-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_7685578-7882934

-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_43686-T1
Valid prediction for Augustus_model.g29272.t1
Valid prediction for Augustus_model.g29288.t1
Valid prediction for snap_scaffold_18-snap.1612-T1
Valid prediction for GeneMark_model.75416_t
Valid prediction for CodingQuarry_transcript_23782-T1
Valid prediction for GeneMark_model.75426_t
Valid prediction for GeneMark_model.75439_t
Valid prediction for snap_scaffold_18-snap.1618-T1
Valid prediction for snap_scaffold_18-snap.1642-T1
Valid prediction for CodingQuarry_transcript_23776-T1
Couldn't classify 184012, 184181
Sorry, prediction pasa_asmbl_20829.p1 fails validation.
(ATG)	 AA	182072-182172	GT	TGG
(TGT)	 AG	182286-182338	GT	AGG
(GTG)	 AG	182412-182543	GT	GGG
(CTT)	 AG	182741-182899	GT	CGG
(CAG)	 AG	183231-183337	GT	AGG
(GTG)	 AG	183538-183676	GT	TGG
(GCA)	 AG	184012-184181	CT	ATC
-recovered pasa_asmbl_20829.p1, initial, 182072, 182172
-recovered pasa_asmbl_20829.p1, internal, 182286, 182338
-recovered pasa_asmbl_20829.p1, internal, 182412, 182543
-recovered pasa_asmbl_20829.p1, internal, 182741, 182899
-recovered pasa_asmbl_20829.p1, internal, 183231, 183337
-recovered pasa_asmbl_20829.p1, internal, 183538, 183676
Valid prediction for Augustus_model.g29262.t1
Valid prediction for Augustus_model.g29278.t1
Valid prediction for snap_scaffold_18-snap.1607-T1
Valid prediction for GlimmerHMM_glimmerT_43697-T1
Valid prediction for snap_scaffold_18-snap.1653-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.1619-T1
Valid prediction for Augustus_model.g29270.t1
Valid prediction for GlimmerHMM_glimmerT_43682-T1
Valid prediction for Augustus_model.g29275.t1
Valid prediction for snap_scaffold_18-snap.1616-T1
Valid prediction for GlimmerHMM_glimmerT_43675-T1
Valid prediction for HiQ_model.g29285.t1
Valid prediction for snap_scaffold_18-snap.1648-T1
Couldn't classify 110787, 110838
Couldn't classify 112221, 112290
Sorry, prediction pasa_asmbl_20817.p1 fails validation.
(GCA)	 TG	110787-110838	GT	TGG
(AGT)	 AG	111164-111303	GT	AGG
(GTG)	 AG	111429-111486	GT	AGG
(GTG)	 AG	111843-111897	GT	CGG
(GAT)	 AG	112221-112290	GT	AGG
-recovered pasa_asmbl_20817.p1, internal, 111164, 111303
-recovered pasa_asmbl_20817.p1, internal, 111429, 111486
-recovered pasa_asmbl_20817.p1, internal, 111843, 111897
-recovered pasa_asmbl_20817.p1, internal, 112221, 112290
Valid prediction for GeneMark_model.75411_t
Valid prediction for CodingQuarry_transcript_23779-T1
Valid prediction for Augustus_model.g29267.t1
Valid prediction for GlimmerHMM_glimmerT_43688-T1
Valid prediction for snap_scaffold_18-snap.1620-T1
Valid prediction for GeneMark_model.75424_t
Valid prediction for CodingQuarry_transcript_23783-T1
Valid prediction for GlimmerHMM_glimmerT_43699-T1
Valid prediction for snap_scaffold_18-snap.1650-T1
Valid prediction for snap_scaffold_18-snap.1621-T1
Valid prediction for CodingQuarry_transcript_23781-T1
Valid prediction for snap_scaffold_18-snap.1652-T1
Valid prediction for Augustus_model.g29269.t1
Valid prediction for GeneMark_model.75443_t
Valid prediction for Augustus_model.g29279.t1
Valid prediction for Augustus_model.g29290.t1
Valid prediction for pasa_asmbl_20812.p1
Valid prediction for snap_scaffold_18-snap.1640-T1
Valid prediction for GlimmerHMM_glimmerT_43705-T1
Couldn't classify 188554, 188713
Sorry, prediction pasa_asmbl_20835.p1 fails validation.
(GCC)	 GA	188554-188713	GT	AGG
(AAA)	 AG	189170-189314	GT	AGG
(GTA)	 AG	189454-189609	GT	AAG
(ATG)	 AG	189829-189928	GT	CTG
(TTC)	 AG	190294-190447	GT	AGG
(AAA)	 AG	191167-191336	TA	GAT
add_exon() Sorry, pasa_asmbl_20835.p1 189829-189928-initial-1 is invalid.
-recovered pasa_asmbl_20835.p1, initial, 189829, 189928
-recovered pasa_asmbl_20835.p1, terminal, 191167, 191336
-recovered pasa_asmbl_20835.p1, internal, 189170, 189314
-recovered pasa_asmbl_20835.p1, internal, 189454, 189609
-recovered pasa_asmbl_20835.p1, internal, 189829, 189928
-recovered pasa_asmbl_20835.p1, internal, 190294, 190447
Valid prediction for snap_scaffold_18-snap.1631-T1
Valid prediction for snap_scaffold_18-snap.1622-T1
Valid prediction for GlimmerHMM_glimmerT_43706-T1
Valid prediction for GlimmerHMM_glimmerT_43691-T1
Valid prediction for CodingQuarry_transcript_23775-T1
Valid prediction for Augustus_model.g29276.t1
Valid prediction for GlimmerHMM_glimmerT_43681-T1
Valid prediction for snap_scaffold_18-snap.1613-T1
Valid prediction for GlimmerHMM_glimmerT_43683-T1
Valid prediction for GeneMark_model.75413_t
Valid prediction for snap_scaffold_18-snap.1615-T1
Valid prediction for CodingQuarry_transcript_23778-T1
Valid prediction for HiQ_model.g29283.t1
Valid prediction for GlimmerHMM_glimmerT_43693-T1
Valid prediction for GeneMark_model.75440_t
Valid prediction for snap_scaffold_18-snap.1645-T1
Valid prediction for GeneMark_model.75419_t
Valid prediction for snap_scaffold_18-snap.1629-T1
Valid prediction for snap_scaffold_18-snap.1605-T1
Valid prediction for GlimmerHMM_glimmerT_43704-T1
Valid prediction for GlimmerHMM_glimmerT_43701-T1
Valid prediction for snap_scaffold_18-snap.1610-T1
Valid prediction for snap_scaffold_18-snap.1626-T1
Valid prediction for GeneMark_model.75429_t
Valid prediction for snap_scaffold_18-snap.1639-T1
Valid prediction for GeneMark_model.75427_t
Valid prediction for snap_scaffold_18-snap.1632-T1
Valid prediction for snap_scaffold_18-snap.1614-T1
Valid prediction for snap_scaffold_18-snap.1637-T1
Valid prediction for GlimmerHMM_glimmerT_43678-T1
Valid prediction for Augustus_model.g29266.t1
Valid prediction for pasa_asmbl_20819.p1
Couldn't classify 64651, 64953
Sorry, prediction pasa_asmbl_20815.p3 fails validation.
(GAG)	 CC	64651-64953	GG	AAG
Valid prediction for GlimmerHMM_glimmerT_43687-T1
Valid prediction for snap_scaffold_18-snap.1627-T1
Valid prediction for GeneMark_model.75423_t
Valid prediction for GlimmerHMM_glimmerT_43703-T1
Valid prediction for CodingQuarry_transcript_23772-T1
Valid prediction for snap_scaffold_18-snap.1628-T1
Valid prediction for Augustus_model.g29264.t1
Valid prediction for snap_scaffold_18-snap.1601-T1
Valid prediction for Augustus_model.g29274.t1
Valid prediction for GeneMark_model.75417_t
Valid prediction for GlimmerHMM_glimmerT_43696-T1
Valid prediction for GeneMark_model.75436_t
Valid prediction for GlimmerHMM_glimmerT_43690-T1
Valid prediction for pasa_asmbl_20813.p1
Couldn't classify 161124, 161286
Sorry, prediction pasa_asmbl_20820.p1 fails validation.
(CAG)	 TC	161124-161286	GT	AGG
(GTG)	 AG	161643-161755	GT	AGG
(GTG)	 AG	163091-163168	GT	AGG
(GAT)	 AG	165598-165679	GT	TGG
(CCT)	 AG	168280-168484	GT	AAG
(CCC)	 AG	170883-171044	GT	AGG
(CGA)	 AG	171988-172087	GT	TGG
(CTG)	 AG	173904-174014	GT	AGG
(GTG)	 AG	174936-174998	GT	AGG
(GGG)	 AG	176318-176421	GT	GGG
(GTC)	 AG	176655-176886	GT	AGG
(ATG)	 AG	177110-177186	GT	AGG
(GCC)	 AG	177427-177553	GT	AGG
(AGA)	 AG	177681-177760	GT	AGG
(GGG)	 AG	178071-178197	GG	GAG
-recovered pasa_asmbl_20820.p1, initial, 177110, 177186
-recovered pasa_asmbl_20820.p1, terminal, 178071, 178197
-recovered pasa_asmbl_20820.p1, internal, 161643, 161755
-recovered pasa_asmbl_20820.p1, internal, 163091, 163168
-recovered pasa_asmbl_20820.p1, internal, 165598, 165679
-recovered pasa_asmbl_20820.p1, internal, 168280, 168484
-recovered pasa_asmbl_20820.p1, internal, 170883, 171044
-recovered pasa_asmbl_20820.p1, internal, 171988, 172087
-recovered pasa_asmbl_20820.p1, internal, 173904, 174014
-recovered pasa_asmbl_20820.p1, internal, 174936, 174998
-recovered pasa_asmbl_20820.p1, internal, 176318, 176421
-recovered pasa_asmbl_20820.p1, internal, 176655, 176886
-recovered pasa_asmbl_20820.p1, internal, 177110, 177186
-recovered pasa_asmbl_20820.p1, internal, 177427, 177553
-recovered pasa_asmbl_20820.p1, internal, 177681, 177760
Valid prediction for GeneMark_model.75420_t
Valid prediction for Augustus_model.g29282.t1
Valid prediction for HiQ_model.g29260.t1
Valid prediction for GeneMark_model.75438_t
Valid prediction for snap_scaffold_18-snap.1604-T1
Valid prediction for GeneMark_model.75446_t
Valid prediction for GeneMark_model.75418_t
Valid prediction for GeneMark_model.75421_t
Valid prediction for Augustus_model.g29289.t1
Valid prediction for snap_scaffold_18-snap.1602-T1
Valid prediction for snap_scaffold_18-snap.1606-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.g29281.t1
Valid prediction for GlimmerHMM_glimmerT_43702-T1
Valid prediction for GeneMark_model.75425_t
Valid prediction for GlimmerHMM_glimmerT_43700-T1
Valid prediction for GlimmerHMM_glimmerT_43679-T1
Valid prediction for GlimmerHMM_glimmerT_43694-T1
Valid prediction for CodingQuarry_transcript_23780-T1
Valid prediction for Augustus_model.g29280.t1
Valid prediction for GeneMark_model.75422_t
Valid prediction for HiQ_model.g29263.t1
Valid prediction for snap_scaffold_18-snap.1611-T1
Valid prediction for snap_scaffold_18-snap.1638-T1
Valid prediction for GeneMark_model.75412_t
Valid prediction for snap_scaffold_18-snap.1603-T1
Valid prediction for HiQ_model.g29277.t1
Valid prediction for GeneMark_model.75444_t
Valid prediction for snap_scaffold_18-snap.1647-T1
Valid prediction for GlimmerHMM_glimmerT_43685-T1
Valid prediction for Augustus_model.g29265.t1
Valid prediction for GeneMark_model.75415_t
Valid prediction for Augustus_model.g29286.t1
Valid prediction for snap_scaffold_18-snap.1609-T1
Valid prediction for GeneMark_model.75432_t
Valid prediction for HiQ_model.g29284.t1
Valid prediction for Augustus_model.g29273.t1
Valid prediction for GeneMark_model.75433_t
Valid prediction for snap_scaffold_18-snap.1617-T1
Valid prediction for snap_scaffold_18-snap.1630-T1
Valid prediction for CodingQuarry_transcript_23777-T1
Valid prediction for Augustus_model.g29261.t1
Valid prediction for GlimmerHMM_glimmerT_43677-T1
Valid prediction for GeneMark_model.75437_t
Valid prediction for GlimmerHMM_glimmerT_43695-T1
Valid prediction for GlimmerHMM_glimmerT_43676-T1
Valid prediction for Augustus_model.g29271.t1
Valid prediction for GeneMark_model.75430_t
Valid prediction for Augustus_model.g29268.t1
Valid prediction for GeneMark_model.75428_t
Valid prediction for pasa_asmbl_20015.p1
Valid prediction for snap_scaffold_18-snap.1635-T1
Valid prediction for GlimmerHMM_glimmerT_43684-T1
Valid prediction for CodingQuarry_transcript_23774-T1
Valid prediction for Augustus_model.g29287.t1
Valid prediction for GlimmerHMM_glimmerT_43689-T1
Valid prediction for snap_scaffold_18-snap.1624-T1
Valid prediction for GeneMark_model.75434_t
Valid prediction for snap_scaffold_18-snap.1623-T1
Valid prediction for snap_scaffold_18-snap.1625-T1
Valid prediction for GeneMark_model.75435_t
Valid prediction for GeneMark_model.75410_t
Valid prediction for snap_scaffold_18-snap.1651-T1
Valid prediction for snap_scaffold_18-snap.1641-T1
Valid prediction for snap_scaffold_18-snap.1608-T1
Valid prediction for snap_scaffold_18-snap.1636-T1
Valid prediction for GlimmerHMM_glimmerT_43680-T1
Couldn't classify 155434, 155748
Sorry, prediction pasa_asmbl_20009.p4 fails validation.
(ATG)	 TA	155434-155748	CA	GCC
Valid prediction for snap_scaffold_18-snap.1649-T1
Valid prediction for GlimmerHMM_glimmerT_43698-T1
Valid prediction for pasa_asmbl_20011.p1
Valid prediction for snap_scaffold_18-snap.1644-T1
Valid prediction for GeneMark_model.75441_t
Valid prediction for GlimmerHMM_glimmerT_43692-T1
Valid prediction for GeneMark_model.75431_t
Valid prediction for GeneMark_model.75414_t
Valid prediction for snap_scaffold_18-snap.1643-T1
Valid prediction for snap_scaffold_18-snap.1633-T1
Valid prediction for GeneMark_model.75442_t
Couldn't classify 15907, 15975
Sorry, prediction pasa_asmbl_20018.p2 fails validation.
(CAC)	 GT	15907-15975	GT	AGG
(ACT)	 AG	16381-16425	GT	ACG
(CGT)	 AG	16537-16653	GT	CGG
(GAG)	 AG	18067-18132	GT	AGG
(GCT)	 AG	18275-18376	TA	AAT
-recovered pasa_asmbl_20018.p2, terminal, 18275, 18376
-recovered pasa_asmbl_20018.p2, internal, 16381, 16425
-recovered pasa_asmbl_20018.p2, internal, 16537, 16653
-recovered pasa_asmbl_20018.p2, internal, 18067, 18132
Valid prediction for snap_scaffold_18-snap.1634-T1
Couldn't classify 11024, 11335
Sorry, prediction pasa_asmbl_20834.p1 fails validation.
(ATG)	 CC	11024-11335	GG	GGG
Valid prediction for snap_scaffold_18-snap.1646-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19905, rend_intergenic: 15563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166593, rend_intergenic: 164065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171273, rend_intergenic: 166923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197357
-exon list size: 500


building trellis

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92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 19905, rend_intergenic: 15563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166593, rend_intergenic: 164065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171273, rend_intergenic: 166923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 40 predictions persist after filtering for low support