-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_10022434-10216419

-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.g8251.t1
Valid prediction for Augustus_model.g8244.t1
Valid prediction for snap_scaffold_5-snap.1893-T1
Valid prediction for GlimmerHMM_glimmerT_12500-T1
Valid prediction for GlimmerHMM_glimmerT_12513-T1
Valid prediction for snap_scaffold_5-snap.1902-T1
Valid prediction for snap_scaffold_5-snap.1881-T1
Valid prediction for GlimmerHMM_glimmerT_12505-T1
Valid prediction for Augustus_model.g8254.t1
Valid prediction for Augustus_model.g8252.t1
Valid prediction for snap_scaffold_5-snap.1879-T1
Valid prediction for snap_scaffold_5-snap.1885-T1
Valid prediction for snap_scaffold_5-snap.1889-T1
Valid prediction for GlimmerHMM_glimmerT_12520-T1
Valid prediction for snap_scaffold_5-snap.1914-T1
Valid prediction for GlimmerHMM_glimmerT_12508-T1
Valid prediction for pasa_asmbl_45663.p1
Valid prediction for HiQ_model.g8253.t1
Valid prediction for GlimmerHMM_glimmerT_12518-T1
Valid prediction for pasa_asmbl_45665.p1
Valid prediction for snap_scaffold_5-snap.1906-T1
Valid prediction for GlimmerHMM_glimmerT_12516-T1
Valid prediction for pasa_asmbl_45656.p1
Valid prediction for GlimmerHMM_glimmerT_12531-T1
Valid prediction for GlimmerHMM_glimmerT_12521-T1
Valid prediction for GlimmerHMM_glimmerT_12523-T1
Valid prediction for Augustus_model.g8258.t1
Valid prediction for snap_scaffold_5-snap.1887-T1
Valid prediction for GlimmerHMM_glimmerT_12524-T1
Valid prediction for Augustus_model.g8246.t1
Valid prediction for snap_scaffold_5-snap.1905-T1
Valid prediction for Augustus_model.g8249.t1
Valid prediction for snap_scaffold_5-snap.1901-T1
Valid prediction for snap_scaffold_5-snap.1890-T1
Valid prediction for Augustus_model.g8257.t1
Valid prediction for Augustus_model.g8248.t1
Valid prediction for snap_scaffold_5-snap.1899-T1
Valid prediction for CodingQuarry_transcript_52201-T1
Valid prediction for HiQ_model.g8261.t1
Valid prediction for snap_scaffold_5-snap.1884-T1
Valid prediction for snap_scaffold_5-snap.1904-T1
Valid prediction for GlimmerHMM_glimmerT_12501-T1
Valid prediction for GlimmerHMM_glimmerT_12525-T1
Valid prediction for CodingQuarry_transcript_52200-T1
Valid prediction for Augustus_model.g8267.t1
Valid prediction for snap_scaffold_5-snap.1896-T1
Valid prediction for CodingQuarry_transcript_52199-T1
Valid prediction for pasa_asmbl_45661.p1
Valid prediction for Augustus_model.g8260.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_5-snap.1913-T1
Valid prediction for snap_scaffold_5-snap.1903-T1
Valid prediction for snap_scaffold_5-snap.1900-T1
Valid prediction for GlimmerHMM_glimmerT_12530-T1
Valid prediction for GlimmerHMM_glimmerT_12511-T1
Valid prediction for CodingQuarry_transcript_52202-T1
Valid prediction for snap_scaffold_5-snap.1891-T1
Valid prediction for GlimmerHMM_glimmerT_12515-T1
Valid prediction for GlimmerHMM_glimmerT_12503-T1
Valid prediction for snap_scaffold_5-snap.1892-T1
Valid prediction for snap_scaffold_5-snap.1912-T1
Valid prediction for snap_scaffold_5-snap.1880-T1
Valid prediction for GlimmerHMM_glimmerT_12517-T1
Valid prediction for CodingQuarry_transcript_52206-T1
Valid prediction for Augustus_model.g8263.t1
Valid prediction for snap_scaffold_5-snap.1888-T1
Valid prediction for HiQ_model.g8266.t1
Valid prediction for pasa_asmbl_44324.p1
Valid prediction for snap_scaffold_5-snap.1878-T1
Valid prediction for Augustus_model.g8245.t1
Valid prediction for GlimmerHMM_glimmerT_12509-T1
Valid prediction for snap_scaffold_5-snap.1907-T1
Valid prediction for GlimmerHMM_glimmerT_12527-T1
Valid prediction for GlimmerHMM_glimmerT_12514-T1
Valid prediction for GlimmerHMM_glimmerT_12504-T1
Valid prediction for snap_scaffold_5-snap.1894-T1
Valid prediction for Augustus_model.g8262.t1
Valid prediction for GlimmerHMM_glimmerT_12526-T1
Valid prediction for CodingQuarry_transcript_52205-T1
Valid prediction for GlimmerHMM_glimmerT_12519-T1
Valid prediction for GlimmerHMM_glimmerT_12528-T1
Couldn't classify 77987, 78037
Couldn't classify 78775, 78843
Sorry, prediction pasa_asmbl_44310.p1 fails validation.
(GTC)	 TA	77987-78037	GT	AAG
(TGG)	 AG	78486-78683	GT	AGG
(GAA)	 AG	78775-78843	AA	GCA
-recovered pasa_asmbl_44310.p1, internal, 78486, 78683
Valid prediction for snap_scaffold_5-snap.1910-T1
Valid prediction for GlimmerHMM_glimmerT_12522-T1
Valid prediction for GlimmerHMM_glimmerT_12502-T1
Valid prediction for Augustus_model.g8250.t1
Valid prediction for snap_scaffold_5-snap.1886-T1
Valid prediction for GlimmerHMM_glimmerT_12506-T1
Couldn't classify 32126, 32243
Sorry, prediction pasa_asmbl_44318.p1 fails validation.
(AGT)	 CC	32126-32243	GT	AGG
(CTT)	 AG	32444-32575	GT	AGG
(TAC)	 AG	32667-32736	GT	CGG
(GTC)	 AG	33157-33168	GT	AGG
(GAT)	 AG	33406-33441	GT	CGG
(AGA)	 AG	34037-34265	CT	AAC
-recovered pasa_asmbl_44318.p1, terminal, 34037, 34265
-recovered pasa_asmbl_44318.p1, internal, 32444, 32575
-recovered pasa_asmbl_44318.p1, internal, 32667, 32736
-recovered pasa_asmbl_44318.p1, internal, 33157, 33168
-recovered pasa_asmbl_44318.p1, internal, 33406, 33441
Valid prediction for snap_scaffold_5-snap.1883-T1
Valid prediction for snap_scaffold_5-snap.1909-T1
Valid prediction for Augustus_model.g8265.t1
Valid prediction for CodingQuarry_transcript_52204-T1
Valid prediction for snap_scaffold_5-snap.1882-T1
Valid prediction for GlimmerHMM_glimmerT_12529-T1
Valid prediction for snap_scaffold_5-snap.1908-T1
Valid prediction for pasa_asmbl_44328.p1
Valid prediction for snap_scaffold_5-snap.1895-T1
Valid prediction for Augustus_model.g8247.t1
Valid prediction for Augustus_model.g8264.t1
Valid prediction for GlimmerHMM_glimmerT_12510-T1
Couldn't classify 41784, 41863
Sorry, prediction pasa_asmbl_44317.p1 fails validation.
(CCC)	 AG	41784-41863	GT	AAG
(GCA)	 AG	41940-42063	GT	CAG
(GAT)	 AG	42161-42343	GT	AGG
(ATC)	 AG	42489-42605	GT	AGG
(GTT)	 AG	42720-42852	GT	TGG
(GAC)	 AG	42948-43402	AC	AAA
-recovered pasa_asmbl_44317.p1, terminal, 42948, 43402
-recovered pasa_asmbl_44317.p1, internal, 41784, 41863
-recovered pasa_asmbl_44317.p1, internal, 41940, 42063
-recovered pasa_asmbl_44317.p1, internal, 42161, 42343
-recovered pasa_asmbl_44317.p1, internal, 42489, 42605
-recovered pasa_asmbl_44317.p1, internal, 42720, 42852
Valid prediction for Augustus_model.g8256.t1
Valid prediction for GlimmerHMM_glimmerT_12512-T1
Valid prediction for Augustus_model.g8259.t1
Valid prediction for GlimmerHMM_glimmerT_12507-T1
Valid prediction for HiQ_model.g8255.t1
Valid prediction for Augustus_model.g8243.t1
Valid prediction for snap_scaffold_5-snap.1898-T1
Valid prediction for snap_scaffold_5-snap.1897-T1
Valid prediction for snap_scaffold_5-snap.1911-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 19870, rend_intergenic: 19867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8273, rend_intergenic: 7775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10366, rend_intergenic: 8413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14321, rend_intergenic: 10761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34546, rend_intergenic: 30156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72394, rend_intergenic: 69241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 193986
-exon list size: 376


building trellis

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28.0    
28.3    
28.6    
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29.4    
29.6    
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30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
45.0    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.8    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.0    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.4    
61.6    
61.9    
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62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.3    
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69.0    
69.3    
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70.1    
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73.3    
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74.1    
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74.6    
74.9    
75.1    
75.4    
75.7    
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76.2    
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77.0    
77.2    
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77.8    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
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79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 31 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 19870, rend_intergenic: 19867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8273, rend_intergenic: 7775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10366, rend_intergenic: 8413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14321, rend_intergenic: 10761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34546, rend_intergenic: 30156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72394, rend_intergenic: 69241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 182123 - 193986
-exon list size: 1


building trellis

33.3    
66.7    
-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