-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_8217154-8428680

-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.g36251.t1
Valid prediction for HiQ_model.g36250.t1
Valid prediction for snap_scaffold_25-snap.1807-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1810-T1
Valid prediction for snap_scaffold_25-snap.1814-T1
Valid prediction for Augustus_model.g36241.t1
Valid prediction for Augustus_model.g36259.t1
Valid prediction for GlimmerHMM_glimmerT_54653-T1
Valid prediction for snap_scaffold_25-snap.1811-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g36245.t1
Valid prediction for GlimmerHMM_glimmerT_54633-T1
Valid prediction for snap_scaffold_25-snap.1825-T1
Valid prediction for snap_scaffold_25-snap.1826-T1
Valid prediction for Augustus_model.g36260.t1
Valid prediction for snap_scaffold_25-snap.1827-T1
Valid prediction for GlimmerHMM_glimmerT_54645-T1
Valid prediction for Augustus_model.g36257.t1
Valid prediction for GlimmerHMM_glimmerT_54635-T1
Valid prediction for snap_scaffold_25-snap.1792-T1
Valid prediction for Augustus_model.g36249.t1
Valid prediction for Augustus_model.g36242.t1
Valid prediction for snap_scaffold_25-snap.1797-T1
Valid prediction for snap_scaffold_25-snap.1802-T1
Valid prediction for snap_scaffold_25-snap.1824-T1
Valid prediction for GlimmerHMM_glimmerT_54646-T1
Valid prediction for pasa_asmbl_33731.p1
Valid prediction for snap_scaffold_25-snap.1834-T1
Valid prediction for snap_scaffold_25-snap.1809-T1
Valid prediction for snap_scaffold_25-snap.1829-T1
Valid prediction for GlimmerHMM_glimmerT_54636-T1
Valid prediction for snap_scaffold_25-snap.1830-T1
Couldn't classify 172507, 172887
Sorry, prediction pasa_asmbl_34437.p2 fails validation.
(GAT)	 GT	172507-172887	TT	GAT
Valid prediction for GlimmerHMM_glimmerT_54657-T1
Valid prediction for GlimmerHMM_glimmerT_54648-T1
Valid prediction for CodingQuarry_transcript_38806-T1
Valid prediction for snap_scaffold_25-snap.1789-T1
Valid prediction for GlimmerHMM_glimmerT_54655-T1
Valid prediction for snap_scaffold_25-snap.1805-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_25-snap.1837-T1
Valid prediction for snap_scaffold_25-snap.1803-T1
Valid prediction for Augustus_model.g36253.t1
Valid prediction for GlimmerHMM_glimmerT_54658-T1
Valid prediction for GlimmerHMM_glimmerT_54644-T1
Valid prediction for snap_scaffold_25-snap.1800-T1
Valid prediction for snap_scaffold_25-snap.1831-T1
Valid prediction for Augustus_model.g36248.t1
Valid prediction for GlimmerHMM_glimmerT_54640-T1
Valid prediction for snap_scaffold_25-snap.1823-T1
Valid prediction for snap_scaffold_25-snap.1798-T1
Couldn't classify 161045, 161045
Sorry, prediction pasa_asmbl_34427.p1 fails validation.
(ATG)	 AC	156122-156184	GT	GGG
(CAC)	 AG	157853-157927	GT	AGG
(ATC)	 AG	158064-158169	GT	AGG
(CGT)	 AG	158315-158425	GT	AGG
(GGT)	 AG	159049-159264	GT	GAG
(TGG)	 AG	159850-159924	GT	AGG
(GTG)	 AG	160751-160940	GT	TGG
(AAA)	 AG	161045-161045	AA	GAA
-recovered pasa_asmbl_34427.p1, initial, 156122, 156184
add_exon() Sorry, pasa_asmbl_34427.p1 158315-158425-terminal-1 is invalid.
-recovered pasa_asmbl_34427.p1, terminal, 158315, 158425
-recovered pasa_asmbl_34427.p1, internal, 157853, 157927
-recovered pasa_asmbl_34427.p1, internal, 158064, 158169
-recovered pasa_asmbl_34427.p1, internal, 158315, 158425
-recovered pasa_asmbl_34427.p1, internal, 159049, 159264
-recovered pasa_asmbl_34427.p1, internal, 159850, 159924
-recovered pasa_asmbl_34427.p1, internal, 160751, 160940
Valid prediction for Augustus_model.g36254.t1
Valid prediction for Augustus_model.g36264.t1
Valid prediction for GlimmerHMM_glimmerT_54642-T1
Valid prediction for GlimmerHMM_glimmerT_54638-T1
Valid prediction for Augustus_model.g36244.t1
Valid prediction for snap_scaffold_25-snap.1832-T1
Valid prediction for Augustus_model.g36246.t1
Valid prediction for snap_scaffold_25-snap.1793-T1
Valid prediction for GlimmerHMM_glimmerT_54639-T1
Valid prediction for GlimmerHMM_glimmerT_54654-T1
Valid prediction for snap_scaffold_25-snap.1815-T1
Valid prediction for Augustus_model.g36243.t1
Valid prediction for GlimmerHMM_glimmerT_54652-T1
Valid prediction for snap_scaffold_25-snap.1794-T1
Valid prediction for snap_scaffold_25-snap.1804-T1
Valid prediction for snap_scaffold_25-snap.1820-T1
Valid prediction for snap_scaffold_25-snap.1795-T1
Couldn't classify 153958, 154011
Couldn't classify 155430, 155681
Sorry, prediction pasa_asmbl_34430.p2 fails validation.
(CAG)	 TC	153958-154011	GT	AGG
(ATA)	 AG	154914-154976	GT	AGG
(ATC)	 AG	155430-155681	GC	GGG
-recovered pasa_asmbl_34430.p2, internal, 154914, 154976
-recovered pasa_asmbl_34430.p2, internal, 155430, 155681
Valid prediction for snap_scaffold_25-snap.1828-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1813-T1
Couldn't classify 16501, 17631
Couldn't classify 20556, 20681
Sorry, prediction pasa_asmbl_34440.p1 fails validation.
(CCC)	 GT	16501-17631	GT	AGG
(GTT)	 AG	20556-20681	GG	CAG
Valid prediction for Augustus_model.g36261.t1
Valid prediction for snap_scaffold_25-snap.1801-T1
Valid prediction for Augustus_model.g36256.t1
Valid prediction for GlimmerHMM_glimmerT_54650-T1
Valid prediction for GlimmerHMM_glimmerT_54651-T1
Valid prediction for snap_scaffold_25-snap.1833-T1
Valid prediction for GlimmerHMM_glimmerT_54647-T1
Couldn't classify 78191, 78247
Couldn't classify 80637, 80771
Sorry, prediction pasa_asmbl_34434.p1 fails validation.
(CAG)	 TC	78191-78247	GT	AGG
(AAA)	 AG	79007-79168	GT	AGG
(GAC)	 AG	79272-79421	GT	ATG
(GTC)	 AG	79601-79687	GT	TGG
(ATC)	 AG	79849-79981	GT	AGG
(GAC)	 AG	80118-80206	GT	AGG
(ATC)	 AG	80336-80551	GT	AGG
(GTC)	 AG	80637-80771	TG	GGT
-recovered pasa_asmbl_34434.p1, internal, 79007, 79168
-recovered pasa_asmbl_34434.p1, internal, 79272, 79421
-recovered pasa_asmbl_34434.p1, internal, 79601, 79687
-recovered pasa_asmbl_34434.p1, internal, 79849, 79981
-recovered pasa_asmbl_34434.p1, internal, 80118, 80206
-recovered pasa_asmbl_34434.p1, internal, 80336, 80551
Valid prediction for HiQ_model.g36252.t1
Valid prediction for snap_scaffold_25-snap.1808-T1
Valid prediction for GlimmerHMM_glimmerT_54649-T1
Valid prediction for snap_scaffold_25-snap.1806-T1
Valid prediction for snap_scaffold_25-snap.1822-T1
Valid prediction for snap_scaffold_25-snap.1812-T1
Valid prediction for snap_scaffold_25-snap.1816-T1
Valid prediction for snap_scaffold_25-snap.1821-T1
Valid prediction for snap_scaffold_25-snap.1835-T1
Couldn't classify 70360, 70472
Sorry, prediction pasa_asmbl_34436.p3 fails validation.
(ATG)	 AT	69647-69830	GT	GGG
(TGG)	 AG	70360-70472	AC	ACA
-recovered pasa_asmbl_34436.p3, initial, 69647, 69830
Valid prediction for snap_scaffold_25-snap.1796-T1
Valid prediction for snap_scaffold_25-snap.1799-T1
Couldn't classify 145526, 145598
Couldn't classify 147688, 147749
Sorry, prediction pasa_asmbl_34643.p2 fails validation.
(AAC)	 AC	145526-145598	GT	CGG
(GGG)	 AG	145702-145878	GT	AGG
(GCT)	 AG	147688-147749	GA	GGG
-recovered pasa_asmbl_34643.p2, internal, 145702, 145878
Valid prediction for GlimmerHMM_glimmerT_54643-T1
Couldn't classify 3352, 3888
Sorry, prediction pasa_asmbl_33734.p1 fails validation.
(ATG)	 GG	3352-3888	AC	TCA
Valid prediction for GlimmerHMM_glimmerT_54641-T1
Couldn't classify 80938, 80985
Sorry, prediction pasa_asmbl_34433.p1 fails validation.
(TTC)	 CC	80938-80985	GT	AGG
(GTC)	 AG	81169-81339	GT	AGG
(GTG)	 AG	81439-81613	GT	TGG
(CGG)	 AG	81817-81932	GT	TGG
(TCT)	 AG	82093-82170	GT	AAG
(ATC)	 AG	82338-82398	GT	TGG
(CCA)	 AG	82510-82670	GA	AAG
-recovered pasa_asmbl_34433.p1, terminal, 82510, 82670
-recovered pasa_asmbl_34433.p1, internal, 81169, 81339
-recovered pasa_asmbl_34433.p1, internal, 81439, 81613
-recovered pasa_asmbl_34433.p1, internal, 81817, 81932
-recovered pasa_asmbl_34433.p1, internal, 82093, 82170
-recovered pasa_asmbl_34433.p1, internal, 82338, 82398
Valid prediction for Augustus_model.g36255.t1
Valid prediction for Augustus_model.g36262.t1
Valid prediction for GlimmerHMM_glimmerT_54656-T1
Valid prediction for CodingQuarry_transcript_38807-T1
Valid prediction for Augustus_model.g36258.t1
Valid prediction for snap_scaffold_25-snap.1819-T1
Couldn't classify 31690, 32034
Sorry, prediction pasa_asmbl_34439.p1 fails validation.
(TAC)	 GC	31690-32034	AG	GAA
Valid prediction for pasa_asmbl_34432.p1
Valid prediction for HiQ_model.g36247.t1
Valid prediction for GlimmerHMM_glimmerT_54659-T1
Valid prediction for Augustus_model.g36263.t1
Valid prediction for snap_scaffold_25-snap.1817-T1
Valid prediction for GlimmerHMM_glimmerT_54637-T1
Valid prediction for snap_scaffold_25-snap.1836-T1
Valid prediction for snap_scaffold_25-snap.1818-T1
Valid prediction for snap_scaffold_25-snap.1790-T1
Valid prediction for GlimmerHMM_glimmerT_54634-T1
Valid prediction for snap_scaffold_25-snap.1791-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9006, rend_intergenic: 5781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12621, rend_intergenic: 9883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24257, rend_intergenic: 19108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26822, rend_intergenic: 24458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41766, rend_intergenic: 39836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52903, rend_intergenic: 52655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56762, rend_intergenic: 52917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61542, rend_intergenic: 59684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63074, rend_intergenic: 61594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74569, rend_intergenic: 63709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76214, rend_intergenic: 74635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148843, rend_intergenic: 145483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211527
-exon list size: 440


building trellis

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18.8    
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20.6    
20.8    
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22.6    
22.9    
23.1    
23.3    
23.5    
23.8    
24.0    
24.2    
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24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
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26.7    
26.9    
27.1    
27.4    
27.6    
27.8    
28.1    
28.3    
28.5    
28.7    
29.0    
29.2    
29.4    
29.6    
29.9    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.4    
31.7    
31.9    
32.1    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.8    
35.1    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.5    
42.8    
43.0    
43.2    
43.4    
43.7    
43.9    
44.1    
44.3    
44.6    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
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46.6    
46.8    
47.1    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.6    
48.9    
49.1    
49.3    
49.5    
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50.0    
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64.0    
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68.6    
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70.4    
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73.5    
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77.6    
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81.0    
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82.8    
83.0    
83.3    
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83.9    
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87.6    
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88.2    
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88.9    
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90.5    
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91.0    
91.2    
91.4    
91.6    
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92.1    
92.3    
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92.8    
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93.4    
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94.8    
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96.6    
96.8    
97.1    
97.3    
97.5    
97.7    
98.0    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 9006, rend_intergenic: 5781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12621, rend_intergenic: 9883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24257, rend_intergenic: 19108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26822, rend_intergenic: 24458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41766, rend_intergenic: 39836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52903, rend_intergenic: 52655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56762, rend_intergenic: 52917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61542, rend_intergenic: 59684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63074, rend_intergenic: 61594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74569, rend_intergenic: 63709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76214, rend_intergenic: 74635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148843, rend_intergenic: 145483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support