-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_11654758-11838628

-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.g17434.t1
Valid prediction for snap_scaffold_10-snap.2274-T1
Valid prediction for GlimmerHMM_glimmerT_25964-T1
Valid prediction for GlimmerHMM_glimmerT_25984-T1
Valid prediction for GeneMark_model.44499_t
Valid prediction for GeneMark_model.44502_t
Valid prediction for GeneMark_model.44504_t
Valid prediction for HiQ_model.g17436.t1
Valid prediction for GeneMark_model.44503_t
Valid prediction for GeneMark_model.44491_t
Valid prediction for GlimmerHMM_glimmerT_25974-T1
Valid prediction for snap_scaffold_10-snap.2273-T1
Valid prediction for snap_scaffold_10-snap.2305-T1
Valid prediction for GeneMark_model.44496_t
Valid prediction for GlimmerHMM_glimmerT_25967-T1
Valid prediction for GeneMark_model.44481_t
Valid prediction for GlimmerHMM_glimmerT_25995-T1
Valid prediction for snap_scaffold_10-snap.2284-T1
Valid prediction for GlimmerHMM_glimmerT_25981-T1
Valid prediction for Augustus_model.g17427.t1
Valid prediction for GeneMark_model.44485_t
Valid prediction for GeneMark_model.44508_t
Valid prediction for GeneMark_model.44478_t
Valid prediction for Augustus_model.g17421.t1
Valid prediction for Augustus_model.g17424.t1
Couldn't classify 169969, 170126
Sorry, prediction pasa_asmbl_4772.p1 fails validation.
(TCC)	 CG	169969-170126	GT	AGG
(TGC)	 AG	170427-170580	GT	CTG
(GTG)	 AG	170856-170969	GT	CAG
(GCA)	 AG	173461-173659	GT	AGG
(GAG)	 AG	175188-175310	GT	CGG
(AGG)	 AG	175952-176065	GT	AGG
(ATT)	 AG	177013-177097	GT	GGG
(TCA)	 AG	177698-177742	GT	AGG
(GTT)	 AG	178361-178553	GT	TGG
(AAT)	 AG	178859-178992	GT	AGG
(TCC)	 AG	180265-180343	GT	AGG
(GTG)	 AG	180633-180767	GT	AGG
(GTT)	 AG	180894-181019	GA	GAG
add_exon() Sorry, pasa_asmbl_4772.p1 175952-176065-terminal-1 is invalid.
-recovered pasa_asmbl_4772.p1, terminal, 175952, 176065
-recovered pasa_asmbl_4772.p1, terminal, 180894, 181019
-recovered pasa_asmbl_4772.p1, internal, 170427, 170580
-recovered pasa_asmbl_4772.p1, internal, 170856, 170969
-recovered pasa_asmbl_4772.p1, internal, 173461, 173659
-recovered pasa_asmbl_4772.p1, internal, 175188, 175310
-recovered pasa_asmbl_4772.p1, internal, 175952, 176065
-recovered pasa_asmbl_4772.p1, internal, 177013, 177097
-recovered pasa_asmbl_4772.p1, internal, 177698, 177742
-recovered pasa_asmbl_4772.p1, internal, 178361, 178553
-recovered pasa_asmbl_4772.p1, internal, 178859, 178992
-recovered pasa_asmbl_4772.p1, internal, 180265, 180343
-recovered pasa_asmbl_4772.p1, internal, 180633, 180767
Valid prediction for GlimmerHMM_glimmerT_25965-T1
Valid prediction for snap_scaffold_10-snap.2294-T1
Valid prediction for snap_scaffold_10-snap.2278-T1
Couldn't classify 101959, 102140
Sorry, prediction pasa_asmbl_4771.p1 fails validation.
(TGT)	 AG	101959-102140	GT	AGG
(AGT)	 AG	103318-103543	GT	AGG
(TTT)	 AG	104428-104638	GT	AGG
(GCC)	 AG	106535-106803	GG	GAG
-recovered pasa_asmbl_4771.p1, terminal, 106535, 106803
-recovered pasa_asmbl_4771.p1, internal, 101959, 102140
-recovered pasa_asmbl_4771.p1, internal, 103318, 103543
-recovered pasa_asmbl_4771.p1, internal, 104428, 104638
Couldn't classify 96905, 97012
Sorry, prediction pasa_asmbl_4770.p1 fails validation.
(ATG)	 AG	90450-90526	GT	AGG
(TCC)	 AG	92616-92751	GT	AGG
(AGC)	 AG	94787-94921	GT	AGG
(CTG)	 AG	95645-95768	GT	GGG
(GCA)	 AG	96106-96242	GT	AGG
(GTG)	 AG	96905-97012	GG	ATG
-recovered pasa_asmbl_4770.p1, initial, 90450, 90526
-recovered pasa_asmbl_4770.p1, internal, 90450, 90526
-recovered pasa_asmbl_4770.p1, internal, 92616, 92751
-recovered pasa_asmbl_4770.p1, internal, 94787, 94921
-recovered pasa_asmbl_4770.p1, internal, 95645, 95768
-recovered pasa_asmbl_4770.p1, internal, 96106, 96242
Valid prediction for Augustus_model.g17433.t1
Valid prediction for Augustus_model.g17428.t1
Valid prediction for GeneMark_model.44493_t
Valid prediction for snap_scaffold_10-snap.2290-T1
Valid prediction for snap_scaffold_10-snap.2298-T1
Valid prediction for GlimmerHMM_glimmerT_25987-T1
Valid prediction for GlimmerHMM_glimmerT_25976-T1
Valid prediction for Augustus_model.g17431.t1
Valid prediction for GlimmerHMM_glimmerT_25986-T1
Valid prediction for GlimmerHMM_glimmerT_25963-T1
Valid prediction for snap_scaffold_10-snap.2300-T1
Valid prediction for GeneMark_model.44498_t
Valid prediction for GlimmerHMM_glimmerT_25990-T1
Valid prediction for snap_scaffold_10-snap.2276-T1
Valid prediction for GeneMark_model.44506_t
Valid prediction for snap_scaffold_10-snap.2295-T1
Valid prediction for snap_scaffold_10-snap.2292-T1
Valid prediction for Augustus_model.g17432.t1
Valid prediction for GlimmerHMM_glimmerT_25993-T1
Valid prediction for snap_scaffold_10-snap.2288-T1
Valid prediction for snap_scaffold_10-snap.2286-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_25991-T1
Valid prediction for GeneMark_model.44480_t
Valid prediction for snap_scaffold_10-snap.2291-T1
Valid prediction for snap_scaffold_10-snap.2283-T1
Valid prediction for snap_scaffold_10-snap.2287-T1
Valid prediction for snap_scaffold_10-snap.2277-T1
Valid prediction for Augustus_model.g17429.t1
Valid prediction for GlimmerHMM_glimmerT_25970-T1
Valid prediction for snap_scaffold_10-snap.2282-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_10-snap.2302-T1
Valid prediction for GeneMark_model.44492_t
Valid prediction for GlimmerHMM_glimmerT_25982-T1
Valid prediction for GeneMark_model.44486_t
Valid prediction for GlimmerHMM_glimmerT_25994-T1
Valid prediction for GeneMark_model.44501_t
Valid prediction for snap_scaffold_10-snap.2281-T1
Valid prediction for snap_scaffold_10-snap.2293-T1
Valid prediction for snap_scaffold_10-snap.2303-T1
Valid prediction for snap_scaffold_10-snap.2307-T1
Valid prediction for GlimmerHMM_glimmerT_25992-T1
Valid prediction for snap_scaffold_10-snap.2275-T1
Valid prediction for GeneMark_model.44487_t
Valid prediction for snap_scaffold_10-snap.2279-T1
Valid prediction for GeneMark_model.44494_t
Valid prediction for Augustus_model.g17423.t1
Valid prediction for snap_scaffold_10-snap.2306-T1
Valid prediction for snap_scaffold_10-snap.2297-T1
Valid prediction for GeneMark_model.44479_t
Valid prediction for Augustus_model.g17422.t1
Valid prediction for snap_scaffold_10-snap.2289-T1
Valid prediction for snap_scaffold_10-snap.2285-T1
Valid prediction for GlimmerHMM_glimmerT_25983-T1
Valid prediction for GlimmerHMM_glimmerT_25989-T1
Valid prediction for GeneMark_model.44500_t
Valid prediction for GlimmerHMM_glimmerT_25969-T1
Valid prediction for GeneMark_model.44484_t
Valid prediction for GeneMark_model.44490_t
Valid prediction for GeneMark_model.44489_t
Valid prediction for GlimmerHMM_glimmerT_25977-T1
Valid prediction for GlimmerHMM_glimmerT_25979-T1
Valid prediction for GlimmerHMM_glimmerT_25988-T1
Valid prediction for GlimmerHMM_glimmerT_25975-T1
Valid prediction for Augustus_model.g17420.t1
Valid prediction for Augustus_model.g17430.t1
Valid prediction for GeneMark_model.44507_t
Valid prediction for snap_scaffold_10-snap.2304-T1
Valid prediction for GeneMark_model.44495_t
Valid prediction for GeneMark_model.44497_t
Valid prediction for GeneMark_model.44482_t
Valid prediction for GeneMark_model.44483_t
Valid prediction for GlimmerHMM_glimmerT_25968-T1
Valid prediction for GlimmerHMM_glimmerT_25978-T1
Valid prediction for snap_scaffold_10-snap.2301-T1
Valid prediction for GlimmerHMM_glimmerT_25980-T1
Valid prediction for GlimmerHMM_glimmerT_25971-T1
Valid prediction for GlimmerHMM_glimmerT_25985-T1
Valid prediction for snap_scaffold_10-snap.2296-T1
Valid prediction for GlimmerHMM_glimmerT_25973-T1
Valid prediction for Augustus_model.g17425.t1
Valid prediction for snap_scaffold_10-snap.2299-T1
Valid prediction for Augustus_model.g17435.t1
Valid prediction for Augustus_model.g17426.t1
Valid prediction for snap_scaffold_10-snap.2280-T1
Valid prediction for GlimmerHMM_glimmerT_25966-T1
Valid prediction for GlimmerHMM_glimmerT_25972-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22653, rend_intergenic: 20527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47671, rend_intergenic: 40890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72472, rend_intergenic: 71402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99033, rend_intergenic: 93728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108570, rend_intergenic: 106355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181019, rend_intergenic: 173422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183871
-exon list size: 469


building trellis

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36.9    
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80.9    
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81.3    
81.5    
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82.0    
82.2    
82.4    
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82.8    
83.0    
83.2    
83.4    
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83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
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86.8    
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87.3    
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87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
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89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
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94.9    
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95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
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97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 22653, rend_intergenic: 20527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47671, rend_intergenic: 40890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72472, rend_intergenic: 71402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99033, rend_intergenic: 93728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108570, rend_intergenic: 106355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181019, rend_intergenic: 173422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support
	-no exons in range 1 - 10403