-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_11835229-12071562

-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_1-snap.2075-T1
Valid prediction for snap_scaffold_1-snap.2059-T1
Valid prediction for snap_scaffold_1-snap.2070-T1
Valid prediction for GlimmerHMM_glimmerT_1590-T1
Couldn't classify 68769, 68843
Sorry, prediction pasa_asmbl_2163.p1 fails validation.
(GTC)	 TA	68769-68843	GT	GGG
(TTT)	 AG	68949-69073	GT	AGG
(TGT)	 AG	69162-69354	GT	AGG
(GAG)	 AG	69453-69842	AC	AGA
-recovered pasa_asmbl_2163.p1, terminal, 69453, 69842
-recovered pasa_asmbl_2163.p1, internal, 68949, 69073
-recovered pasa_asmbl_2163.p1, internal, 69162, 69354
Valid prediction for CodingQuarry_transcript_2813-T1
Valid prediction for Augustus_model.g1173.t1
Valid prediction for snap_scaffold_1-snap.2064-T1
Couldn't classify 59240, 59323
Sorry, prediction pasa_asmbl_2161.p1 fails validation.
(CAG)	 AC	59240-59323	GT	AGG
(GAA)	 AG	59690-59792	GT	TGG
(GAA)	 AG	59889-59920	GT	CTG
(ATG)	 AG	60133-60207	GT	AGG
(AAT)	 AG	60302-60407	GT	AGG
(CTG)	 AG	60502-60581	TC	AGT
-recovered pasa_asmbl_2161.p1, initial, 60133, 60207
-recovered pasa_asmbl_2161.p1, terminal, 60502, 60581
-recovered pasa_asmbl_2161.p1, internal, 59690, 59792
-recovered pasa_asmbl_2161.p1, internal, 59889, 59920
-recovered pasa_asmbl_2161.p1, internal, 60133, 60207
-recovered pasa_asmbl_2161.p1, internal, 60302, 60407
Valid prediction for snap_scaffold_1-snap.2046-T1
Valid prediction for Augustus_model.g1184.t1
Valid prediction for GlimmerHMM_glimmerT_1580-T1
Couldn't classify 103446, 103469
Sorry, prediction pasa_asmbl_2169.p1 fails validation.
(CTA)	 CT	103446-103469	GT	AGG
(ATC)	 AG	103561-103735	GT	GGG
(ATC)	 AG	103991-104114	GT	AGG
(TGC)	 AG	104328-104580	GG	GAG
-recovered pasa_asmbl_2169.p1, terminal, 104328, 104580
-recovered pasa_asmbl_2169.p1, internal, 103561, 103735
-recovered pasa_asmbl_2169.p1, internal, 103991, 104114
Valid prediction for pasa_asmbl_2172.p1
Valid prediction for GlimmerHMM_glimmerT_1581-T1
Valid prediction for snap_scaffold_1-snap.2080-T1
Valid prediction for Augustus_model.g1186.t1
Valid prediction for Augustus_model.g1174.t1
Valid prediction for HiQ_model.g1169.t1
Valid prediction for Augustus_model.g1171.t1
Valid prediction for Augustus_model.g1187.t1
Valid prediction for GlimmerHMM_glimmerT_1584-T1
Couldn't classify 44893, 45011
Sorry, prediction pasa_asmbl_2763.p1 fails validation.
(GGC)	 AA	44893-45011	GC	AGG
(CTG)	 AG	45531-45744	CA	AGC
-recovered pasa_asmbl_2763.p1, terminal, 45531, 45744
Valid prediction for pasa_asmbl_2166.p1
Valid prediction for snap_scaffold_1-snap.2078-T1
Valid prediction for snap_scaffold_1-snap.2054-T1
Valid prediction for Augustus_model.g1183.t1
Valid prediction for snap_scaffold_1-snap.2053-T1
Valid prediction for GlimmerHMM_glimmerT_1597-T1
Valid prediction for snap_scaffold_1-snap.2065-T1
Couldn't classify 98005, 98058
Couldn't classify 101815, 101867
Sorry, prediction pasa_asmbl_2168.p1 fails validation.
(CCG)	 CT	98005-98058	GT	CGG
(GGC)	 AG	98167-98294	GT	AGG
(GAT)	 AG	98550-98664	GT	AGG
(GCC)	 AG	98867-99068	GT	AGG
(TGG)	 AG	99330-99442	GT	AGG
(CAC)	 AG	100452-100532	GT	AGG
(GGG)	 AG	100817-100940	GT	TGG
(GTG)	 AG	101075-101196	GT	ACG
(GTC)	 AG	101366-101477	GT	AGG
(ATG)	 AG	101815-101867	AT	AGA
-recovered pasa_asmbl_2168.p1, internal, 98167, 98294
-recovered pasa_asmbl_2168.p1, internal, 98550, 98664
-recovered pasa_asmbl_2168.p1, internal, 98867, 99068
-recovered pasa_asmbl_2168.p1, internal, 99330, 99442
-recovered pasa_asmbl_2168.p1, internal, 100452, 100532
-recovered pasa_asmbl_2168.p1, internal, 100817, 100940
-recovered pasa_asmbl_2168.p1, internal, 101075, 101196
-recovered pasa_asmbl_2168.p1, internal, 101366, 101477
Couldn't classify 77360, 77473
Couldn't classify 77648, 77701
Sorry, prediction CodingQuarry_transcript_2812-T1 fails validation.
(ATG)	 AA	74618-74665	GT	AGG
(AGA)	 AG	74749-74845	GT	AGG
(ACC)	 AG	75009-75136	GT	CGG
(CTT)	 AG	75226-75366	GT	TGG
(GAG)	 AG	75707-75864	GT	AGG
(TTC)	 AG	76019-76115	GT	CAG
(CTG)	 AG	76226-76345	GT	TGG
(CGA)	 AG	76566-76700	GT	AGG
(GTG)	 AG	76931-77119	GT	CTG
(AAT)	 AG	77360-77473	AC	TGA
(TCT)	 TT	77648-77701	GC	GAG
-recovered CodingQuarry_transcript_2812-T1, initial, 74618, 74665
-recovered CodingQuarry_transcript_2812-T1, internal, 74749, 74845
-recovered CodingQuarry_transcript_2812-T1, internal, 75009, 75136
-recovered CodingQuarry_transcript_2812-T1, internal, 75226, 75366
-recovered CodingQuarry_transcript_2812-T1, internal, 75707, 75864
-recovered CodingQuarry_transcript_2812-T1, internal, 76019, 76115
-recovered CodingQuarry_transcript_2812-T1, internal, 76226, 76345
-recovered CodingQuarry_transcript_2812-T1, internal, 76566, 76700
-recovered CodingQuarry_transcript_2812-T1, internal, 76931, 77119
Valid prediction for snap_scaffold_1-snap.2049-T1
Valid prediction for HiQ_model.g1179.t1
Valid prediction for Augustus_model.g1191.t1
Valid prediction for snap_scaffold_1-snap.2056-T1
Valid prediction for pasa_asmbl_2733.p1
Valid prediction for HiQ_model.g1172.t1
Valid prediction for GlimmerHMM_glimmerT_1577-T1
Valid prediction for snap_scaffold_1-snap.2066-T1
Valid prediction for snap_scaffold_1-snap.2068-T1
Valid prediction for GlimmerHMM_glimmerT_1576-T1
Valid prediction for GlimmerHMM_glimmerT_1578-T1
Valid prediction for snap_scaffold_1-snap.2050-T1
Valid prediction for Augustus_model.g1185.t1
Valid prediction for snap_scaffold_1-snap.2062-T1
Valid prediction for GlimmerHMM_glimmerT_1587-T1
Valid prediction for snap_scaffold_1-snap.2052-T1
Valid prediction for Augustus_model.g1170.t1
Valid prediction for GlimmerHMM_glimmerT_1583-T1
Valid prediction for snap_scaffold_1-snap.2073-T1
Valid prediction for snap_scaffold_1-snap.2076-T1
Valid prediction for snap_scaffold_1-snap.2051-T1
Valid prediction for snap_scaffold_1-snap.2071-T1
Valid prediction for Augustus_model.g1178.t1
Valid prediction for GlimmerHMM_glimmerT_1596-T1
Valid prediction for GlimmerHMM_glimmerT_1582-T1
Valid prediction for HiQ_model.g1175.t1
Valid prediction for snap_scaffold_1-snap.2055-T1
Valid prediction for snap_scaffold_1-snap.2047-T1
Valid prediction for CodingQuarry_transcript_2811-T1
Valid prediction for CodingQuarry_transcript_2810-T1
Valid prediction for GlimmerHMM_glimmerT_1588-T1
Valid prediction for Augustus_model.g1177.t1
Valid prediction for GlimmerHMM_glimmerT_1575-T1
Valid prediction for GlimmerHMM_glimmerT_1589-T1
Valid prediction for GlimmerHMM_glimmerT_1579-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 CodingQuarry_transcript_2817-T1
Valid prediction for GlimmerHMM_glimmerT_1574-T1
Valid prediction for snap_scaffold_1-snap.2069-T1
Valid prediction for snap_scaffold_1-snap.2048-T1
Valid prediction for snap_scaffold_1-snap.2063-T1
Valid prediction for GlimmerHMM_glimmerT_1573-T1
Valid prediction for snap_scaffold_1-snap.2044-T1
Valid prediction for HiQ_model.g1181.t1
Valid prediction for Augustus_model.g1167.t1
Valid prediction for CodingQuarry_transcript_2816-T1
Valid prediction for Augustus_model.g1168.t1
Valid prediction for GlimmerHMM_glimmerT_1598-T1
Valid prediction for pasa_asmbl_679.p1
Valid prediction for GlimmerHMM_glimmerT_1594-T1
Valid prediction for snap_scaffold_1-snap.2074-T1
Valid prediction for snap_scaffold_1-snap.2067-T1
Valid prediction for GlimmerHMM_glimmerT_1591-T1
Valid prediction for GlimmerHMM_glimmerT_1595-T1
Valid prediction for snap_scaffold_1-snap.2072-T1
Valid prediction for GlimmerHMM_glimmerT_1586-T1
Valid prediction for snap_scaffold_1-snap.2058-T1
Valid prediction for Augustus_model.g1180.t1
Valid prediction for snap_scaffold_1-snap.2045-T1
Valid prediction for CodingQuarry_transcript_2815-T1
Valid prediction for Augustus_model.g1190.t1
Valid prediction for GlimmerHMM_glimmerT_1585-T1
Valid prediction for snap_scaffold_1-snap.2061-T1
Valid prediction for Augustus_model.g1176.t1
Valid prediction for HiQ_model.g1192.t1
Valid prediction for CodingQuarry_transcript_2814-T1
Valid prediction for snap_scaffold_1-snap.2057-T1
Valid prediction for Augustus_model.g1189.t1
Valid prediction for pasa_asmbl_677.p1
Valid prediction for snap_scaffold_1-snap.2077-T1
Valid prediction for pasa_asmbl_683.p2
Valid prediction for HiQ_model.g1193.t1
Valid prediction for snap_scaffold_1-snap.2060-T1
Valid prediction for Augustus_model.g1182.t1
Valid prediction for pasa_asmbl_684.p2
Valid prediction for GlimmerHMM_glimmerT_1592-T1
Valid prediction for GlimmerHMM_glimmerT_1593-T1
Valid prediction for Augustus_model.g1188.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28358, rend_intergenic: 25084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32785, rend_intergenic: 30077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85101, rend_intergenic: 82428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104580, rend_intergenic: 85346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130237, rend_intergenic: 124031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176729, rend_intergenic: 171354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181483, rend_intergenic: 177724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188363, rend_intergenic: 184178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192466, rend_intergenic: 189286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195314, rend_intergenic: 192657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200649, rend_intergenic: 195394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 236334
-exon list size: 500


building trellis

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20.1    
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27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
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37.1    
37.3    
37.5    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
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40.8    
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41.2    
41.4    
41.6    
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42.0    
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42.8    
43.0    
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43.8    
44.0    
44.2    
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44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
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46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.2    
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48.6    
48.8    
49.0    
49.2    
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49.6    
49.8    
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55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
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58.4    
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58.8    
59.0    
59.2    
59.4    
59.6    
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60.8    
61.0    
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61.6    
61.8    
62.0    
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62.7    
62.9    
63.1    
63.3    
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63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
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65.9    
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67.1    
67.3    
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68.1    
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68.9    
69.1    
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71.1    
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73.1    
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73.9    
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76.9    
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79.1    
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80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
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81.9    
82.1    
82.3    
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82.9    
83.1    
83.3    
83.5    
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84.1    
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84.7    
84.9    
85.1    
85.3    
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85.9    
86.1    
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86.9    
87.1    
87.3    
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87.6    
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88.0    
88.2    
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88.6    
88.8    
89.0    
89.2    
89.4    
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89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
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95.0    
95.2    
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96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
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98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 28358, rend_intergenic: 25084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32785, rend_intergenic: 30077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85101, rend_intergenic: 82428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104580, rend_intergenic: 85346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130237, rend_intergenic: 124031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176729, rend_intergenic: 171354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181483, rend_intergenic: 177724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188363, rend_intergenic: 184178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192466, rend_intergenic: 189286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195314, rend_intergenic: 192657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200649, rend_intergenic: 195394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13381
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 - 13065
-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