-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_10888343-11200430

-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 GlimmerHMM_glimmerT_32353-T1
Valid prediction for snap_scaffold_13-snap.2058-T1
Valid prediction for Augustus_model.g21593.t1
Valid prediction for snap_scaffold_13-snap.2039-T1
Valid prediction for GlimmerHMM_glimmerT_32350-T1
Valid prediction for HiQ_model.g21601.t1
Valid prediction for GlimmerHMM_glimmerT_32341-T1
Valid prediction for snap_scaffold_13-snap.2025-T1
Valid prediction for GlimmerHMM_glimmerT_32332-T1
Valid prediction for snap_scaffold_13-snap.2027-T1
Valid prediction for GlimmerHMM_glimmerT_32347-T1
Valid prediction for snap_scaffold_13-snap.2048-T1
Couldn't classify 308361, 308447
Sorry, prediction pasa_asmbl_11252.p1 fails validation.
(GAG)	 CA	308361-308447	GT	TGG
(GAG)	 AG	308762-308882	GC	AGG
(GTG)	 AG	309004-309098	GT	AGG
(CCC)	 AG	309336-309456	GT	AGG
(CTT)	 AG	309920-310008	GT	AGG
(GTC)	 AG	310231-310320	GA	AAG
add_exon() Sorry, pasa_asmbl_11252.p1 308762-308882-terminal-3 is invalid.
-recovered pasa_asmbl_11252.p1, terminal, 308762, 308882
add_exon() Sorry, pasa_asmbl_11252.p1 309336-309456-terminal-3 is invalid.
-recovered pasa_asmbl_11252.p1, terminal, 309336, 309456
-recovered pasa_asmbl_11252.p1, terminal, 310231, 310320
-recovered pasa_asmbl_11252.p1, internal, 308762, 308882
-recovered pasa_asmbl_11252.p1, internal, 309004, 309098
-recovered pasa_asmbl_11252.p1, internal, 309336, 309456
-recovered pasa_asmbl_11252.p1, internal, 309920, 310008
Valid prediction for snap_scaffold_13-snap.2036-T1
Valid prediction for snap_scaffold_13-snap.2046-T1
Valid prediction for Augustus_model.g21600.t1
Valid prediction for snap_scaffold_13-snap.2055-T1
Valid prediction for Augustus_model.g21583.t1
Valid prediction for snap_scaffold_13-snap.2024-T1
Valid prediction for GlimmerHMM_glimmerT_32330-T1
Valid prediction for GlimmerHMM_glimmerT_32340-T1
Valid prediction for Augustus_model.g21599.t1
Valid prediction for snap_scaffold_13-snap.2026-T1
Valid prediction for Augustus_model.g21596.t1
Valid prediction for snap_scaffold_13-snap.2047-T1
Valid prediction for snap_scaffold_13-snap.2052-T1
Valid prediction for Augustus_model.g21592.t1
Valid prediction for Augustus_model.g21591.t1
Valid prediction for CodingQuarry_transcript_13235-T1
Valid prediction for snap_scaffold_13-snap.2028-T1
Valid prediction for GlimmerHMM_glimmerT_32342-T1
Valid prediction for CodingQuarry_transcript_13238-T1
Valid prediction for snap_scaffold_13-snap.2021-T1
Valid prediction for snap_scaffold_13-snap.2063-T1
Valid prediction for snap_scaffold_13-snap.2059-T1
Valid prediction for snap_scaffold_13-snap.2020-T1
Valid prediction for snap_scaffold_13-snap.2038-T1
Valid prediction for snap_scaffold_13-snap.2051-T1
Valid prediction for snap_scaffold_13-snap.2053-T1
Valid prediction for GlimmerHMM_glimmerT_32331-T1
Valid prediction for snap_scaffold_13-snap.2022-T1
Valid prediction for GlimmerHMM_glimmerT_32335-T1
Valid prediction for Augustus_model.g21594.t1
Valid prediction for snap_scaffold_13-snap.2062-T1
Valid prediction for snap_scaffold_13-snap.2049-T1
Valid prediction for snap_scaffold_13-snap.2030-T1
Valid prediction for snap_scaffold_13-snap.2044-T1
Valid prediction for GlimmerHMM_glimmerT_32345-T1
Valid prediction for snap_scaffold_13-snap.2050-T1
Valid prediction for GlimmerHMM_glimmerT_32354-T1
Valid prediction for snap_scaffold_13-snap.2057-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32351-T1
Valid prediction for snap_scaffold_13-snap.2029-T1
Valid prediction for Augustus_model.g21598.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.g21586.t1
Valid prediction for Augustus_model.g21589.t1
Valid prediction for snap_scaffold_13-snap.2033-T1
Valid prediction for CodingQuarry_transcript_13234-T1
Valid prediction for GlimmerHMM_glimmerT_32348-T1
Valid prediction for GlimmerHMM_glimmerT_32349-T1
Valid prediction for snap_scaffold_13-snap.2040-T1
Valid prediction for snap_scaffold_13-snap.2037-T1
Valid prediction for snap_scaffold_13-snap.2061-T1
Valid prediction for pasa_asmbl_10074.p2
Valid prediction for snap_scaffold_13-snap.2054-T1
Valid prediction for GlimmerHMM_glimmerT_32352-T1
Valid prediction for snap_scaffold_13-snap.2042-T1
Valid prediction for GlimmerHMM_glimmerT_32328-T1
Valid prediction for snap_scaffold_13-snap.2041-T1
Valid prediction for GlimmerHMM_glimmerT_32346-T1
Valid prediction for snap_scaffold_13-snap.2045-T1
Valid prediction for snap_scaffold_13-snap.2065-T1
Valid prediction for snap_scaffold_13-snap.2064-T1
Valid prediction for CodingQuarry_transcript_13237-T1
Valid prediction for GlimmerHMM_glimmerT_32334-T1
Valid prediction for snap_scaffold_13-snap.2019-T1
Valid prediction for snap_scaffold_13-snap.2034-T1
Valid prediction for Augustus_model.g21587.t1
Valid prediction for snap_scaffold_13-snap.2032-T1
Valid prediction for GlimmerHMM_glimmerT_32337-T1
Couldn't classify 46211, 46390
Sorry, prediction pasa_asmbl_10070.p1 fails validation.
(CAG)	 AC	46211-46390	GT	AGG
(GTC)	 AG	46737-46847	GT	AGG
(GAG)	 AG	47494-47569	GT	GGG
(GAC)	 AG	47734-47912	AG	AGA
-recovered pasa_asmbl_10070.p1, terminal, 47734, 47912
-recovered pasa_asmbl_10070.p1, internal, 46737, 46847
-recovered pasa_asmbl_10070.p1, internal, 47494, 47569
Valid prediction for snap_scaffold_13-snap.2056-T1
Valid prediction for GlimmerHMM_glimmerT_32333-T1
Valid prediction for Augustus_model.g21588.t1
Couldn't classify 282353, 282630
Sorry, prediction pasa_asmbl_10068.p1 fails validation.
(ACT)	 GT	282353-282630	GT	TGG
(CCC)	 AG	282946-283005	GT	TGG
(CTA)	 AG	283142-283239	GT	TGG
(TTA)	 AG	283416-283480	GT	CTG
(AAT)	 AG	283574-283693	GT	CGG
(GAG)	 AG	283846-283914	GT	AGG
(CAA)	 AG	284033-284092	GT	AGG
(GAA)	 AG	284305-284384	GT	AGG
(TAG)	 AG	284692-284749	GT	AGG
(GGT)	 AG	284878-284992	GT	AGG
(ATG)	 AG	285086-285221	GT	AGG
(CAT)	 AG	285421-285564	GT	AGG
(CTG)	 AG	285712-285820	GT	AGG
(GAG)	 AG	286131-286212	GT	AGG
(TGA)	 AG	286380-286496	GT	CGG
(ACC)	 AG	286622-286739	GT	GCG
(ATC)	 AG	286851-286975	GT	CGG
(GCA)	 AG	287243-287403	GT	GGG
(GAG)	 AG	287586-287630	GT	AGG
(GTG)	 AG	287874-287891	TG	GAT
add_exon() Sorry, pasa_asmbl_10068.p1 285086-285221-initial-1 is invalid.
-recovered pasa_asmbl_10068.p1, initial, 285086, 285221
add_exon() Sorry, pasa_asmbl_10068.p1 285086-285221-terminal-3 is invalid.
-recovered pasa_asmbl_10068.p1, terminal, 285086, 285221
-recovered pasa_asmbl_10068.p1, terminal, 287874, 287891
-recovered pasa_asmbl_10068.p1, internal, 282946, 283005
-recovered pasa_asmbl_10068.p1, internal, 283142, 283239
-recovered pasa_asmbl_10068.p1, internal, 283416, 283480
-recovered pasa_asmbl_10068.p1, internal, 283574, 283693
-recovered pasa_asmbl_10068.p1, internal, 283846, 283914
-recovered pasa_asmbl_10068.p1, internal, 284033, 284092
-recovered pasa_asmbl_10068.p1, internal, 284305, 284384
-recovered pasa_asmbl_10068.p1, internal, 284692, 284749
-recovered pasa_asmbl_10068.p1, internal, 284878, 284992
-recovered pasa_asmbl_10068.p1, internal, 285086, 285221
-recovered pasa_asmbl_10068.p1, internal, 285421, 285564
-recovered pasa_asmbl_10068.p1, internal, 285712, 285820
-recovered pasa_asmbl_10068.p1, internal, 286131, 286212
-recovered pasa_asmbl_10068.p1, internal, 286380, 286496
-recovered pasa_asmbl_10068.p1, internal, 286622, 286739
-recovered pasa_asmbl_10068.p1, internal, 286851, 286975
-recovered pasa_asmbl_10068.p1, internal, 287243, 287403
-recovered pasa_asmbl_10068.p1, internal, 287586, 287630
Valid prediction for GlimmerHMM_glimmerT_32336-T1
Valid prediction for GlimmerHMM_glimmerT_32339-T1
Valid prediction for snap_scaffold_13-snap.2031-T1
Valid prediction for Augustus_model.g21595.t1
Valid prediction for snap_scaffold_13-snap.2060-T1
Valid prediction for HiQ_model.g21597.t1
Valid prediction for GlimmerHMM_glimmerT_32329-T1
Valid prediction for snap_scaffold_13-snap.2067-T1
Valid prediction for snap_scaffold_13-snap.2035-T1
Valid prediction for snap_scaffold_13-snap.2066-T1
Valid prediction for Augustus_model.g21584.t1
Valid prediction for snap_scaffold_13-snap.2043-T1
Valid prediction for Augustus_model.g21590.t1
Valid prediction for GlimmerHMM_glimmerT_32343-T1
Valid prediction for GlimmerHMM_glimmerT_32344-T1
Valid prediction for Augustus_model.g21585.t1
Valid prediction for HiQ_model.g21582.t1
Valid prediction for GlimmerHMM_glimmerT_32338-T1
Valid prediction for snap_scaffold_13-snap.2023-T1
Couldn't classify 45185, 45292
Sorry, prediction pasa_asmbl_10072.p1 fails validation.
(ATG)	 TC	43069-43088	GT	AGG
(GTA)	 AG	43477-43546	GT	AGG
(GTC)	 AG	43821-44000	GT	AGG
(CTG)	 AG	44179-44286	GT	CAG
(TCA)	 AG	44553-44615	GT	AGG
(GAC)	 AG	45185-45292	CC	GGC
-recovered pasa_asmbl_10072.p1, initial, 43069, 43088
-recovered pasa_asmbl_10072.p1, internal, 43477, 43546
-recovered pasa_asmbl_10072.p1, internal, 43821, 44000
-recovered pasa_asmbl_10072.p1, internal, 44179, 44286
-recovered pasa_asmbl_10072.p1, internal, 44553, 44615

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11079, rend_intergenic: 8305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 268331, rend_intergenic: 264177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 289028, rend_intergenic: 285296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 293890, rend_intergenic: 291160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 310320, rend_intergenic: 298507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 312088
-exon list size: 398


building trellis

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48.8    
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49.2    
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51.2    
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52.2    
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54.5    
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61.3    
61.5    
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84.2    
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88.8    
89.0    
89.2    
89.5    
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90.2    
90.5    
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91.0    
91.2    
91.5    
91.8    
92.0    
92.2    
92.5    
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93.2    
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94.2    
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95.2    
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96.0    
96.2    
96.5    
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97.2    
97.5    
97.8    
98.0    
98.2    
98.5    
98.8    
99.0    
99.2    
99.5    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 11079, rend_intergenic: 8305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 268331, rend_intergenic: 264177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 289028, rend_intergenic: 285296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 293890, rend_intergenic: 291160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 310320, rend_intergenic: 298507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 20924
-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 2 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 - 17764
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-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 - 17302
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

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