-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_7968754-8167003

-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 HiQ_model.g33112.t1
Valid prediction for GeneMark_model.85469_t
Valid prediction for snap_scaffold_21-snap.1706-T1
Valid prediction for GeneMark_model.85472_t
Valid prediction for snap_scaffold_21-snap.1731-T1
Valid prediction for Augustus_model.g33099.t1
Valid prediction for snap_scaffold_21-snap.1697-T1
Valid prediction for Augustus_model.g33120.t1
Valid prediction for CodingQuarry_transcript_32594-T1
Valid prediction for GeneMark_model.85461_t
Valid prediction for GeneMark_model.85443_t
Valid prediction for HiQ_model.g33098.t1
Valid prediction for GeneMark_model.85458_t
Valid prediction for CodingQuarry_transcript_32593-T1
Valid prediction for Augustus_model.g33100.t1
Valid prediction for snap_scaffold_21-snap.1730-T1
Valid prediction for snap_scaffold_21-snap.1713-T1
Valid prediction for Augustus_model.g33110.t1
Valid prediction for GlimmerHMM_glimmerT_49369-T1
Valid prediction for GeneMark_model.85452_t
Valid prediction for snap_scaffold_21-snap.1699-T1
Valid prediction for GeneMark_model.85449_t
Valid prediction for snap_scaffold_21-snap.1696-T1
Valid prediction for CodingQuarry_transcript_32595-T1
Valid prediction for GlimmerHMM_glimmerT_49345-T1
Valid prediction for pasa_asmbl_28797.p1
Valid prediction for snap_scaffold_21-snap.1690-T1
Valid prediction for GeneMark_model.85479_t
Valid prediction for snap_scaffold_21-snap.1729-T1
Valid prediction for GeneMark_model.85482_t
Valid prediction for GlimmerHMM_glimmerT_49357-T1
Valid prediction for snap_scaffold_21-snap.1708-T1
Valid prediction for GlimmerHMM_glimmerT_49352-T1
Valid prediction for GeneMark_model.85444_t
Valid prediction for GeneMark_model.85441_t
Valid prediction for GlimmerHMM_glimmerT_49344-T1
Valid prediction for snap_scaffold_21-snap.1695-T1
Valid prediction for GlimmerHMM_glimmerT_49353-T1
Couldn't classify 104249, 104302
Couldn't classify 105115, 105363
Sorry, prediction pasa_asmbl_28800.p1 fails validation.
(TGT)	 AC	104249-104302	GT	AGG
(GTG)	 AG	104785-104925	GT	AGG
(GAG)	 AG	105115-105363	TG	AGT
-recovered pasa_asmbl_28800.p1, internal, 104785, 104925
Valid prediction for GeneMark_model.85473_t
Valid prediction for snap_scaffold_21-snap.1712-T1
Valid prediction for Augustus_model.g33107.t1
Valid prediction for CodingQuarry_transcript_32597-T1
Valid prediction for GeneMark_model.85465_t
Valid prediction for HiQ_model.g33102.t1
Valid prediction for snap_scaffold_21-snap.1714-T1
Valid prediction for Augustus_model.g33108.t1
Valid prediction for GeneMark_model.85455_t
Valid prediction for GeneMark_model.85480_t
Valid prediction for snap_scaffold_21-snap.1728-T1
Valid prediction for GeneMark_model.85477_t
Valid prediction for GlimmerHMM_glimmerT_49359-T1
Valid prediction for GlimmerHMM_glimmerT_49349-T1
Valid prediction for snap_scaffold_21-snap.1698-T1
Valid prediction for Augustus_model.g33105.t1
Valid prediction for snap_scaffold_21-snap.1718-T1
Valid prediction for snap_scaffold_21-snap.1722-T1
Valid prediction for GlimmerHMM_glimmerT_49348-T1
Valid prediction for GlimmerHMM_glimmerT_49346-T1
Valid prediction for GeneMark_model.85454_t
Valid prediction for GeneMark_model.85463_t
Valid prediction for GlimmerHMM_glimmerT_49350-T1
Valid prediction for snap_scaffold_21-snap.1694-T1
Valid prediction for GlimmerHMM_glimmerT_49356-T1
Valid prediction for snap_scaffold_21-snap.1701-T1
Valid prediction for pasa_asmbl_28802.p1
Couldn't classify 16398, 16457
Sorry, prediction pasa_asmbl_28789.p1 fails validation.
(GTG)	 GC	16398-16457	GT	TGG
(GCA)	 AG	17918-18228	GT	TGG
(GGC)	 AG	19308-19384	GT	AGG
(GGA)	 AG	19528-19640	AA	AAA
-recovered pasa_asmbl_28789.p1, terminal, 19528, 19640
-recovered pasa_asmbl_28789.p1, internal, 17918, 18228
-recovered pasa_asmbl_28789.p1, internal, 19308, 19384
Valid prediction for pasa_asmbl_28791.p1
Valid prediction for GlimmerHMM_glimmerT_49368-T1
Valid prediction for pasa_asmbl_28803.p1
Valid prediction for GlimmerHMM_glimmerT_49363-T1
Valid prediction for Augustus_model.g33104.t1
Valid prediction for Augustus_model.g33119.t1
Valid prediction for snap_scaffold_21-snap.1703-T1
Valid prediction for GeneMark_model.85450_t
Valid prediction for HiQ_model.g33103.t1
Valid prediction for GeneMark_model.85447_t
Valid prediction for snap_scaffold_21-snap.1693-T1
Valid prediction for GeneMark_model.85448_t
Valid prediction for Augustus_model.g33111.t1
Valid prediction for GlimmerHMM_glimmerT_49362-T1
Valid prediction for GeneMark_model.85474_t
Couldn't classify 95955, 96164
Couldn't classify 96878, 97123
Sorry, prediction pasa_asmbl_28799.p1 fails validation.
(GAC)	 TG	95955-96164	GT	AGG
(GAC)	 AG	96878-97123	AC	ACA
Valid prediction for GeneMark_model.85464_t
Valid prediction for snap_scaffold_21-snap.1721-T1
Valid prediction for HiQ_model.g33116.t1
Valid prediction for snap_scaffold_21-snap.1732-T1
Valid prediction for snap_scaffold_21-snap.1715-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 GlimmerHMM_glimmerT_49347-T1
Valid prediction for GeneMark_model.85459_t
Valid prediction for GeneMark_model.85451_t
Valid prediction for snap_scaffold_21-snap.1723-T1
Valid prediction for Augustus_model.g33106.t1
Valid prediction for HiQ_model.g33101.t1
Valid prediction for snap_scaffold_21-snap.1725-T1
Valid prediction for GlimmerHMM_glimmerT_49358-T1
Valid prediction for CodingQuarry_transcript_32592-T1
Valid prediction for Augustus_model.g33118.t1
Valid prediction for HiQ_model.g33097.t1
Valid prediction for GlimmerHMM_glimmerT_49366-T1
Valid prediction for GeneMark_model.85471_t
Valid prediction for GeneMark_model.85483_t
Couldn't classify 69236, 69348
Sorry, prediction GlimmerHMM_glimmerT_49360-T1 fails validation.
(ATG)	 TC	67068-67255	GT	AGG
(GAA)	 AG	68163-68269	GT	CGG
(GAG)	 AG	69236-69348	NT	CNN
(AAC)	 AG	69796-69895	GT	CGG
(GTG)	 AG	70331-70603	GT	AGG
(ACA)	 AG	70974-71353	AC	GAA
-recovered GlimmerHMM_glimmerT_49360-T1, initial, 67068, 67255
-recovered GlimmerHMM_glimmerT_49360-T1, terminal, 70974, 71353
-recovered GlimmerHMM_glimmerT_49360-T1, internal, 68163, 68269
-recovered GlimmerHMM_glimmerT_49360-T1, internal, 69796, 69895
-recovered GlimmerHMM_glimmerT_49360-T1, internal, 70331, 70603
Valid prediction for CodingQuarry_transcript_32596-T1
Valid prediction for GeneMark_model.85457_t
Couldn't classify 185198, 185317
Couldn't classify 187192, 187234
Sorry, prediction pasa_asmbl_27896.p1 fails validation.
(GAG)	 AT	185198-185317	GT	AGG
(TTT)	 AG	185529-185629	GT	AGG
(GGA)	 AG	185834-185967	GT	GGG
(ACA)	 AG	186235-186343	GT	AGG
(TCT)	 AG	186441-186504	GT	AAG
(CAT)	 AG	186600-186686	GT	GGG
(TTC)	 AG	186896-186993	GT	AGG
(GTA)	 AG	187192-187234	TG	GCT
-recovered pasa_asmbl_27896.p1, internal, 185529, 185629
-recovered pasa_asmbl_27896.p1, internal, 185834, 185967
-recovered pasa_asmbl_27896.p1, internal, 186235, 186343
-recovered pasa_asmbl_27896.p1, internal, 186441, 186504
-recovered pasa_asmbl_27896.p1, internal, 186600, 186686
-recovered pasa_asmbl_27896.p1, internal, 186896, 186993
Valid prediction for GlimmerHMM_glimmerT_49343-T1
Valid prediction for GeneMark_model.85440_t
Valid prediction for GeneMark_model.85439_t
Valid prediction for snap_scaffold_21-snap.1711-T1
Valid prediction for snap_scaffold_21-snap.1704-T1
Couldn't classify 33070, 33098
Sorry, prediction pasa_asmbl_27910.p1 fails validation.
(CCC)	 GC	33070-33098	GC	AGG
(CAC)	 AG	34615-34878	GT	AGG
(AAA)	 AG	35550-35576	GT	AGG
(ACC)	 AG	37844-38270	GA	GAG
-recovered pasa_asmbl_27910.p1, terminal, 37844, 38270
-recovered pasa_asmbl_27910.p1, internal, 34615, 34878
-recovered pasa_asmbl_27910.p1, internal, 35550, 35576
Valid prediction for Augustus_model.g33109.t1
Valid prediction for Augustus_model.g33114.t1
Valid prediction for snap_scaffold_21-snap.1720-T1
Valid prediction for GlimmerHMM_glimmerT_49355-T1
Valid prediction for GeneMark_model.85475_t
Valid prediction for GeneMark_model.85478_t
Valid prediction for snap_scaffold_21-snap.1705-T1
Valid prediction for GeneMark_model.85476_t
Valid prediction for pasa_asmbl_27905.p2
Valid prediction for GeneMark_model.85462_t
Valid prediction for GlimmerHMM_glimmerT_49351-T1
Valid prediction for snap_scaffold_21-snap.1709-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49367-T1
Valid prediction for snap_scaffold_21-snap.1710-T1
Valid prediction for snap_scaffold_21-snap.1719-T1
Valid prediction for GeneMark_model.85481_t
Valid prediction for snap_scaffold_21-snap.1702-T1
Valid prediction for pasa_asmbl_27900.p1
Valid prediction for Augustus_model.g33117.t1
Valid prediction for snap_scaffold_21-snap.1726-T1
Valid prediction for GeneMark_model.85453_t
Valid prediction for snap_scaffold_21-snap.1724-T1
Valid prediction for Augustus_model.g33095.t1
Valid prediction for GlimmerHMM_glimmerT_49364-T1
Valid prediction for snap_scaffold_21-snap.1692-T1
Valid prediction for snap_scaffold_21-snap.1691-T1
Valid prediction for snap_scaffold_21-snap.1716-T1
Valid prediction for snap_scaffold_21-snap.1717-T1
Valid prediction for GlimmerHMM_glimmerT_49361-T1
Valid prediction for GlimmerHMM_glimmerT_49354-T1
Valid prediction for GlimmerHMM_glimmerT_49365-T1
Valid prediction for HiQ_model.g33113.t1
Valid prediction for snap_scaffold_21-snap.1727-T1
Valid prediction for Augustus_model.g33115.t1
Valid prediction for GeneMark_model.85468_t
Valid prediction for GeneMark_model.85470_t
Valid prediction for pasa_asmbl_27908.p1
Valid prediction for GeneMark_model.85456_t
Valid prediction for snap_scaffold_21-snap.1700-T1
Valid prediction for GeneMark_model.85442_t
Valid prediction for GeneMark_model.85460_t
Valid prediction for snap_scaffold_21-snap.1707-T1
Valid prediction for Augustus_model.g33096.t1
Valid prediction for GeneMark_model.85466_t
Valid prediction for GeneMark_model.85467_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8697, rend_intergenic: 4736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62246, rend_intergenic: 60857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65013, rend_intergenic: 64348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68223, rend_intergenic: 65689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73788, rend_intergenic: 71342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75308, rend_intergenic: 73833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76323, rend_intergenic: 75429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82388, rend_intergenic: 76490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132410, rend_intergenic: 129671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139939, rend_intergenic: 133324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141882, rend_intergenic: 140163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175035, rend_intergenic: 166833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198250
-exon list size: 592


building trellis

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97.0    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 8697, rend_intergenic: 4736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62246, rend_intergenic: 60857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65013, rend_intergenic: 64348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68223, rend_intergenic: 65689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73788, rend_intergenic: 71342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75308, rend_intergenic: 73833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76323, rend_intergenic: 75429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82388, rend_intergenic: 76490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132410, rend_intergenic: 129671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139939, rend_intergenic: 133324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141882, rend_intergenic: 140163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175035, rend_intergenic: 166833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support