-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_7831609-8030306

-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_6-snap.1749-T1
Valid prediction for HiQ_model.g9966.t1
Valid prediction for Augustus_model.g9946.t1
Valid prediction for GlimmerHMM_glimmerT_15018-T1
Valid prediction for GlimmerHMM_glimmerT_15021-T1
Valid prediction for snap_scaffold_6-snap.1745-T1
Valid prediction for snap_scaffold_6-snap.1763-T1
Valid prediction for HiQ_model.g9952.t1
Valid prediction for snap_scaffold_6-snap.1734-T1
Valid prediction for GlimmerHMM_glimmerT_15032-T1
Valid prediction for snap_scaffold_6-snap.1765-T1
Valid prediction for GlimmerHMM_glimmerT_15038-T1
Valid prediction for snap_scaffold_6-snap.1738-T1
Valid prediction for snap_scaffold_6-snap.1737-T1
Valid prediction for snap_scaffold_6-snap.1761-T1
Valid prediction for snap_scaffold_6-snap.1769-T1
Valid prediction for Augustus_model.g9959.t1
Valid prediction for GlimmerHMM_glimmerT_15017-T1
Valid prediction for pasa_asmbl_47088.p2
Valid prediction for pasa_asmbl_47089.p1
Valid prediction for snap_scaffold_6-snap.1748-T1
Valid prediction for snap_scaffold_6-snap.1752-T1
Valid prediction for GlimmerHMM_glimmerT_15015-T1
Valid prediction for snap_scaffold_6-snap.1743-T1
Couldn't classify 179863, 179923
Couldn't classify 180108, 180166
Sorry, prediction pasa_asmbl_47090.p1 fails validation.
(ATG)	 AA	179863-179923	AT	GAA
(AGC)	 AC	180108-180166	GT	CGG
(GTT)	 AG	180289-180405	GT	TTG
(TTT)	 AG	180585-180700	GT	AGG
(GGA)	 AG	180827-180992	CC	GAC
-recovered pasa_asmbl_47090.p1, terminal, 180827, 180992
-recovered pasa_asmbl_47090.p1, internal, 180289, 180405
-recovered pasa_asmbl_47090.p1, internal, 180585, 180700
Valid prediction for Augustus_model.g9960.t1
Valid prediction for GlimmerHMM_glimmerT_15023-T1
Valid prediction for snap_scaffold_6-snap.1770-T1
Valid prediction for snap_scaffold_6-snap.1774-T1
Valid prediction for Augustus_model.g9963.t1
Valid prediction for GlimmerHMM_glimmerT_15030-T1
Valid prediction for snap_scaffold_6-snap.1750-T1
Valid prediction for CodingQuarry_transcript_55113-T1
Valid prediction for snap_scaffold_6-snap.1771-T1
Valid prediction for Augustus_model.g9950.t1
Valid prediction for Augustus_model.g9951.t1
Valid prediction for CodingQuarry_transcript_55112-T1
Valid prediction for GlimmerHMM_glimmerT_15035-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 Augustus_model.g9955.t1
Valid prediction for CodingQuarry_transcript_55116-T1
Valid prediction for GlimmerHMM_glimmerT_15022-T1
Couldn't classify 73679, 74003
Sorry, prediction pasa_asmbl_48519.p1 fails validation.
(ATG)	 AC	71691-71788	GT	AGG
(TGG)	 AG	73679-74003	AT	AGA
-recovered pasa_asmbl_48519.p1, initial, 71691, 71788
Valid prediction for Augustus_model.g9961.t1
Couldn't classify 77457, 77460
Sorry, prediction pasa_asmbl_48518.p1 fails validation.
(TTT)	 AC	77457-77460	GT	TGG
(TGG)	 AG	77617-77930	GC	GAG
-recovered pasa_asmbl_48518.p1, terminal, 77617, 77930
-recovered pasa_asmbl_48518.p1, internal, 77617, 77930
Valid prediction for snap_scaffold_6-snap.1756-T1
Valid prediction for Augustus_model.g9945.t1
Couldn't classify 8420, 8899
Sorry, prediction pasa_asmbl_48528.p1 fails validation.
(ATG)	 AC	8420-8899	CG	GGC
Valid prediction for snap_scaffold_6-snap.1776-T1
Valid prediction for snap_scaffold_6-snap.1746-T1
Valid prediction for Augustus_model.g9953.t1
Valid prediction for snap_scaffold_6-snap.1764-T1
Valid prediction for GlimmerHMM_glimmerT_15040-T1
Valid prediction for GlimmerHMM_glimmerT_15016-T1
Valid prediction for snap_scaffold_6-snap.1759-T1
Valid prediction for GlimmerHMM_glimmerT_15026-T1
Valid prediction for snap_scaffold_6-snap.1753-T1
Valid prediction for snap_scaffold_6-snap.1757-T1
Valid prediction for Augustus_model.g9958.t1
Valid prediction for Augustus_model.g9949.t1
Valid prediction for GlimmerHMM_glimmerT_15019-T1
Valid prediction for snap_scaffold_6-snap.1735-T1
Valid prediction for snap_scaffold_6-snap.1760-T1
Valid prediction for GlimmerHMM_glimmerT_15014-T1
Valid prediction for snap_scaffold_6-snap.1751-T1
Valid prediction for Augustus_model.g9967.t1
Couldn't classify 42160, 42207
Sorry, prediction pasa_asmbl_48521.p1 fails validation.
(TGT)	 CC	42160-42207	GT	GGG
(GTT)	 AG	42304-42425	GT	CGG
(GGT)	 AG	42571-42648	GT	GAG
(TCA)	 AG	42768-42857	GT	GTG
(GTT)	 AG	42972-43059	GT	TGG
(ATC)	 AG	43168-43277	GT	TGG
(GGA)	 AG	43388-43472	GT	AGG
(AGC)	 AG	43798-43812	AG	AGA
-recovered pasa_asmbl_48521.p1, terminal, 43798, 43812
-recovered pasa_asmbl_48521.p1, internal, 42304, 42425
-recovered pasa_asmbl_48521.p1, internal, 42571, 42648
-recovered pasa_asmbl_48521.p1, internal, 42768, 42857
-recovered pasa_asmbl_48521.p1, internal, 42972, 43059
-recovered pasa_asmbl_48521.p1, internal, 43168, 43277
-recovered pasa_asmbl_48521.p1, internal, 43388, 43472
Valid prediction for snap_scaffold_6-snap.1762-T1
Valid prediction for snap_scaffold_6-snap.1747-T1
Valid prediction for Augustus_model.g9948.t1
Valid prediction for snap_scaffold_6-snap.1767-T1
Valid prediction for GlimmerHMM_glimmerT_15024-T1
Couldn't classify 15196, 15229
Sorry, prediction pasa_asmbl_48527.p1 fails validation.
(AGC)	 CC	15196-15229	GT	AGG
(GTG)	 AG	15312-15380	GT	GGG
(ATG)	 AG	15473-15709	GT	AGG
(GAC)	 AG	15883-16178	GG	GAG
add_exon() Sorry, pasa_asmbl_48527.p1 15473-15709-initial-1 is invalid.
-recovered pasa_asmbl_48527.p1, initial, 15473, 15709
-recovered pasa_asmbl_48527.p1, terminal, 15883, 16178
-recovered pasa_asmbl_48527.p1, internal, 15312, 15380
-recovered pasa_asmbl_48527.p1, internal, 15473, 15709
Valid prediction for Augustus_model.g9964.t1
Couldn't classify 22211, 22272
Sorry, prediction pasa_asmbl_48523.p1 fails validation.
(ATG)	 CC	21766-21952	GT	GGG
(TCA)	 AG	22083-22133	GT	GGG
(AAT)	 AG	22211-22272	CA	CCC
-recovered pasa_asmbl_48523.p1, initial, 21766, 21952
-recovered pasa_asmbl_48523.p1, internal, 22083, 22133
Valid prediction for Augustus_model.g9957.t1
Valid prediction for GlimmerHMM_glimmerT_15029-T1
Valid prediction for snap_scaffold_6-snap.1739-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.1754-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.1740-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g9944.t1
Valid prediction for GlimmerHMM_glimmerT_15028-T1
Valid prediction for Augustus_model.g9956.t1
Valid prediction for GlimmerHMM_glimmerT_15031-T1
Valid prediction for GlimmerHMM_glimmerT_15027-T1
Valid prediction for snap_scaffold_6-snap.1742-T1
Valid prediction for Augustus_model.g9962.t1
Valid prediction for snap_scaffold_6-snap.1736-T1
Valid prediction for snap_scaffold_6-snap.1773-T1
Valid prediction for snap_scaffold_6-snap.1755-T1
Valid prediction for GlimmerHMM_glimmerT_15033-T1
Valid prediction for Augustus_model.g9947.t1
Valid prediction for pasa_asmbl_48524.p1
Valid prediction for GlimmerHMM_glimmerT_15020-T1
Valid prediction for snap_scaffold_6-snap.1768-T1
Valid prediction for GlimmerHMM_glimmerT_15041-T1
Couldn't classify 22953, 22990
Couldn't classify 25411, 25477
Sorry, prediction pasa_asmbl_48522.p1 fails validation.
(GAC)	 GT	22953-22990	GT	AAG
(GTT)	 AG	23236-23368	GT	TGG
(GCA)	 AG	24155-24200	GT	CGG
(CCC)	 AG	24300-24432	GT	AGG
(ATA)	 AG	24542-24684	GT	CGG
(AGC)	 AG	24803-24863	GT	GGG
(AAT)	 AG	25120-25194	GT	AGG
(TTT)	 AG	25411-25477	CT	GCC
-recovered pasa_asmbl_48522.p1, internal, 23236, 23368
-recovered pasa_asmbl_48522.p1, internal, 24155, 24200
-recovered pasa_asmbl_48522.p1, internal, 24300, 24432
-recovered pasa_asmbl_48522.p1, internal, 24542, 24684
-recovered pasa_asmbl_48522.p1, internal, 24803, 24863
-recovered pasa_asmbl_48522.p1, internal, 25120, 25194
Valid prediction for snap_scaffold_6-snap.1775-T1
Valid prediction for snap_scaffold_6-snap.1772-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for HiQ_model.g9965.t1
Valid prediction for GlimmerHMM_glimmerT_15036-T1
Valid prediction for GlimmerHMM_glimmerT_15039-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for HiQ_model.g9954.t1
Valid prediction for snap_scaffold_6-snap.1758-T1
Valid prediction for pasa_asmbl_48511.p1
Valid prediction for GlimmerHMM_glimmerT_15025-T1
Valid prediction for snap_scaffold_6-snap.1741-T1
Valid prediction for CodingQuarry_transcript_55119-T1
Couldn't classify 35417, 35514
Sorry, prediction pasa_asmbl_48520.p1 fails validation.
(CTG)	 CA	35417-35514	GT	AGG
(GCC)	 AG	35696-35756	GT	AGG
(CTG)	 AG	35985-36007	GT	AGG
(GGG)	 AG	36108-36139	GT	AGG
(TCT)	 AG	36253-36315	GT	CGG
(CTG)	 AG	36553-36629	GT	AGG
(GAG)	 AG	36749-36830	GT	GGG
(AGG)	 AG	36966-37084	GT	GGG
(ATC)	 AG	37224-37315	GT	CAG
(GGT)	 AG	37554-37694	GT	TGG
(GGT)	 AG	38352-38435	GT	CTG
(CGT)	 AG	38605-38763	GT	CTG
(GGA)	 AG	39906-40044	GT	CGG
(GTT)	 AG	42304-42425	GT	CGG
(GGT)	 AG	42571-42648	GT	GAG
(TCA)	 AG	42768-42857	GT	GTG
(GTT)	 AG	42972-43059	GT	TGG
(ATC)	 AG	43168-43277	GT	TGG
(GGA)	 AG	43388-43472	GT	AGG
(AGC)	 AG	43798-43812	AG	AGA
add_exon() Sorry, pasa_asmbl_48520.p1 35985-36007-terminal-2 is invalid.
-recovered pasa_asmbl_48520.p1, terminal, 35985, 36007
-recovered pasa_asmbl_48520.p1, terminal, 43798, 43812
-recovered pasa_asmbl_48520.p1, internal, 35696, 35756
-recovered pasa_asmbl_48520.p1, internal, 35985, 36007
-recovered pasa_asmbl_48520.p1, internal, 36108, 36139
-recovered pasa_asmbl_48520.p1, internal, 36253, 36315
-recovered pasa_asmbl_48520.p1, internal, 36553, 36629
-recovered pasa_asmbl_48520.p1, internal, 36749, 36830
-recovered pasa_asmbl_48520.p1, internal, 36966, 37084
-recovered pasa_asmbl_48520.p1, internal, 37224, 37315
-recovered pasa_asmbl_48520.p1, internal, 37554, 37694
-recovered pasa_asmbl_48520.p1, internal, 38352, 38435
-recovered pasa_asmbl_48520.p1, internal, 38605, 38763
-recovered pasa_asmbl_48520.p1, internal, 39906, 40044
-recovered pasa_asmbl_48520.p1, internal, 42304, 42425
-recovered pasa_asmbl_48520.p1, internal, 42571, 42648
-recovered pasa_asmbl_48520.p1, internal, 42768, 42857
-recovered pasa_asmbl_48520.p1, internal, 42972, 43059
-recovered pasa_asmbl_48520.p1, internal, 43168, 43277
-recovered pasa_asmbl_48520.p1, internal, 43388, 43472
Valid prediction for GlimmerHMM_glimmerT_15037-T1
Valid prediction for snap_scaffold_6-snap.1744-T1
Valid prediction for snap_scaffold_6-snap.1766-T1
Valid prediction for GlimmerHMM_glimmerT_15034-T1
Valid prediction for CodingQuarry_transcript_55115-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 95163, rend_intergenic: 93763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130357, rend_intergenic: 129775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135549, rend_intergenic: 133415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137513, rend_intergenic: 135587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144905, rend_intergenic: 137721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168766, rend_intergenic: 156970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198698
-exon list size: 416


building trellis

0.2    
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1.0    
1.2    
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3.6    
3.8    
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11.2    
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11.7    
12.0    
12.2    
12.4    
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13.6    
13.9    
14.1    
14.4    
14.6    
14.8    
15.1    
15.3    
15.6    
15.8    
16.0    
16.3    
16.5    
16.7    
17.0    
17.2    
17.5    
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17.9    
18.2    
18.4    
18.7    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
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21.3    
21.5    
21.8    
22.0    
22.2    
22.5    
22.7    
23.0    
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23.4    
23.7    
23.9    
24.2    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.8    
26.1    
26.3    
26.6    
26.8    
27.0    
27.3    
27.5    
27.8    
28.0    
28.2    
28.5    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.3    
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    
34.7    
34.9    
35.2    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.5    
54.8    
55.0    
55.3    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.4    
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62.9    
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63.9    
64.1    
64.4    
64.6    
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66.3    
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66.7    
67.0    
67.2    
67.5    
67.7    
67.9    
68.2    
68.4    
68.7    
68.9    
69.1    
69.4    
69.6    
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70.6    
70.8    
71.1    
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71.8    
72.0    
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73.0    
73.2    
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73.9    
74.2    
74.4    
74.6    
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75.1    
75.4    
75.6    
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76.1    
76.3    
76.6    
76.8    
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77.3    
77.5    
77.8    
78.0    
78.2    
78.5    
78.7    
78.9    
79.2    
79.4    
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79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
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82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
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84.9    
85.2    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
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87.1    
87.3    
87.6    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.1    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 95163, rend_intergenic: 93763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130357, rend_intergenic: 129775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135549, rend_intergenic: 133415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137513, rend_intergenic: 135587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144905, rend_intergenic: 137721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168766, rend_intergenic: 156970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support