validation.
(AAG)	 AC	189889-189915	GT	AAG
(GTG)	 AG	190439-190595	GC	AGG
(AGG)	 AG	191108-191254	GT	AGG
(AGC)	 AG	191609-191653	GT	GGG
(ACA)	 AG	191909-191988	GT	AGG
(AAC)	 AG	192377-192489	GT	AGG
(GTG)	 AG	193245-193428	GT	TTG
(GAG)	 AG	193676-193760	GT	AGG
(GGT)	 AG	194287-194432	GT	ACG
(ATA)	 AG	195461-195551	GT	TGG
(AGG)	 AG	195663-195811	GT	AGG
(TGC)	 AG	196047-196147	GT	CGG
(ACC)	 AG	196327-196396	GT	AGG
(TTT)	 AG	196640-196758	GT	AGG
(AGT)	 AG	196984-197125	AT	AGA
-recovered pasa_asmbl_6724.p1, terminal, 196984, 197125
-recovered pasa_asmbl_6724.p1, internal, 190439, 190595
-recovered pasa_asmbl_6724.p1, internal, 191108, 191254
-recovered pasa_asmbl_6724.p1, internal, 191609, 191653
-recovered pasa_asmbl_6724.p1, internal, 191909, 191988
-recovered pasa_asmbl_6724.p1, internal, 192377, 192489
-recovered pasa_asmbl_6724.p1, internal, 193245, 193428
-recovered pasa_asmbl_6724.p1, internal, 193676, 193760
-recovered pasa_asmbl_6724.p1, internal, 194287, 194432
-recovered pasa_asmbl_6724.p1, internal, 195461, 195551
-recovered pasa_asmbl_6724.p1, internal, 195663, 195811
-recovered pasa_asmbl_6724.p1, internal, 196047, 196147
-recovered pasa_asmbl_6724.p1, internal, 196327, 196396
-recovered pasa_asmbl_6724.p1, internal, 196640, 196758
Valid prediction for Augustus_model.g18056.t1
Valid prediction for GlimmerHMM_glimmerT_27283-T1
Valid prediction for snap_scaffold_11-snap.1570-T1
Valid prediction for snap_scaffold_11-snap.1569-T1
Valid prediction for snap_scaffold_11-snap.1540-T1
Valid prediction for snap_scaffold_11-snap.1538-T1
Valid prediction for snap_scaffold_11-snap.1564-T1
Couldn't classify 178462, 178770
Sorry, prediction pasa_asmbl_6728.p2 fails validation.
(ATG)	 CA	173141-173218	GT	TGG
(AGC)	 AG	175585-175674	GT	CTG
(CAG)	 AG	178462-178770	GA	TGG
-recovered pasa_asmbl_6728.p2, initial, 173141, 173218
-recovered pasa_asmbl_6728.p2, internal, 175585, 175674
Couldn't classify 139794, 139869
Couldn't classify 140234, 141062
Sorry, prediction pasa_asmbl_6732.p1 fails validation.
(AAG)	 TC	139794-139869	GT	AGG
(GGG)	 AG	140044-140149	GT	AAG
(TTC)	 AG	140234-141062	TC	CGT
-recovered pasa_asmbl_6732.p1, internal, 140044, 140149
Valid prediction for GlimmerHMM_glimmerT_27287-T1
Valid prediction for CodingQuarry_transcript_8105-T1
Valid prediction for snap_scaffold_11-snap.1549-T1
Valid prediction for GlimmerHMM_glimmerT_27292-T1
Valid prediction for GlimmerHMM_glimmerT_27298-T1
Valid prediction for Augustus_model.g18054.t1
Valid prediction for snap_scaffold_11-snap.1573-T1
Valid prediction for snap_scaffold_11-snap.1554-T1
Valid prediction for CodingQuarry_transcript_8106-T1
Valid prediction for snap_scaffold_11-snap.1539-T1
Valid prediction for snap_scaffold_11-snap.1536-T1
Valid prediction for Augustus_model.g18058.t1
Valid prediction for CodingQuarry_transcript_8100-T1
Valid prediction for snap_scaffold_11-snap.1546-T1
Valid prediction for GlimmerHMM_glimmerT_27290-T1
Valid prediction for GlimmerHMM_glimmerT_27285-T1
Valid prediction for GlimmerHMM_glimmerT_27279-T1
Valid prediction for GlimmerHMM_glimmerT_27288-T1
Valid prediction for Augustus_model.g18072.t1
Valid prediction for CodingQuarry_transcript_8099-T1
Valid prediction for snap_scaffold_11-snap.1571-T1
Valid prediction for snap_scaffold_11-snap.1550-T1
Valid prediction for Augustus_model.g18064.t1
Valid prediction for snap_scaffold_11-snap.1551-T1
Valid prediction for Augustus_model.g18057.t1
Valid prediction for snap_scaffold_11-snap.1577-T1
Valid prediction for GlimmerHMM_glimmerT_27276-T1
Valid prediction for snap_scaffold_11-snap.1543-T1
Valid prediction for Augustus_model.g18059.t1
Valid prediction for GlimmerHMM_glimmerT_27289-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25608, rend_intergenic: 22023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59405, rend_intergenic: 56588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77682, rend_intergenic: 74455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126808, rend_intergenic: 122337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144409, rend_intergenic: 143653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146617, rend_intergenic: 145458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147495, rend_intergenic: 147027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149345, rend_intergenic: 148159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153399, rend_intergenic: 153274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155071, rend_intergenic: 153519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159082, rend_intergenic: 155671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228514, rend_intergenic: 208462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234203, rend_intergenic: 231056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 237055
-exon list size: 415


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
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2.4    
2.6    
2.9    
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3.4    
3.6    
3.8    
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5.3    
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7.0    
7.2    
7.4    
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7.9    
8.2    
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8.6    
8.9    
9.1    
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9.6    
9.8    
10.1    
10.3    
10.6    
10.8    
11.0    
11.3    
11.5    
11.8    
12.0    
12.2    
12.5    
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13.2    
13.4    
13.7    
13.9    
14.1    
14.4    
14.6    
14.9    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.5    
16.8    
17.0    
17.3    
17.5    
17.7    
18.0    
18.2    
18.5    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.1    
26.4    
26.6    
26.9    
27.1    
27.3    
27.6    
27.8    
28.1    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
30.9    
31.2    
31.4    
31.7    
31.9    
32.1    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.9    
38.1    
38.4    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.0    
46.3    
46.5    
46.8    
47.0    
47.2    
47.5    
47.7    
48.0    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.6    
51.8    
52.0    
52.3    
52.5    
52.8    
53.0    
53.2    
53.5    
53.7    
54.0    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.2    
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61.6    
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62.1    
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62.6    
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63.1    
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64.0    
64.3    
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65.2    
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65.9    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.9    
68.1    
68.3    
68.6    
68.8    
69.1    
69.3    
69.5    
69.8    
70.0    
70.3    
70.5    
70.7    
71.0    
71.2    
71.5    
71.7    
71.9    
72.2    
72.4    
72.7    
72.9    
73.1    
73.4    
73.6    
73.9    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.1    
85.4    
85.6    
85.9    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.5    
87.8    
88.0    
88.2    
88.5    
88.7    
89.0    
89.2    
89.4    
89.7    
89.9    
90.2    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.6    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 25608, rend_intergenic: 22023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59405, rend_intergenic: 56588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77682, rend_intergenic: 74455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126808, rend_intergenic: 122337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144409, rend_intergenic: 143653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146617, rend_intergenic: 145458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147495, rend_intergenic: 147027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149345, rend_intergenic: 148159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153399, rend_intergenic: 153274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155071, rend_intergenic: 153519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159082, rend_intergenic: 155671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228514, rend_intergenic: 208462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234203, rend_intergenic: 231056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support