-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_6088138-6315262

-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.1479-T1
Valid prediction for snap_scaffold_11-snap.1491-T1
Valid prediction for Augustus_model.g18536.t1
Valid prediction for snap_scaffold_11-snap.1467-T1
Valid prediction for snap_scaffold_11-snap.1500-T1
Valid prediction for CodingQuarry_transcript_8060-T1
Valid prediction for GeneMark_model.48050_t
Valid prediction for GlimmerHMM_glimmerT_27801-T1
Valid prediction for snap_scaffold_11-snap.1504-T1
Valid prediction for GlimmerHMM_glimmerT_27800-T1
Valid prediction for GeneMark_model.48064_t
Valid prediction for snap_scaffold_11-snap.1489-T1
Valid prediction for GeneMark_model.48066_t
Valid prediction for GlimmerHMM_glimmerT_27787-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g18530.t1
Valid prediction for Augustus_model.g18527.t1
Valid prediction for GeneMark_model.48070_t
Valid prediction for snap_scaffold_11-snap.1501-T1
Valid prediction for GlimmerHMM_glimmerT_27788-T1
Valid prediction for snap_scaffold_11-snap.1488-T1
Valid prediction for Augustus_model.g18523.t1
Valid prediction for GeneMark_model.48073_t
Valid prediction for snap_scaffold_11-snap.1499-T1
Valid prediction for GeneMark_model.48065_t
Valid prediction for snap_scaffold_11-snap.1498-T1
Valid prediction for Augustus_model.g18529.t1
Valid prediction for GlimmerHMM_glimmerT_27786-T1
Valid prediction for pasa_asmbl_5588.p1
Valid prediction for GeneMark_model.48055_t
Valid prediction for snap_scaffold_11-snap.1490-T1
Valid prediction for Augustus_model.g18541.t1
Valid prediction for Augustus_model.g18537.t1
Valid prediction for GlimmerHMM_glimmerT_27783-T1
Valid prediction for GlimmerHMM_glimmerT_27804-T1
Valid prediction for snap_scaffold_11-snap.1476-T1
Valid prediction for snap_scaffold_11-snap.1475-T1
Valid prediction for GeneMark_model.48075_t
Valid prediction for snap_scaffold_11-snap.1494-T1
Valid prediction for snap_scaffold_11-snap.1487-T1
Valid prediction for HiQ_model.g18540.t1
Valid prediction for GlimmerHMM_glimmerT_27798-T1
Valid prediction for snap_scaffold_11-snap.1506-T1
Valid prediction for CodingQuarry_transcript_8061-T1
Valid prediction for HiQ_model.g18543.t1
Valid prediction for snap_scaffold_11-snap.1473-T1
Valid prediction for GeneMark_model.48062_t
Valid prediction for Augustus_model.g18544.t1
Valid prediction for Augustus_model.g18548.t1
Valid prediction for snap_scaffold_11-snap.1471-T1
Valid prediction for GlimmerHMM_glimmerT_27797-T1
Valid prediction for GeneMark_model.48056_t
Valid prediction for HiQ_model.g18539.t1
Valid prediction for GeneMark_model.48047_t
Valid prediction for GeneMark_model.48054_t
Couldn't classify 151730, 151863
Sorry, prediction pasa_asmbl_5581.p1 fails validation.
(ATC)	 GG	151730-151863	GT	CTG
(GTC)	 AG	152274-152337	GT	AGG
(CTC)	 AG	152427-152510	GT	AGG
(GCC)	 AG	152932-153055	GT	TGG
(GTA)	 AG	153315-153393	GT	GGG
(GGA)	 AG	153474-153628	GT	CGG
(ATT)	 AG	153762-153834	GT	GGG
(ATA)	 AG	153977-154124	GT	AGG
(GAT)	 AG	154254-154321	GT	GGG
(ACA)	 AG	154418-154484	TG	AAT
-recovered pasa_asmbl_5581.p1, terminal, 154418, 154484
-recovered pasa_asmbl_5581.p1, internal, 152274, 152337
-recovered pasa_asmbl_5581.p1, internal, 152427, 152510
-recovered pasa_asmbl_5581.p1, internal, 152932, 153055
-recovered pasa_asmbl_5581.p1, internal, 153315, 153393
-recovered pasa_asmbl_5581.p1, internal, 153474, 153628
-recovered pasa_asmbl_5581.p1, internal, 153762, 153834
-recovered pasa_asmbl_5581.p1, internal, 153977, 154124
-recovered pasa_asmbl_5581.p1, internal, 154254, 154321
Valid prediction for GlimmerHMM_glimmerT_27810-T1
Valid prediction for snap_scaffold_11-snap.1481-T1
Valid prediction for Augustus_model.g18532.t1
Valid prediction for GlimmerHMM_glimmerT_27802-T1
Valid prediction for GlimmerHMM_glimmerT_27789-T1
Valid prediction for GlimmerHMM_glimmerT_27796-T1
Valid prediction for snap_scaffold_11-snap.1496-T1
Valid prediction for GlimmerHMM_glimmerT_27805-T1
Valid prediction for snap_scaffold_11-snap.1478-T1
Valid prediction for GlimmerHMM_glimmerT_27793-T1
Valid prediction for GeneMark_model.48069_t
Valid prediction for Augustus_model.g18538.t1
Valid prediction for GlimmerHMM_glimmerT_27809-T1
Valid prediction for GlimmerHMM_glimmerT_27777-T1
Valid prediction for snap_scaffold_11-snap.1497-T1
Valid prediction for GlimmerHMM_glimmerT_27803-T1
Couldn't classify 14954, 15310
Sorry, prediction pasa_asmbl_5575.p1 fails validation.
(TTC)	 AC	14954-15310	AC	AGA
Couldn't classify 161837, 162034
Sorry, prediction pasa_asmbl_5583.p1 fails validation.
(CTG)	 AG	161837-162034	GT	CGG
(CTC)	 AG	162816-163003	GT	AAG
(GGT)	 AG	163130-163255	GT	CTG
(AGT)	 AG	163448-163712	CA	AAC
-recovered pasa_asmbl_5583.p1, terminal, 163448, 163712
-recovered pasa_asmbl_5583.p1, internal, 161837, 162034
-recovered pasa_asmbl_5583.p1, internal, 162816, 163003
-recovered pasa_asmbl_5583.p1, internal, 163130, 163255
Valid prediction for GeneMark_model.48060_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 GlimmerHMM_glimmerT_27811-T1
Valid prediction for snap_scaffold_11-snap.1495-T1
Valid prediction for GeneMark_model.48072_t
Valid prediction for pasa_asmbl_6672.p1
Valid prediction for Augustus_model.g18526.t1
Valid prediction for snap_scaffold_11-snap.1477-T1
Valid prediction for GlimmerHMM_glimmerT_27781-T1
Valid prediction for GeneMark_model.48049_t
Valid prediction for snap_scaffold_11-snap.1480-T1
Valid prediction for GlimmerHMM_glimmerT_27780-T1
Valid prediction for Augustus_model.g18546.t1
Valid prediction for snap_scaffold_11-snap.1507-T1
Valid prediction for CodingQuarry_transcript_8058-T1
Valid prediction for Augustus_model.g18533.t1
Valid prediction for GlimmerHMM_glimmerT_27785-T1
Valid prediction for GlimmerHMM_glimmerT_27775-T1
Valid prediction for GlimmerHMM_glimmerT_27799-T1
Couldn't classify 6203, 6330
Sorry, prediction pasa_asmbl_6678.p1 fails validation.
(CTT)	 AT	6203-6330	GT	GGG
(GTG)	 AG	6431-6607	GT	AGG
(GTT)	 AG	6724-7282	TG	GAT
-recovered pasa_asmbl_6678.p1, terminal, 6724, 7282
-recovered pasa_asmbl_6678.p1, internal, 6431, 6607
Valid prediction for GeneMark_model.48074_t
Valid prediction for GlimmerHMM_glimmerT_27776-T1
Valid prediction for GlimmerHMM_glimmerT_27778-T1
Valid prediction for Augustus_model.g18535.t1
Valid prediction for Augustus_model.g18531.t1
Valid prediction for GlimmerHMM_glimmerT_27807-T1
Valid prediction for GeneMark_model.48058_t
Valid prediction for GeneMark_model.48061_t
Valid prediction for GeneMark_model.48067_t
Valid prediction for Augustus_model.g18534.t1
Valid prediction for GeneMark_model.48051_t
Valid prediction for GlimmerHMM_glimmerT_27779-T1
Valid prediction for GlimmerHMM_glimmerT_27808-T1
Valid prediction for snap_scaffold_11-snap.1483-T1
Valid prediction for GeneMark_model.48046_t
Valid prediction for snap_scaffold_11-snap.1482-T1
Valid prediction for snap_scaffold_11-snap.1503-T1
Valid prediction for pasa_asmbl_6675.p1
Valid prediction for Augustus_model.g18549.t1
Valid prediction for snap_scaffold_11-snap.1474-T1
Valid prediction for GlimmerHMM_glimmerT_27813-T1
Valid prediction for GeneMark_model.48052_t
Valid prediction for GeneMark_model.48059_t
Valid prediction for HiQ_model.g18528.t1
Valid prediction for snap_scaffold_11-snap.1502-T1
Valid prediction for GlimmerHMM_glimmerT_27812-T1
Valid prediction for GlimmerHMM_glimmerT_27782-T1
Valid prediction for GeneMark_model.48045_t
Valid prediction for snap_scaffold_11-snap.1485-T1
Valid prediction for GeneMark_model.48057_t
Valid prediction for Augustus_model.g18550.t1
Valid prediction for snap_scaffold_11-snap.1470-T1
Valid prediction for Augustus_model.g18525.t1
Valid prediction for GlimmerHMM_glimmerT_27794-T1
Valid prediction for snap_scaffold_11-snap.1472-T1
Valid prediction for Augustus_model.g18547.t1
Valid prediction for Augustus_model.g18545.t1
Couldn't classify 192639, 192661
Sorry, prediction pasa_asmbl_6673.p1 fails validation.
(CAC)	 CC	192639-192661	GT	AAG
(GTT)	 AG	192752-192925	GT	AAG
(CTG)	 AG	193051-193113	GT	ACG
(GGT)	 AG	193247-193472	GT	AGG
(GTG)	 AG	193954-194091	GT	AGG
(GTG)	 AG	194785-194886	GT	AGG
(TCT)	 AG	195282-195353	GT	AGG
(TGG)	 AG	196035-196223	GT	AGG
(GGA)	 AG	196531-196623	GT	CGG
(TGG)	 AG	196709-196795	GT	AGG
(GAG)	 AG	196936-197114	GT	AAG
(ACC)	 AG	197381-197461	GT	AGG
(TCA)	 AG	197611-197707	AT	GAA
-recovered pasa_asmbl_6673.p1, terminal, 197611, 197707
-recovered pasa_asmbl_6673.p1, internal, 192752, 192925
-recovered pasa_asmbl_6673.p1, internal, 193051, 193113
-recovered pasa_asmbl_6673.p1, internal, 193247, 193472
-recovered pasa_asmbl_6673.p1, internal, 193954, 194091
-recovered pasa_asmbl_6673.p1, internal, 194785, 194886
-recovered pasa_asmbl_6673.p1, internal, 195282, 195353
-recovered pasa_asmbl_6673.p1, internal, 196035, 196223
-recovered pasa_asmbl_6673.p1, internal, 196531, 196623
-recovered pasa_asmbl_6673.p1, internal, 196709, 196795
-recovered pasa_asmbl_6673.p1, internal, 196936, 197114
-recovered pasa_asmbl_6673.p1, internal, 197381, 197461
Valid prediction for GlimmerHMM_glimmerT_27791-T1
Valid prediction for snap_scaffold_11-snap.1484-T1
Valid prediction for snap_scaffold_11-snap.1493-T1
Valid prediction for GlimmerHMM_glimmerT_27792-T1
Valid prediction for Augustus_model.g18542.t1
Valid prediction for snap_scaffold_11-snap.1505-T1
Valid prediction for snap_scaffold_11-snap.1466-T1
Valid prediction for snap_scaffold_11-snap.1469-T1
Valid prediction for GlimmerHMM_glimmerT_27795-T1
Valid prediction for GeneMark_model.48048_t
Valid prediction for GeneMark_model.48071_t
Valid prediction for snap_scaffold_11-snap.1486-T1
Valid prediction for GlimmerHMM_glimmerT_27806-T1
Valid prediction for snap_scaffold_11-snap.1492-T1
Valid prediction for HiQ_model.g18524.t1
Valid prediction for GlimmerHMM_glimmerT_27790-T1
Valid prediction for snap_scaffold_11-snap.1468-T1
Valid prediction for GlimmerHMM_glimmerT_27784-T1
Valid prediction for GeneMark_model.48053_t
Valid prediction for GeneMark_model.48077_t
Valid prediction for CodingQuarry_transcript_8059-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32401, rend_intergenic: 30072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35798, rend_intergenic: 33026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37343, rend_intergenic: 36462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42530, rend_intergenic: 38568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227125
-exon list size: 531


building trellis

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27.0    
27.2    
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28.1    
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29.1    
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29.5    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.6    
32.8    
33.0    
33.2    
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33.6    
33.8    
34.0    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
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40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
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42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
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46.2    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
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48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
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50.8    
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51.2    
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51.6    
51.8    
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52.9    
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53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
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57.8    
58.0    
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58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.8    
60.0    
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60.4    
60.6    
60.8    
61.0    
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61.4    
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62.1    
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63.2    
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63.8    
64.0    
64.2    
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72.8    
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76.5    
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76.9    
77.1    
77.3    
77.5    
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78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.5    
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79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
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83.9    
84.1    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
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85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.5    
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95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 32401, rend_intergenic: 30072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35798, rend_intergenic: 33026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37343, rend_intergenic: 36462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42530, rend_intergenic: 38568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14551
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-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 1 - 14392
-exon list size: 20


building trellis

4.5    
9.1    
13.6    
18.2    
22.7    
27.3    
31.8    
36.4    
40.9    
45.5    
50.0    
54.5    
59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
95.5    
-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 1 - 13059
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-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

-building DP trellis

-building trellis in range 1 - 10109
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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