-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_6549054-6757785

-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.48136_t
Valid prediction for snap_scaffold_11-snap.1559-T1
Valid prediction for GeneMark_model.48118_t
Valid prediction for GeneMark_model.48109_t
Valid prediction for GlimmerHMM_glimmerT_27854-T1
Valid prediction for GeneMark_model.48098_t
Valid prediction for snap_scaffold_11-snap.1576-T1
Valid prediction for snap_scaffold_11-snap.1567-T1
Valid prediction for snap_scaffold_11-snap.1557-T1
Valid prediction for GeneMark_model.48121_t
Valid prediction for GeneMark_model.48124_t
Valid prediction for snap_scaffold_11-snap.1570-T1
Valid prediction for Augustus_model.g18579.t1
Valid prediction for GeneMark_model.48132_t
Valid prediction for snap_scaffold_11-snap.1548-T1
Valid prediction for snap_scaffold_11-snap.1574-T1
Valid prediction for snap_scaffold_11-snap.1572-T1
Valid prediction for snap_scaffold_11-snap.1549-T1
Valid prediction for GeneMark_model.48130_t
Valid prediction for Augustus_model.g18568.t1
Valid prediction for snap_scaffold_11-snap.1583-T1
Valid prediction for GeneMark_model.48108_t
Valid prediction for GlimmerHMM_glimmerT_27858-T1
Valid prediction for GeneMark_model.48106_t
Valid prediction for snap_scaffold_11-snap.1568-T1
Valid prediction for GeneMark_model.48097_t
Valid prediction for Augustus_model.g18583.t1
Valid prediction for GeneMark_model.48103_t
Valid prediction for GeneMark_model.48128_t
Valid prediction for snap_scaffold_11-snap.1560-T1
Valid prediction for GeneMark_model.48114_t
Valid prediction for GlimmerHMM_glimmerT_27843-T1
Valid prediction for snap_scaffold_11-snap.1550-T1
Valid prediction for GeneMark_model.48111_t
Valid prediction for GeneMark_model.48122_t
Valid prediction for snap_scaffold_11-snap.1551-T1
Valid prediction for snap_scaffold_11-snap.1575-T1
Valid prediction for GeneMark_model.48120_t
Valid prediction for Augustus_model.g18577.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.1579-T1
Valid prediction for GlimmerHMM_glimmerT_27861-T1
Valid prediction for GeneMark_model.48115_t
Valid prediction for GlimmerHMM_glimmerT_27862-T1
Valid prediction for GlimmerHMM_glimmerT_27849-T1
Valid prediction for snap_scaffold_11-snap.1562-T1
Valid prediction for GlimmerHMM_glimmerT_27846-T1
Valid prediction for GeneMark_model.48137_t
Valid prediction for GeneMark_model.48100_t
Valid prediction for GeneMark_model.48099_t
Valid prediction for Augustus_model.g18571.t1
Valid prediction for snap_scaffold_11-snap.1573-T1
Valid prediction for GlimmerHMM_glimmerT_27851-T1
Valid prediction for GlimmerHMM_glimmerT_27844-T1
Valid prediction for GeneMark_model.48116_t
Valid prediction for GlimmerHMM_glimmerT_27852-T1
Couldn't classify 110725, 110800
Couldn't classify 111165, 111993
Sorry, prediction pasa_asmbl_6707.p1 fails validation.
(AAG)	 TC	110725-110800	GT	AGG
(GGG)	 AG	110975-111080	GT	AAG
(TTC)	 AG	111165-111993	TC	CGT
-recovered pasa_asmbl_6707.p1, internal, 110975, 111080
Valid prediction for GeneMark_model.48110_t
Valid prediction for CodingQuarry_transcript_8066-T1
Valid prediction for GeneMark_model.48125_t
Valid prediction for Augustus_model.g18574.t1
Valid prediction for GeneMark_model.48107_t
Valid prediction for GeneMark_model.48134_t
Valid prediction for GlimmerHMM_glimmerT_27859-T1
Valid prediction for CodingQuarry_transcript_8072-T1
Valid prediction for CodingQuarry_transcript_8067-T1
Valid prediction for Augustus_model.g18572.t1
Valid prediction for GeneMark_model.48123_t
Valid prediction for HiQ_model.g18576.t1
Valid prediction for GlimmerHMM_glimmerT_27855-T1
Valid prediction for snap_scaffold_11-snap.1565-T1
Valid prediction for Augustus_model.g18569.t1
Valid prediction for CodingQuarry_transcript_8073-T1
Valid prediction for GeneMark_model.48129_t
Valid prediction for GeneMark_model.48126_t
Valid prediction for CodingQuarry_transcript_8068-T1
Valid prediction for GeneMark_model.48104_t
Valid prediction for snap_scaffold_11-snap.1582-T1
Valid prediction for GeneMark_model.48119_t
Couldn't classify 112524, 114026
Sorry, prediction pasa_asmbl_6706.p1 fails validation.
(GCT)	 CA	112524-114026	AA	AAA
Valid prediction for snap_scaffold_11-snap.1555-T1
Valid prediction for snap_scaffold_11-snap.1581-T1
Valid prediction for GeneMark_model.48105_t
Valid prediction for CodingQuarry_transcript_8069-T1
Couldn't classify 149393, 149701
Sorry, prediction pasa_asmbl_6703.p2 fails validation.
(ATG)	 CA	144072-144149	GT	TGG
(AGC)	 AG	146516-146605	GT	CTG
(CAG)	 AG	149393-149701	GA	TGG
-recovered pasa_asmbl_6703.p2, initial, 144072, 144149
-recovered pasa_asmbl_6703.p2, internal, 146516, 146605
Valid prediction for GlimmerHMM_glimmerT_27847-T1
Valid prediction for snap_scaffold_11-snap.1580-T1
Valid prediction for GlimmerHMM_glimmerT_27845-T1
Valid prediction for GeneMark_model.48131_t
Valid prediction for GeneMark_model.48113_t
Couldn't classify 159803, 160096
Couldn't classify 160352, 160375
Sorry, prediction pasa_asmbl_6702.p1 fails validation.
(CAT)	 AC	159803-160096	GT	AGG
(GAT)	 AG	160352-160375	GA	GGG
Valid prediction for snap_scaffold_11-snap.1553-T1
Valid prediction for snap_scaffold_11-snap.1556-T1
Valid prediction for Augustus_model.g18573.t1
Valid prediction for pasa_asmbl_6710.p1
Valid prediction for Augustus_model.g18581.t1
Valid prediction for Augustus_model.g18570.t1
Valid prediction for snap_scaffold_11-snap.1554-T1
Valid prediction for GlimmerHMM_glimmerT_27853-T1
Valid prediction for CodingQuarry_transcript_8070-T1
Valid prediction for Augustus_model.g18575.t1
Valid prediction for pasa_asmbl_6699.p1
Valid prediction for GlimmerHMM_glimmerT_27860-T1
Valid prediction for GeneMark_model.48127_t
Valid prediction for GeneMark_model.48102_t
Valid prediction for GeneMark_model.48112_t
Valid prediction for snap_scaffold_11-snap.1564-T1
Valid prediction for snap_scaffold_11-snap.1566-T1
Valid prediction for snap_scaffold_11-snap.1578-T1
Valid prediction for GlimmerHMM_glimmerT_27850-T1
Valid prediction for snap_scaffold_11-snap.1552-T1
Couldn't classify 42801, 42893
Sorry, prediction pasa_asmbl_6713.p1 fails validation.
(GCG)	 AT	42801-42893	GT	CAG
(CTT)	 AG	43448-43564	GT	AGG
(ACT)	 AG	43752-43973	GT	AGG
(ATT)	 AG	44569-44665	GT	GGG
(AGA)	 AG	45133-45198	GT	AGG
(TCA)	 AG	45396-45563	GT	AGG
(AAG)	 AG	45714-45811	GT	ACG
(AGT)	 AG	46250-46288	GT	AGG
(GGC)	 AG	46430-46537	TC	GAT
-recovered pasa_asmbl_6713.p1, terminal, 46430, 46537
-recovered pasa_asmbl_6713.p1, internal, 43448, 43564
-recovered pasa_asmbl_6713.p1, internal, 43752, 43973
-recovered pasa_asmbl_6713.p1, internal, 44569, 44665
-recovered pasa_asmbl_6713.p1, internal, 45133, 45198
-recovered pasa_asmbl_6713.p1, internal, 45396, 45563
-recovered pasa_asmbl_6713.p1, internal, 45714, 45811
-recovered pasa_asmbl_6713.p1, internal, 46250, 46288
Valid prediction for snap_scaffold_11-snap.1571-T1
Valid prediction for snap_scaffold_11-snap.1561-T1
Valid prediction for snap_scaffold_11-snap.1563-T1
Valid prediction for GeneMark_model.48135_t
Valid prediction for pasa_asmbl_6697.p1
Valid prediction for Augustus_model.g18578.t1
Valid prediction for GeneMark_model.48117_t
Valid prediction for HiQ_model.g18580.t1
Valid prediction for snap_scaffold_11-snap.1569-T1
Valid prediction for snap_scaffold_11-snap.1577-T1
Valid prediction for GlimmerHMM_glimmerT_27857-T1
Valid prediction for Augustus_model.g18582.t1
Valid prediction for GlimmerHMM_glimmerT_27856-T1
Valid prediction for GlimmerHMM_glimmerT_27848-T1
Valid prediction for snap_scaffold_11-snap.1558-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 60151, rend_intergenic: 57334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78428, rend_intergenic: 75201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127554, rend_intergenic: 123083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145155, rend_intergenic: 144059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150411, rend_intergenic: 146204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159065, rend_intergenic: 156417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208732
-exon list size: 552


building trellis

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25.3    
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25.8    
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27.6    
27.8    
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28.2    
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28.5    
28.7    
28.9    
29.1    
29.2    
29.4    
29.6    
29.8    
30.0    
30.1    
30.3    
30.5    
30.7    
30.9    
31.0    
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31.8    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.0    
33.2    
33.4    
33.6    
33.8    
33.9    
34.1    
34.3    
34.5    
34.7    
34.8    
35.0    
35.2    
35.4    
35.6    
35.7    
35.9    
36.1    
36.3    
36.5    
36.6    
36.8    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.1    
38.3    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.5    
39.7    
39.9    
40.1    
40.3    
40.4    
40.6    
40.8    
41.0    
41.2    
41.3    
41.5    
41.7    
41.9    
42.1    
42.2    
42.4    
42.6    
42.8    
43.0    
43.1    
43.3    
43.5    
43.7    
43.9    
44.0    
44.2    
44.4    
44.6    
44.8    
44.9    
45.1    
45.3    
45.5    
45.7    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
46.9    
47.1    
47.3    
47.5    
47.7    
47.8    
48.0    
48.2    
48.4    
48.6    
48.7    
48.9    
49.1    
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49.8    
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50.2    
50.4    
50.5    
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50.9    
51.1    
51.3    
51.4    
51.6    
51.8    
52.0    
52.2    
52.3    
52.5    
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52.9    
53.1    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
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54.9    
55.1    
55.2    
55.4    
55.6    
55.8    
56.0    
56.1    
56.3    
56.5    
56.7    
56.9    
57.0    
57.2    
57.4    
57.6    
57.8    
57.9    
58.1    
58.3    
58.5    
58.7    
58.8    
59.0    
59.2    
59.4    
59.6    
59.7    
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60.1    
60.3    
60.5    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.7    
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62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.2    
63.4    
63.5    
63.7    
63.9    
64.1    
64.3    
64.4    
64.6    
64.8    
65.0    
65.2    
65.3    
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65.7    
65.9    
66.1    
66.2    
66.4    
66.6    
66.8    
67.0    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
69.0    
69.1    
69.3    
69.5    
69.7    
69.9    
70.0    
70.2    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.3    
77.4    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.5    
86.6    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 60151, rend_intergenic: 57334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78428, rend_intergenic: 75201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127554, rend_intergenic: 123083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145155, rend_intergenic: 144059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150411, rend_intergenic: 146204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159065, rend_intergenic: 156417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13590
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-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 - 13292
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 1 predictions from path traversal

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