-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_9276580-9422508

-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 snap_scaffold_13-snap.1699-T1
Valid prediction for GeneMark_model.56017_t
Valid prediction for Augustus_model.g22049.t1
Valid prediction for snap_scaffold_13-snap.1693-T1
Valid prediction for GlimmerHMM_glimmerT_32829-T1
Valid prediction for GlimmerHMM_glimmerT_32832-T1
Valid prediction for GlimmerHMM_glimmerT_32830-T1
Valid prediction for GlimmerHMM_glimmerT_32844-T1
Valid prediction for CodingQuarry_transcript_13166-T1
Valid prediction for snap_scaffold_13-snap.1701-T1
Valid prediction for snap_scaffold_13-snap.1688-T1
Valid prediction for snap_scaffold_13-snap.1675-T1
Valid prediction for GlimmerHMM_glimmerT_32836-T1
Valid prediction for GeneMark_model.56008_t
Valid prediction for GlimmerHMM_glimmerT_32845-T1
Valid prediction for snap_scaffold_13-snap.1694-T1
Valid prediction for GlimmerHMM_glimmerT_32841-T1
Valid prediction for GeneMark_model.55994_t
Valid prediction for Augustus_model.g22048.t1
Valid prediction for GeneMark_model.56019_t
Valid prediction for snap_scaffold_13-snap.1692-T1
Valid prediction for GeneMark_model.56002_t
Couldn't classify 101746, 101952
Couldn't classify 102237, 102542
Sorry, prediction pasa_asmbl_11187.p1 fails validation.
(TTC)	 AC	101746-101952	GT	AAG
(TTT)	 AG	102237-102542	GG	CAG
Valid prediction for GlimmerHMM_glimmerT_32848-T1
Valid prediction for GeneMark_model.55995_t
Valid prediction for GeneMark_model.56015_t
Valid prediction for snap_scaffold_13-snap.1680-T1
Valid prediction for Augustus_model.g22034.t1
Valid prediction for snap_scaffold_13-snap.1700-T1
Valid prediction for HiQ_model.g22043.t1
Valid prediction for HiQ_model.g22037.t1
Valid prediction for GeneMark_model.55993_t
Valid prediction for snap_scaffold_13-snap.1695-T1
Valid prediction for snap_scaffold_13-snap.1676-T1
Valid prediction for GlimmerHMM_glimmerT_32849-T1
Valid prediction for GlimmerHMM_glimmerT_32843-T1
Valid prediction for snap_scaffold_13-snap.1682-T1
Valid prediction for Augustus_model.g22035.t1
Valid prediction for GeneMark_model.56007_t
Valid prediction for GlimmerHMM_glimmerT_32837-T1
Valid prediction for Augustus_model.g22039.t1
Valid prediction for GlimmerHMM_glimmerT_32828-T1
Valid prediction for GeneMark_model.56009_t
Valid prediction for GlimmerHMM_glimmerT_32834-T1
Valid prediction for CodingQuarry_transcript_13163-T1
Valid prediction for snap_scaffold_13-snap.1684-T1
Valid prediction for GlimmerHMM_glimmerT_32846-T1
Couldn't classify 35040, 35188
Couldn't classify 38235, 38410
Sorry, prediction pasa_asmbl_11177.p1 fails validation.
(GTC)	 AG	35040-35188	GT	AGG
(TGC)	 AG	35492-35614	GT	TCG
(TAT)	 AG	35984-36291	GT	TGG
(GTA)	 AG	36503-36664	GT	TGG
(GGT)	 AG	36929-37092	GT	AGG
(GAC)	 AG	37225-37363	GT	AGG
(GAG)	 AG	37469-37619	GT	AAG
(GTA)	 AG	37924-38039	GT	AGG
(GAC)	 AG	38235-38410	CG	ACC
-recovered pasa_asmbl_11177.p1, internal, 35040, 35188
-recovered pasa_asmbl_11177.p1, internal, 35492, 35614
-recovered pasa_asmbl_11177.p1, internal, 35984, 36291
-recovered pasa_asmbl_11177.p1, internal, 36503, 36664
-recovered pasa_asmbl_11177.p1, internal, 36929, 37092
-recovered pasa_asmbl_11177.p1, internal, 37225, 37363
-recovered pasa_asmbl_11177.p1, internal, 37469, 37619
-recovered pasa_asmbl_11177.p1, internal, 37924, 38039
Valid prediction for snap_scaffold_13-snap.1672-T1
Valid prediction for GeneMark_model.56004_t
Valid prediction for Augustus_model.g22046.t1
Valid prediction for GeneMark_model.55998_t
Valid prediction for snap_scaffold_13-snap.1696-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_32833-T1
Valid prediction for Augustus_model.g22040.t1
Valid prediction for CodingQuarry_transcript_13164-T1
Valid prediction for GeneMark_model.56006_t
Valid prediction for CodingQuarry_transcript_13162-T1
Valid prediction for GeneMark_model.56016_t
Valid prediction for snap_scaffold_13-snap.1677-T1
Couldn't classify 62313, 62377
Sorry, prediction pasa_asmbl_9987.p1 fails validation.
(GCA)	 AT	62313-62377	GT	CGG
(CCG)	 AG	62495-62635	GT	AGG
(GTA)	 AG	62923-62977	GT	CGG
(GCA)	 AG	63317-63439	GT	AGG
(CAA)	 AG	63554-63643	GT	AGG
(GTG)	 AG	63832-63959	GT	GAG
(TCG)	 AG	64153-64257	GT	AGG
(GGC)	 AG	64461-64608	GT	AGG
(GTG)	 AG	64759-64930	GT	AGG
(CAC)	 AG	65046-65197	GT	AGG
(AGT)	 AG	65409-65507	GT	AGG
(GTC)	 AG	65680-65781	CA	GAC
-recovered pasa_asmbl_9987.p1, terminal, 65680, 65781
-recovered pasa_asmbl_9987.p1, internal, 62495, 62635
-recovered pasa_asmbl_9987.p1, internal, 62923, 62977
-recovered pasa_asmbl_9987.p1, internal, 63317, 63439
-recovered pasa_asmbl_9987.p1, internal, 63554, 63643
-recovered pasa_asmbl_9987.p1, internal, 63832, 63959
-recovered pasa_asmbl_9987.p1, internal, 64153, 64257
-recovered pasa_asmbl_9987.p1, internal, 64461, 64608
-recovered pasa_asmbl_9987.p1, internal, 64759, 64930
-recovered pasa_asmbl_9987.p1, internal, 65046, 65197
-recovered pasa_asmbl_9987.p1, internal, 65409, 65507
Valid prediction for GeneMark_model.56005_t
Valid prediction for GeneMark_model.56010_t
Couldn't classify 46366, 46475
Sorry, prediction pasa_asmbl_10371.p1 fails validation.
(ACT)	 TC	46366-46475	GT	GGG
(GTT)	 AG	46905-47023	GT	AGG
(ATT)	 AG	47218-47303	GT	CGG
(GCT)	 AG	47416-47550	GT	TGG
(TTC)	 AG	47662-47774	GT	TGG
(GTG)	 AG	47857-47906	GT	GGG
(CCA)	 AG	48003-48166	GT	AGG
(CTG)	 AG	48268-48429	GT	AGG
(CCT)	 AG	48516-48593	GT	AGG
(GCT)	 AG	48684-48742	GT	CAG
(GGT)	 AG	48835-48957	GT	ACG
(ACT)	 AG	49064-49239	GT	AGG
(AGA)	 AG	49422-49625	GT	AGG
(ATA)	 AG	49792-49902	GT	GAG
(GTA)	 AG	50011-50075	GT	AGG
(CAA)	 AG	50219-50371	AG	GAA
add_exon() Sorry, pasa_asmbl_10371.p1 49792-49902-terminal-1 is invalid.
-recovered pasa_asmbl_10371.p1, terminal, 49792, 49902
-recovered pasa_asmbl_10371.p1, terminal, 50219, 50371
-recovered pasa_asmbl_10371.p1, internal, 46905, 47023
-recovered pasa_asmbl_10371.p1, internal, 47218, 47303
-recovered pasa_asmbl_10371.p1, internal, 47416, 47550
-recovered pasa_asmbl_10371.p1, internal, 47662, 47774
-recovered pasa_asmbl_10371.p1, internal, 47857, 47906
-recovered pasa_asmbl_10371.p1, internal, 48003, 48166
-recovered pasa_asmbl_10371.p1, internal, 48268, 48429
-recovered pasa_asmbl_10371.p1, internal, 48516, 48593
-recovered pasa_asmbl_10371.p1, internal, 48684, 48742
-recovered pasa_asmbl_10371.p1, internal, 48835, 48957
-recovered pasa_asmbl_10371.p1, internal, 49064, 49239
-recovered pasa_asmbl_10371.p1, internal, 49422, 49625
-recovered pasa_asmbl_10371.p1, internal, 49792, 49902
-recovered pasa_asmbl_10371.p1, internal, 50011, 50075
Valid prediction for pasa_asmbl_9982.p1
Valid prediction for GlimmerHMM_glimmerT_32831-T1
Couldn't classify 89549, 89701
Sorry, prediction pasa_asmbl_9976.p1 fails validation.
(CTA)	 AG	89549-89701	GT	GGG
(GCC)	 AG	90536-90601	GT	AGG
(ATT)	 AG	90719-90830	GT	CGG
(AAC)	 AG	90994-91046	GT	AGG
(GAT)	 AG	91237-94101	GT	GGG
(TCT)	 AG	94552-94695	GT	AGG
(AAG)	 AG	94879-94979	GT	AGG
(GGA)	 AG	95658-95715	GT	AGG
(AGC)	 AG	97802-97847	GT	CAG
(GCA)	 AG	98011-98153	GT	AGG
(TCT)	 AG	98272-98415	GT	AGG
(GTG)	 AG	98587-98791	GT	AGG
(CCA)	 AG	98931-99076	GT	TGG
(GTG)	 AG	99275-99382	GT	CTG
(TAC)	 AG	99484-99591	GT	AGG
(CTG)	 AG	99683-99986	GT	GGG
(AGA)	 AG	100073-100173	GT	AGG
(TTT)	 AG	100310-100672	GC	AAG
-recovered pasa_asmbl_9976.p1, terminal, 100310, 100672
-recovered pasa_asmbl_9976.p1, internal, 89549, 89701
-recovered pasa_asmbl_9976.p1, internal, 90536, 90601
-recovered pasa_asmbl_9976.p1, internal, 90719, 90830
-recovered pasa_asmbl_9976.p1, internal, 90994, 91046
-recovered pasa_asmbl_9976.p1, internal, 91237, 94101
-recovered pasa_asmbl_9976.p1, internal, 94552, 94695
-recovered pasa_asmbl_9976.p1, internal, 94879, 94979
-recovered pasa_asmbl_9976.p1, internal, 95658, 95715
-recovered pasa_asmbl_9976.p1, internal, 97802, 97847
-recovered pasa_asmbl_9976.p1, internal, 98011, 98153
-recovered pasa_asmbl_9976.p1, internal, 98272, 98415
-recovered pasa_asmbl_9976.p1, internal, 98587, 98791
-recovered pasa_asmbl_9976.p1, internal, 98931, 99076
-recovered pasa_asmbl_9976.p1, internal, 99275, 99382
-recovered pasa_asmbl_9976.p1, internal, 99484, 99591
-recovered pasa_asmbl_9976.p1, internal, 99683, 99986
-recovered pasa_asmbl_9976.p1, internal, 100073, 100173
-recovered pasa_asmbl_9976.p1, internal, 100310, 100672
Valid prediction for snap_scaffold_13-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_32826-T1
Valid prediction for GlimmerHMM_glimmerT_32840-T1
Valid prediction for Augustus_model.g22033.t1
Valid prediction for CodingQuarry_transcript_13167-T1
Valid prediction for snap_scaffold_13-snap.1678-T1
Valid prediction for CodingQuarry_transcript_13165-T1
Couldn't classify 72020, 72108
Sorry, prediction pasa_asmbl_10348.p1 fails validation.
(GTA)	 AG	72020-72108	GT	AGG
(GCC)	 AG	72185-72273	GT	TGG
(CCA)	 AG	72350-72530	GT	GGG
(ATG)	 AG	72610-72715	GT	AAG
(GTG)	 AG	72789-72874	GT	GGG
(CTG)	 AG	72980-73071	GT	AGG
(GAC)	 AG	73157-73221	GC	AAG
add_exon() Sorry, pasa_asmbl_10348.p1 72610-72715-initial-1 is invalid.
-recovered pasa_asmbl_10348.p1, initial, 72610, 72715
-recovered pasa_asmbl_10348.p1, terminal, 73157, 73221
-recovered pasa_asmbl_10348.p1, internal, 72020, 72108
-recovered pasa_asmbl_10348.p1, internal, 72185, 72273
-recovered pasa_asmbl_10348.p1, internal, 72350, 72530
-recovered pasa_asmbl_10348.p1, internal, 72610, 72715
-recovered pasa_asmbl_10348.p1, internal, 72789, 72874
-recovered pasa_asmbl_10348.p1, internal, 72980, 73071
-recovered pasa_asmbl_10348.p1, internal, 73157, 73221
Valid prediction for GlimmerHMM_glimmerT_32838-T1
Valid prediction for GeneMark_model.55997_t
Valid prediction for snap_scaffold_13-snap.1674-T1
Valid prediction for GeneMark_model.55999_t
Valid prediction for GeneMark_model.56001_t
Valid prediction for GeneMark_model.56013_t
Valid prediction for snap_scaffold_13-snap.1685-T1
Valid prediction for snap_scaffold_13-snap.1697-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32825-T1
Valid prediction for snap_scaffold_13-snap.1687-T1
Valid prediction for Augustus_model.g22050.t1
Valid prediction for GeneMark_model.55996_t
Valid prediction for GlimmerHMM_glimmerT_32842-T1
Valid prediction for snap_scaffold_13-snap.1673-T1
Valid prediction for Augustus_model.g22041.t1
Valid prediction for GeneMark_model.56000_t
Valid prediction for HiQ_model.g22036.t1
Valid prediction for GeneMark_model.56018_t
Valid prediction for GeneMark_model.56014_t
Valid prediction for GeneMark_model.55992_t
Valid prediction for snap_scaffold_13-snap.1702-T1
Valid prediction for Augustus_model.g22032.t1
Couldn't classify 141129, 141266
Couldn't classify 141760, 141811
Sorry, prediction pasa_asmbl_10326.p1 fails validation.
(GAC)	 AG	141129-141266	GT	TGG
(GAA)	 AG	141424-141492	GT	AGG
(GTC)	 AG	141599-141654	GT	TAG
(TTC)	 AG	141760-141811	AG	AGA
-recovered pasa_asmbl_10326.p1, internal, 141129, 141266
-recovered pasa_asmbl_10326.p1, internal, 141424, 141492
-recovered pasa_asmbl_10326.p1, internal, 141599, 141654
Valid prediction for snap_scaffold_13-snap.1679-T1
Valid prediction for Augustus_model.g22045.t1
Valid prediction for snap_scaffold_13-snap.1689-T1
Valid prediction for GlimmerHMM_glimmerT_32847-T1
Valid prediction for snap_scaffold_13-snap.1698-T1
Valid prediction for snap_scaffold_13-snap.1681-T1
Valid prediction for snap_scaffold_13-snap.1686-T1
Valid prediction for snap_scaffold_13-snap.1683-T1
Valid prediction for GeneMark_model.56003_t
Valid prediction for HiQ_model.g22038.t1
Valid prediction for Augustus_model.g22047.t1
Valid prediction for snap_scaffold_13-snap.1690-T1
Valid prediction for GlimmerHMM_glimmerT_32839-T1
Valid prediction for CodingQuarry_transcript_13168-T1
Valid prediction for Augustus_model.g22044.t1
Valid prediction for GlimmerHMM_glimmerT_32835-T1
Valid prediction for GeneMark_model.56020_t
Valid prediction for GlimmerHMM_glimmerT_32827-T1
Valid prediction for GeneMark_model.56012_t
Valid prediction for Augustus_model.g22042.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 54737, rend_intergenic: 51199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116708, rend_intergenic: 111157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142578, rend_intergenic: 134282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 145929
-exon list size: 449


building trellis

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93.6    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 54737, rend_intergenic: 51199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116708, rend_intergenic: 111157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142578, rend_intergenic: 134282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support