-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_5925255-6089705

-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 GeneMark_model.48035_t
Valid prediction for HiQ_model.g18516.t1
Valid prediction for Augustus_model.g18513.t1
Valid prediction for GlimmerHMM_glimmerT_27760-T1
Valid prediction for CodingQuarry_transcript_8053-T1
Valid prediction for GlimmerHMM_glimmerT_27767-T1
Valid prediction for snap_scaffold_11-snap.1440-T1
Valid prediction for GeneMark_model.48029_t
Valid prediction for snap_scaffold_11-snap.1459-T1
Valid prediction for GeneMark_model.48042_t
Valid prediction for snap_scaffold_11-snap.1456-T1
Valid prediction for snap_scaffold_11-snap.1442-T1
Valid prediction for snap_scaffold_11-snap.1452-T1
Valid prediction for GlimmerHMM_glimmerT_27759-T1
Valid prediction for CodingQuarry_transcript_8055-T1
Valid prediction for snap_scaffold_11-snap.1451-T1
Valid prediction for snap_scaffold_11-snap.1462-T1
Valid prediction for GeneMark_model.48033_t
Valid prediction for HiQ_model.g18521.t1
Couldn't classify 111670, 111699
Couldn't classify 113382, 113615
Sorry, prediction pasa_asmbl_6244.p1 fails validation.
(CAA)	 TG	111670-111699	GT	AGG
(CTT)	 AG	112148-112264	GT	GGG
(GTG)	 AG	113382-113615	GG	AGG
-recovered pasa_asmbl_6244.p1, internal, 112148, 112264
Valid prediction for GlimmerHMM_glimmerT_27774-T1
Couldn't classify 76570, 76593
Sorry, prediction pasa_asmbl_5562.p2 fails validation.
(CAC)	 GA	76570-76593	GT	AGG
(AAT)	 AG	77020-77111	GT	AGG
(ATT)	 AG	77310-77499	TG	GAT
-recovered pasa_asmbl_5562.p2, terminal, 77310, 77499
-recovered pasa_asmbl_5562.p2, internal, 77020, 77111
Valid prediction for CodingQuarry_transcript_8056-T1
Valid prediction for GlimmerHMM_glimmerT_27770-T1
Valid prediction for snap_scaffold_11-snap.1443-T1
Valid prediction for GlimmerHMM_glimmerT_27771-T1
Valid prediction for GeneMark_model.48023_t
Valid prediction for Augustus_model.g18519.t1
Valid prediction for GeneMark_model.48039_t
Valid prediction for snap_scaffold_11-snap.1448-T1
Valid prediction for GlimmerHMM_glimmerT_27768-T1
Valid prediction for GlimmerHMM_glimmerT_27773-T1
Valid prediction for CodingQuarry_transcript_8057-T1
Valid prediction for HiQ_model.g18517.t1
Valid prediction for GlimmerHMM_glimmerT_27764-T1
Valid prediction for GeneMark_model.48014_t
Valid prediction for Augustus_model.g18522.t1
Couldn't classify 95154, 95261
Sorry, prediction pasa_asmbl_5567.p1 fails validation.
(AAC)	 TC	95154-95261	GT	GGG
(AAC)	 AG	95371-95667	GT	AGG
(CTG)	 AG	95878-96693	AT	AGA
-recovered pasa_asmbl_5567.p1, terminal, 95878, 96693
-recovered pasa_asmbl_5567.p1, internal, 95371, 95667
Valid prediction for GeneMark_model.48011_t
Valid prediction for Augustus_model.g18509.t1
Valid prediction for GlimmerHMM_glimmerT_27762-T1
Valid prediction for snap_scaffold_11-snap.1463-T1
Valid prediction for snap_scaffold_11-snap.1438-T1
Valid prediction for GeneMark_model.48015_t
Valid prediction for GeneMark_model.48027_t
Valid prediction for GeneMark_model.48016_t
Valid prediction for pasa_asmbl_5564.p1
Valid prediction for Augustus_model.g18520.t1
Valid prediction for GeneMark_model.48037_t
Valid prediction for snap_scaffold_11-snap.1454-T1
Valid prediction for GeneMark_model.48020_t
Valid prediction for snap_scaffold_11-snap.1461-T1
Valid prediction for snap_scaffold_11-snap.1439-T1
Valid prediction for GeneMark_model.48024_t
Valid prediction for GlimmerHMM_glimmerT_27772-T1
Couldn't classify 137786, 137969
Sorry, prediction pasa_asmbl_5569.p1 fails validation.
(GAT)	 CA	137786-137969	GT	AGG
(CCA)	 AG	139554-139686	GT	AGG
(CAC)	 AG	142072-142203	GT	AGG
(TAA)	 AG	142644-142672	GT	AGG
(GGA)	 AG	143479-143505	GT	AGG
(AGG)	 AG	145767-145896	GT	GTG
(GTA)	 AG	146253-146402	GT	TGG
(CCT)	 AG	147704-147773	GT	AAG
(CAG)	 AG	148026-148136	GT	CGG
(AAT)	 AG	148665-148760	GT	AGG
(TGC)	 AG	148889-149023	GT	AGG
(AAA)	 AG	149677-149776	GT	AGG
(GGA)	 AG	150308-150459	GT	AGG
(GTC)	 AG	150876-151001	GT	AGG
(GGT)	 AG	151109-151240	GT	AGG
(GAC)	 AG	151412-151479	GT	AGG
(GTG)	 AG	151635-151723	GT	AGG
(ATG)	 AG	151880-151977	GT	CGG
(GGC)	 AG	152187-152274	GT	CTG
(GGA)	 AG	152405-152500	GT	CGG
(GGC)	 AG	152637-152767	GT	GGG
(GCT)	 AG	152938-153063	TT	GAT
-recovered pasa_asmbl_5569.p1, initial, 151880, 151977
-recovered pasa_asmbl_5569.p1, terminal, 152938, 153063
-recovered pasa_asmbl_5569.p1, internal, 139554, 139686
-recovered pasa_asmbl_5569.p1, internal, 142072, 142203
-recovered pasa_asmbl_5569.p1, internal, 142644, 142672
-recovered pasa_asmbl_5569.p1, internal, 143479, 143505
-recovered pasa_asmbl_5569.p1, internal, 145767, 145896
-recovered pasa_asmbl_5569.p1, internal, 146253, 146402
-recovered pasa_asmbl_5569.p1, internal, 147704, 147773
-recovered pasa_asmbl_5569.p1, internal, 148026, 148136
-recovered pasa_asmbl_5569.p1, internal, 148665, 148760
-recovered pasa_asmbl_5569.p1, internal, 148889, 149023
-recovered pasa_asmbl_5569.p1, internal, 149677, 149776
-recovered pasa_asmbl_5569.p1, internal, 150308, 150459
-recovered pasa_asmbl_5569.p1, internal, 150876, 151001
-recovered pasa_asmbl_5569.p1, internal, 151109, 151240
-recovered pasa_asmbl_5569.p1, internal, 151412, 151479
-recovered pasa_asmbl_5569.p1, internal, 151635, 151723
-recovered pasa_asmbl_5569.p1, internal, 151880, 151977
-recovered pasa_asmbl_5569.p1, internal, 152187, 152274
-recovered pasa_asmbl_5569.p1, internal, 152405, 152500
-recovered pasa_asmbl_5569.p1, internal, 152637, 152767
Valid prediction for GlimmerHMM_glimmerT_27758-T1
Valid prediction for pasa_asmbl_5560.p1
Valid prediction for snap_scaffold_11-snap.1458-T1
Valid prediction for GeneMark_model.48043_t
Valid prediction for GeneMark_model.48018_t
Valid prediction for snap_scaffold_11-snap.1446-T1
Valid prediction for snap_scaffold_11-snap.1436-T1
Valid prediction for GeneMark_model.48022_t
Valid prediction for snap_scaffold_11-snap.1465-T1
Valid prediction for GeneMark_model.48031_t
Valid prediction for HiQ_model.g18512.t1
Valid prediction for GeneMark_model.48044_t

-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 HiQ_model.g18515.t1
Valid prediction for Augustus_model.g18518.t1
Valid prediction for snap_scaffold_11-snap.1464-T1
Valid prediction for snap_scaffold_11-snap.1445-T1
Valid prediction for GeneMark_model.48034_t
Valid prediction for Augustus_model.g18510.t1
Valid prediction for GlimmerHMM_glimmerT_27763-T1
Valid prediction for snap_scaffold_11-snap.1447-T1
Valid prediction for GeneMark_model.48019_t
Valid prediction for snap_scaffold_11-snap.1455-T1
Valid prediction for GeneMark_model.48021_t
Valid prediction for snap_scaffold_11-snap.1450-T1
Valid prediction for snap_scaffold_11-snap.1437-T1
Valid prediction for GlimmerHMM_glimmerT_27766-T1
Valid prediction for GeneMark_model.48012_t
Valid prediction for GeneMark_model.48010_t
Valid prediction for GeneMark_model.48013_t
Valid prediction for CodingQuarry_transcript_8054-T1
Valid prediction for snap_scaffold_11-snap.1457-T1
Valid prediction for GlimmerHMM_glimmerT_27765-T1
Valid prediction for GeneMark_model.48041_t
Valid prediction for GeneMark_model.48036_t
Valid prediction for Augustus_model.g18511.t1
Valid prediction for snap_scaffold_11-snap.1449-T1
Valid prediction for snap_scaffold_11-snap.1453-T1
Valid prediction for GeneMark_model.48038_t
Valid prediction for GlimmerHMM_glimmerT_27761-T1
Valid prediction for snap_scaffold_11-snap.1460-T1
Valid prediction for snap_scaffold_11-snap.1441-T1
Valid prediction for Augustus_model.g18514.t1
Valid prediction for GeneMark_model.48026_t
Valid prediction for snap_scaffold_11-snap.1444-T1
Valid prediction for GlimmerHMM_glimmerT_27769-T1
Valid prediction for pasa_asmbl_6670.p1
Valid prediction for GeneMark_model.48032_t
Valid prediction for GeneMark_model.48028_t
Valid prediction for GeneMark_model.48030_t
Valid prediction for GeneMark_model.48040_t
Valid prediction for GeneMark_model.48017_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 40473, rend_intergenic: 36584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77850, rend_intergenic: 73222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105336, rend_intergenic: 102980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118856, rend_intergenic: 117488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127715, rend_intergenic: 127032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138417, rend_intergenic: 127865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153063, rend_intergenic: 146200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 164451
-exon list size: 464


building trellis

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2.8    
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3.9    
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8.6    
8.8    
9.0    
9.2    
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10.9    
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21.2    
21.5    
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22.5    
22.7    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
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25.8    
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26.6    
26.8    
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27.3    
27.5    
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27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
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29.4    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
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52.4    
52.6    
52.8    
53.0    
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53.6    
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55.6    
55.8    
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56.7    
56.9    
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59.4    
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59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
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62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 40473, rend_intergenic: 36584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77850, rend_intergenic: 73222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105336, rend_intergenic: 102980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118856, rend_intergenic: 117488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127715, rend_intergenic: 127032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138417, rend_intergenic: 127865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153063, rend_intergenic: 146200  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