-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_1549641-1656143

-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 Augustus_model.g18081.t1
Valid prediction for Augustus_model.g18085.t1
Valid prediction for GeneMark_model.46734_t
Valid prediction for GlimmerHMM_glimmerT_27047-T1
Valid prediction for CodingQuarry_transcript_7946-T1
Valid prediction for GlimmerHMM_glimmerT_27065-T1
Valid prediction for GlimmerHMM_glimmerT_27046-T1
Valid prediction for GlimmerHMM_glimmerT_27061-T1
Couldn't classify 80375, 80535
Sorry, prediction pasa_asmbl_5298.p1 fails validation.
(ATG)	 AG	79031-79060	GT	AGG
(GTC)	 AG	79260-79307	GT	AAG
(AGT)	 AG	79417-79549	GT	AGG
(GTG)	 AG	80375-80535	GA	GGG
-recovered pasa_asmbl_5298.p1, initial, 79031, 79060
-recovered pasa_asmbl_5298.p1, internal, 79031, 79060
-recovered pasa_asmbl_5298.p1, internal, 79260, 79307
-recovered pasa_asmbl_5298.p1, internal, 79417, 79549
Valid prediction for GeneMark_model.46716_t
Valid prediction for GlimmerHMM_glimmerT_27062-T1
Valid prediction for GeneMark_model.46731_t
Valid prediction for GlimmerHMM_glimmerT_27054-T1
Valid prediction for GeneMark_model.46728_t
Valid prediction for snap_scaffold_11-snap.386-T1
Valid prediction for snap_scaffold_11-snap.375-T1
Valid prediction for Augustus_model.g18083.t1
Valid prediction for GeneMark_model.46726_t
Valid prediction for Augustus_model.g18082.t1
Couldn't classify 81280, 81760
Sorry, prediction pasa_asmbl_5299.p1 fails validation.
(CAG)	 CC	81280-81760	GT	CGG
(GAA)	 AG	81851-81940	GT	AGG
(AGA)	 AG	82085-82167	GT	CGG
(GCT)	 AG	82526-82621	GT	AGG
(TTG)	 AG	82794-82904	CG	AGC
-recovered pasa_asmbl_5299.p1, terminal, 82794, 82904
-recovered pasa_asmbl_5299.p1, internal, 81851, 81940
-recovered pasa_asmbl_5299.p1, internal, 82085, 82167
-recovered pasa_asmbl_5299.p1, internal, 82526, 82621
Valid prediction for snap_scaffold_11-snap.379-T1
Valid prediction for pasa_asmbl_6267.p1
Valid prediction for GeneMark_model.46720_t
Valid prediction for HiQ_model.g18079.t1
Valid prediction for snap_scaffold_11-snap.381-T1
Valid prediction for snap_scaffold_11-snap.392-T1
Valid prediction for GlimmerHMM_glimmerT_27060-T1
Valid prediction for snap_scaffold_11-snap.395-T1
Couldn't classify 21918, 21987
Sorry, prediction pasa_asmbl_5294.p1 fails validation.
(ACG)	 AG	21918-21987	GT	AGG
(GTA)	 AG	22426-22715	AA	AAA
-recovered pasa_asmbl_5294.p1, terminal, 22426, 22715
-recovered pasa_asmbl_5294.p1, internal, 21918, 21987
Valid prediction for snap_scaffold_11-snap.374-T1
Valid prediction for GlimmerHMM_glimmerT_27056-T1
Valid prediction for snap_scaffold_11-snap.384-T1
Valid prediction for snap_scaffold_11-snap.388-T1
Valid prediction for GeneMark_model.46715_t
Valid prediction for snap_scaffold_11-snap.397-T1
Valid prediction for snap_scaffold_11-snap.389-T1
Valid prediction for GlimmerHMM_glimmerT_27044-T1
Valid prediction for snap_scaffold_11-snap.393-T1
Valid prediction for GeneMark_model.46730_t
Valid prediction for GlimmerHMM_glimmerT_27050-T1
Valid prediction for snap_scaffold_11-snap.373-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 43973, 44116
Sorry, prediction pasa_asmbl_5296.p1 fails validation.
(GGA)	 AC	43973-44116	GT	AGG
(ATT)	 AG	45948-46036	GT	CAG
(GTA)	 AG	47230-47286	GT	GCG
(GTT)	 AG	47925-47999	GT	ATG
(TTA)	 AG	48641-49022	GT	AGG
(ATT)	 AG	50857-50966	GT	CGG
(TCC)	 AG	51710-51782	TC	GAT
-recovered pasa_asmbl_5296.p1, terminal, 51710, 51782
-recovered pasa_asmbl_5296.p1, internal, 45948, 46036
-recovered pasa_asmbl_5296.p1, internal, 47230, 47286
-recovered pasa_asmbl_5296.p1, internal, 47925, 47999
-recovered pasa_asmbl_5296.p1, internal, 48641, 49022
-recovered pasa_asmbl_5296.p1, internal, 50857, 50966
Valid prediction for GlimmerHMM_glimmerT_27058-T1
Valid prediction for snap_scaffold_11-snap.372-T1
Valid prediction for snap_scaffold_11-snap.378-T1
Valid prediction for GlimmerHMM_glimmerT_27049-T1
Valid prediction for GeneMark_model.46713_t
Valid prediction for GlimmerHMM_glimmerT_27064-T1
Valid prediction for snap_scaffold_11-snap.391-T1
Valid prediction for GeneMark_model.46718_t
Valid prediction for snap_scaffold_11-snap.398-T1
Valid prediction for GlimmerHMM_glimmerT_27055-T1
Valid prediction for snap_scaffold_11-snap.383-T1
Valid prediction for snap_scaffold_11-snap.380-T1
Valid prediction for CodingQuarry_transcript_7947-T1
Valid prediction for GlimmerHMM_glimmerT_27053-T1
Valid prediction for GeneMark_model.46723_t
Valid prediction for GlimmerHMM_glimmerT_27059-T1
Valid prediction for HiQ_model.g18078.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: -)Couldn't classify 83948, 84078
Couldn't classify 84118, 84172
Sorry, prediction CodingQuarry_transcript_7944-T1 fails validation.
(ATG)	 AA	83948-84078	CT	ACC
(CTT)	 AC	84118-84172	GA	GAG
Valid prediction for snap_scaffold_11-snap.387-T1
Valid prediction for GlimmerHMM_glimmerT_27045-T1
Valid prediction for GeneMark_model.46719_t
Couldn't classify 83948, 84078
Couldn't classify 84443, 84497
Sorry, prediction CodingQuarry_transcript_7943-T1 fails validation.
(ATG)	 AA	83948-84078	CT	ACC
(CTG)	 AC	84443-84497	GA	GAG
Couldn't classify 78133, 78258
Couldn't classify 80703, 80745
Sorry, prediction pasa_asmbl_6414.p1 fails validation.
(TAT)	 AG	78133-78258	GT	AGG
(GTG)	 AG	78962-79091	GT	AGG
(GTC)	 AG	79214-79272	GT	AGG
(CTG)	 AG	79410-79499	GT	AGG
(GTG)	 AG	79687-79862	GT	TGG
(TTT)	 AG	80703-80745	CT	AGC
-recovered pasa_asmbl_6414.p1, internal, 78133, 78258
-recovered pasa_asmbl_6414.p1, internal, 78962, 79091
-recovered pasa_asmbl_6414.p1, internal, 79214, 79272
-recovered pasa_asmbl_6414.p1, internal, 79410, 79499
-recovered pasa_asmbl_6414.p1, internal, 79687, 79862
Valid prediction for pasa_asmbl_6419.p1
Valid prediction for GeneMark_model.46729_t
Valid prediction for Augustus_model.g18076.t1
Valid prediction for snap_scaffold_11-snap.396-T1
Valid prediction for Augustus_model.g18080.t1
Valid prediction for GeneMark_model.46727_t
Valid prediction for snap_scaffold_11-snap.371-T1
Couldn't classify 75776, 75917
Couldn't classify 76795, 76904
Sorry, prediction pasa_asmbl_6415.p1 fails validation.
(TTC)	 AG	75776-75917	GT	CGG
(GAG)	 AG	76374-76495	GT	CAG
(TCT)	 AG	76581-76656	GT	GGG
(CAC)	 AG	76795-76904	GT	TGG
-recovered pasa_asmbl_6415.p1, internal, 75776, 75917
-recovered pasa_asmbl_6415.p1, internal, 76374, 76495
-recovered pasa_asmbl_6415.p1, internal, 76581, 76656
-recovered pasa_asmbl_6415.p1, internal, 76795, 76904
Valid prediction for GeneMark_model.46733_t
Couldn't classify 13788, 13916
Sorry, prediction pasa_asmbl_6420.p1 fails validation.
(CTA)	 AG	13788-13916	GT	AGG
(GGA)	 AG	14952-14985	GT	AGG
(CCC)	 AG	15064-15103	GT	GTG
(GCA)	 AG	15243-15304	GT	CAG
(AGA)	 AG	15414-15488	GT	AGG
(GTG)	 AG	15723-15778	GT	AGG
(ACG)	 AG	16526-16634	GT	AGG
(CAG)	 AG	17052-17219	GT	AGG
(TGT)	 AG	17358-17443	GT	GGG
(GTC)	 AG	17823-17920	GT	AGG
(TAA)	 AG	19351-19481	GT	CGG
(TCA)	 AG	20156-20229	GT	AGG
(GGT)	 AG	20339-20422	GT	AAG
(GCC)	 AG	21490-21657	GT	AGG
(GTG)	 AG	22135-22269	AC	GAA
-recovered pasa_asmbl_6420.p1, terminal, 22135, 22269
-recovered pasa_asmbl_6420.p1, internal, 13788, 13916
-recovered pasa_asmbl_6420.p1, internal, 14952, 14985
-recovered pasa_asmbl_6420.p1, internal, 15064, 15103
-recovered pasa_asmbl_6420.p1, internal, 15243, 15304
-recovered pasa_asmbl_6420.p1, internal, 15414, 15488
-recovered pasa_asmbl_6420.p1, internal, 15723, 15778
-recovered pasa_asmbl_6420.p1, internal, 16526, 16634
-recovered pasa_asmbl_6420.p1, internal, 17052, 17219
-recovered pasa_asmbl_6420.p1, internal, 17358, 17443
-recovered pasa_asmbl_6420.p1, internal, 17823, 17920
-recovered pasa_asmbl_6420.p1, internal, 19351, 19481
-recovered pasa_asmbl_6420.p1, internal, 20156, 20229
-recovered pasa_asmbl_6420.p1, internal, 20339, 20422
-recovered pasa_asmbl_6420.p1, internal, 21490, 21657
Valid prediction for snap_scaffold_11-snap.399-T1
Couldn't classify 73016, 73117
Couldn't classify 74140, 74369
Sorry, prediction pasa_asmbl_6416.p1 fails validation.
(CAG)	 AG	73016-73117	GT	CGG
(CTG)	 AG	73753-73933	GT	CGG
(AGA)	 AG	74140-74369	AT	ACA
-recovered pasa_asmbl_6416.p1, internal, 73016, 73117
-recovered pasa_asmbl_6416.p1, internal, 73753, 73933
Valid prediction for GeneMark_model.46717_t
Couldn't classify 83948, 84078
Couldn't classify 84262, 84372
Couldn't classify 84517, 84571
Sorry, prediction CodingQuarry_transcript_7945-T1 fails validation.
(ATG)	 AA	83948-84078	CT	ACC
(CTG)	 AC	84262-84372	CT	ACC
(CTG)	 AC	84517-84571	GA	GAG
Valid prediction for Augustus_model.g18077.t1
Valid prediction for GlimmerHMM_glimmerT_27052-T1
Valid prediction for GlimmerHMM_glimmerT_27048-T1
Valid prediction for Augustus_model.g18075.t1
Valid prediction for snap_scaffold_11-snap.394-T1
Valid prediction for GeneMark_model.46721_t
Valid prediction for snap_scaffold_11-snap.370-T1
Valid prediction for snap_scaffold_11-snap.390-T1
Valid prediction for GeneMark_model.46724_t
Valid prediction for GeneMark_model.46725_t
Valid prediction for GeneMark_model.46714_t
Valid prediction for snap_scaffold_11-snap.400-T1
Valid prediction for snap_scaffold_11-snap.382-T1
Valid prediction for GlimmerHMM_glimmerT_27063-T1
Valid prediction for GeneMark_model.46735_t
Valid prediction for GeneMark_model.46732_t
Valid prediction for snap_scaffold_11-snap.376-T1
Valid prediction for snap_scaffold_11-snap.377-T1
Valid prediction for HiQ_model.g18084.t1
Valid prediction for snap_scaffold_11-snap.385-T1
Valid prediction for GlimmerHMM_glimmerT_27051-T1
Valid prediction for GeneMark_model.46722_t
Valid prediction for snap_scaffold_11-snap.401-T1
Valid prediction for GlimmerHMM_glimmerT_27057-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10953, rend_intergenic: 8482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38596, rend_intergenic: 25706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47936, rend_intergenic: 46347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54801, rend_intergenic: 53863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59205, rend_intergenic: 56141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65732, rend_intergenic: 62572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78020, rend_intergenic: 75637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92099, rend_intergenic: 84857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97069, rend_intergenic: 95578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 106503
-exon list size: 419


building trellis

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26.4    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.0    
28.3    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
29.9    
30.2    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
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34.9    
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35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.2    
43.5    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.1    
45.4    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
48.0    
48.2    
48.5    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.5    
51.8    
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52.3    
52.5    
52.7    
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53.9    
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55.6    
55.8    
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56.5    
56.8    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
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59.6    
59.9    
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60.8    
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64.4    
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73.9    
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77.2    
77.4    
77.7    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.2    
82.4    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.9    
88.1    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.5    
94.8    
95.0    
95.2    
95.5    
95.7    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 12 predictions from path traversal
Error with prediction: snap lend_intergenic: 10953, rend_intergenic: 8482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38596, rend_intergenic: 25706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47936, rend_intergenic: 46347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54801, rend_intergenic: 53863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59205, rend_intergenic: 56141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65732, rend_intergenic: 62572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78020, rend_intergenic: 75637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92099, rend_intergenic: 84857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97069, rend_intergenic: 95578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21917
-exon list size: 79


building trellis

1.2    
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12.3    
13.6    
14.8    
16.0    
17.3    
18.5    
19.8    
21.0    
22.2    
23.5    
24.7    
25.9    
27.2    
28.4    
29.6    
30.9    
32.1    
33.3    
34.6    
35.8    
37.0    
38.3    
39.5    
40.7    
42.0    
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44.4    
45.7    
46.9    
48.1    
49.4    
50.6    
51.9    
53.1    
54.3    
55.6    
56.8    
58.0    
59.3    
60.5    
61.7    
63.0    
64.2    
65.4    
66.7    
67.9    
69.1    
70.4    
71.6    
72.8    
74.1    
75.3    
76.5    
77.8    
79.0    
80.2    
81.5    
82.7    
84.0    
85.2    
86.4    
87.7    
88.9    
90.1    
91.4    
92.6    
93.8    
95.1    
96.3    
97.5    
98.8    
-found 7 predictions from path traversal
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 4 predictions persist after filtering for low support