-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_11984007-12166594

-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.g21696.t1
Valid prediction for Augustus_model.g21695.t1
Valid prediction for snap_scaffold_13-snap.2272-T1
Valid prediction for snap_scaffold_13-snap.2267-T1
Valid prediction for GlimmerHMM_glimmerT_32482-T1
Valid prediction for snap_scaffold_13-snap.2264-T1
Valid prediction for snap_scaffold_13-snap.2277-T1
Valid prediction for snap_scaffold_13-snap.2248-T1
Couldn't classify 102760, 102840
Sorry, prediction pasa_asmbl_11327.p1 fails validation.
(ATG)	 TC	102112-102218	GT	CAG
(GGA)	 AG	102367-102589	GT	GGG
(AGA)	 AG	102760-102840	CC	ACC
-recovered pasa_asmbl_11327.p1, initial, 102112, 102218
-recovered pasa_asmbl_11327.p1, internal, 102367, 102589
Valid prediction for snap_scaffold_13-snap.2281-T1
Valid prediction for snap_scaffold_13-snap.2259-T1
Valid prediction for Augustus_model.g21704.t1
Valid prediction for GlimmerHMM_glimmerT_32480-T1
Couldn't classify 103552, 103750
Couldn't classify 111293, 111509
Couldn't classify 111917, 111995
Sorry, prediction pasa_asmbl_11328.p1 fails validation.
(ACG)	 AG	103552-103750	GT	AGG
(ATT)	 AG	104737-104872	GT	AGG
(CCA)	 AG	105109-105195	GT	AGG
(GTT)	 AG	105303-105480	GT	AGG
(GTG)	 AG	107897-108281	GT	AGG
(GAG)	 AG	108480-108644	GT	CGG
(AGG)	 AG	110489-110632	GT	AGG
(TGC)	 AG	111293-111509	AT	GGA
(GTT)	 AC	111917-111995	GT	AGG
(ATT)	 AG	112324-112434	CA	AGC
-recovered pasa_asmbl_11328.p1, terminal, 112324, 112434
-recovered pasa_asmbl_11328.p1, internal, 103552, 103750
-recovered pasa_asmbl_11328.p1, internal, 104737, 104872
-recovered pasa_asmbl_11328.p1, internal, 105109, 105195
-recovered pasa_asmbl_11328.p1, internal, 105303, 105480
-recovered pasa_asmbl_11328.p1, internal, 107897, 108281
-recovered pasa_asmbl_11328.p1, internal, 108480, 108644
-recovered pasa_asmbl_11328.p1, internal, 110489, 110632
Valid prediction for CodingQuarry_transcript_13268-T1
Valid prediction for GlimmerHMM_glimmerT_32490-T1
Valid prediction for snap_scaffold_13-snap.2247-T1
Valid prediction for snap_scaffold_13-snap.2257-T1
Valid prediction for GlimmerHMM_glimmerT_32477-T1
Valid prediction for snap_scaffold_13-snap.2242-T1
Valid prediction for snap_scaffold_13-snap.2263-T1
Valid prediction for Augustus_model.g21698.t1
Valid prediction for pasa_asmbl_11338.p1
Valid prediction for GlimmerHMM_glimmerT_32481-T1
Valid prediction for GlimmerHMM_glimmerT_32473-T1
Valid prediction for GlimmerHMM_glimmerT_32489-T1
Valid prediction for HiQ_model.g21705.t1
Couldn't classify 17339, 17944
Sorry, prediction pasa_asmbl_11320.p1 fails validation.
(AGA)	 TT	17339-17944	GT	AGG
(GAG)	 AG	18058-18120	GT	AGG
(GAG)	 AG	18287-18408	GT	GGG
(AAT)	 AG	18641-18707	GT	TGG
(GTG)	 AG	19501-19640	GT	AGG
(ATC)	 AG	20315-20525	CA	GAC
-recovered pasa_asmbl_11320.p1, terminal, 20315, 20525
-recovered pasa_asmbl_11320.p1, internal, 18058, 18120
-recovered pasa_asmbl_11320.p1, internal, 18287, 18408
-recovered pasa_asmbl_11320.p1, internal, 18641, 18707
-recovered pasa_asmbl_11320.p1, internal, 19501, 19640
Valid prediction for GlimmerHMM_glimmerT_32493-T1
Valid prediction for Augustus_model.g21691.t1
Couldn't classify 50037, 50243
Sorry, prediction pasa_asmbl_11322.p1 fails validation.
(ATG)	 GG	44621-44818	GT	AGG
(GTC)	 AG	45040-45186	GT	AGG
(GGA)	 AG	45433-45588	GT	AGG
(GAA)	 AG	45766-45822	GT	AGG
(GGG)	 AG	46384-46561	GT	CGG
(TTA)	 AG	46919-47081	GT	AGG
(TTC)	 AG	47759-47901	GT	TGG
(AGT)	 AG	48094-48266	GT	AGG
(TGG)	 AG	48549-48782	GT	GGG
(GAT)	 AG	48997-49323	GT	AGG
(GTG)	 AG	49525-49710	GT	AGG
(CGT)	 AG	50037-50243	GT	AGG
-recovered pasa_asmbl_11322.p1, initial, 44621, 44818
-recovered pasa_asmbl_11322.p1, internal, 45040, 45186
-recovered pasa_asmbl_11322.p1, internal, 45433, 45588
-recovered pasa_asmbl_11322.p1, internal, 45766, 45822
-recovered pasa_asmbl_11322.p1, internal, 46384, 46561
-recovered pasa_asmbl_11322.p1, internal, 46919, 47081
-recovered pasa_asmbl_11322.p1, internal, 47759, 47901
-recovered pasa_asmbl_11322.p1, internal, 48094, 48266
-recovered pasa_asmbl_11322.p1, internal, 48549, 48782
-recovered pasa_asmbl_11322.p1, internal, 48997, 49323
-recovered pasa_asmbl_11322.p1, internal, 49525, 49710
-recovered pasa_asmbl_11322.p1, internal, 50037, 50243
Valid prediction for GlimmerHMM_glimmerT_32483-T1
Valid prediction for HiQ_model.g21701.t1
Valid prediction for Augustus_model.g21706.t1
Valid prediction for Augustus_model.g21697.t1
Valid prediction for Augustus_model.g21689.t1
Valid prediction for snap_scaffold_13-snap.2280-T1
Valid prediction for snap_scaffold_13-snap.2245-T1
Valid prediction for Augustus_model.g21703.t1
Valid prediction for snap_scaffold_13-snap.2244-T1
Valid prediction for GlimmerHMM_glimmerT_32486-T1
Valid prediction for snap_scaffold_13-snap.2271-T1
Couldn't classify 51794, 51895
Sorry, prediction pasa_asmbl_11323.p1 fails validation.
(CAG)	 CA	51794-51895	GT	ATG
(TGC)	 AG	52118-52207	GT	CTG
(TGG)	 AG	52327-52441	GT	TAG
(CGT)	 AG	52633-52745	GT	CCG
(ACG)	 AG	53243-53353	GT	TGG
(AAC)	 AG	53666-53714	GT	AGG
(GGC)	 AG	54018-54114	GT	GAG
(GAA)	 AG	54251-54416	GT	AGG
(AAG)	 AG	54675-54725	CA	GAC
-recovered pasa_asmbl_11323.p1, terminal, 54675, 54725
-recovered pasa_asmbl_11323.p1, internal, 52118, 52207
-recovered pasa_asmbl_11323.p1, internal, 52327, 52441
-recovered pasa_asmbl_11323.p1, internal, 52633, 52745
-recovered pasa_asmbl_11323.p1, internal, 53243, 53353
-recovered pasa_asmbl_11323.p1, internal, 53666, 53714
-recovered pasa_asmbl_11323.p1, internal, 54018, 54114
-recovered pasa_asmbl_11323.p1, internal, 54251, 54416
Valid prediction for snap_scaffold_13-snap.2279-T1
Valid prediction for GlimmerHMM_glimmerT_32471-T1
Valid prediction for snap_scaffold_13-snap.2273-T1
Valid prediction for snap_scaffold_13-snap.2256-T1
Valid prediction for snap_scaffold_13-snap.2252-T1
Valid prediction for GlimmerHMM_glimmerT_32470-T1
Valid prediction for GlimmerHMM_glimmerT_32492-T1
Valid prediction for Augustus_model.g21707.t1
Valid prediction for snap_scaffold_13-snap.2274-T1
Valid prediction for GlimmerHMM_glimmerT_32479-T1
Valid prediction for GlimmerHMM_glimmerT_32487-T1
Valid prediction for GlimmerHMM_glimmerT_32491-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 pasa_asmbl_10399.p1
Valid prediction for snap_scaffold_13-snap.2260-T1
Valid prediction for Augustus_model.g21688.t1
Valid prediction for GlimmerHMM_glimmerT_32475-T1
Valid prediction for snap_scaffold_13-snap.2249-T1
Couldn't classify 172056, 172176
Couldn't classify 177730, 177827
Sorry, prediction pasa_asmbl_10120.p1 fails validation.
(GAC)	 GG	172056-172176	GT	AGG
(GTG)	 AG	172767-172856	GT	CGG
(TCT)	 AG	173666-173716	GT	CAG
(AGT)	 AG	173857-173942	GT	GGG
(CGT)	 AG	174210-174338	GT	CGG
(GAG)	 AG	174541-174601	GT	AGG
(GCC)	 AG	174928-174983	GT	AGG
(GCG)	 AG	175676-175852	GT	AGG
(GAC)	 AG	176716-176813	GT	AGG
(GCT)	 AG	176970-177056	GT	AGG
(GTT)	 AG	177146-177281	GT	AGG
(GAG)	 AG	177491-177578	GT	TGG
(GCT)	 AG	177730-177827	CA	ACC
add_exon() Sorry, pasa_asmbl_10120.p1 176970-177056-terminal-1 is invalid.
-recovered pasa_asmbl_10120.p1, terminal, 176970, 177056
-recovered pasa_asmbl_10120.p1, internal, 172767, 172856
-recovered pasa_asmbl_10120.p1, internal, 173666, 173716
-recovered pasa_asmbl_10120.p1, internal, 173857, 173942
-recovered pasa_asmbl_10120.p1, internal, 174210, 174338
-recovered pasa_asmbl_10120.p1, internal, 174541, 174601
-recovered pasa_asmbl_10120.p1, internal, 174928, 174983
-recovered pasa_asmbl_10120.p1, internal, 175676, 175852
-recovered pasa_asmbl_10120.p1, internal, 176716, 176813
-recovered pasa_asmbl_10120.p1, internal, 176970, 177056
-recovered pasa_asmbl_10120.p1, internal, 177146, 177281
-recovered pasa_asmbl_10120.p1, internal, 177491, 177578
Valid prediction for snap_scaffold_13-snap.2262-T1
Valid prediction for Augustus_model.g21693.t1
Valid prediction for snap_scaffold_13-snap.2241-T1
Valid prediction for snap_scaffold_13-snap.2268-T1
Valid prediction for Augustus_model.g21700.t1
Valid prediction for GlimmerHMM_glimmerT_32469-T1
Valid prediction for snap_scaffold_13-snap.2255-T1
Valid prediction for Augustus_model.g21690.t1
Valid prediction for Augustus_model.g21702.t1
Valid prediction for snap_scaffold_13-snap.2276-T1
Valid prediction for snap_scaffold_13-snap.2266-T1
Valid prediction for snap_scaffold_13-snap.2246-T1
Couldn't classify 141696, 141715
Couldn't classify 141794, 141905
Sorry, prediction CodingQuarry_transcript_13266-T1 fails validation.
(ATG)	 CA	141696-141715	AA	GTA
(CCA)	 GT	141794-141905	CA	GAC
Valid prediction for Augustus_model.g21699.t1
Valid prediction for snap_scaffold_13-snap.2275-T1
Valid prediction for GlimmerHMM_glimmerT_32476-T1
Valid prediction for Augustus_model.g21692.t1
Valid prediction for CodingQuarry_transcript_13267-T1
Valid prediction for GlimmerHMM_glimmerT_32468-T1
Valid prediction for snap_scaffold_13-snap.2278-T1
Valid prediction for snap_scaffold_13-snap.2240-T1
Valid prediction for snap_scaffold_13-snap.2239-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32478-T1
Valid prediction for snap_scaffold_13-snap.2270-T1
Valid prediction for Augustus_model.g21694.t1
Valid prediction for GlimmerHMM_glimmerT_32472-T1
Valid prediction for snap_scaffold_13-snap.2258-T1
Valid prediction for GlimmerHMM_glimmerT_32485-T1
Valid prediction for GlimmerHMM_glimmerT_32474-T1
Valid prediction for GlimmerHMM_glimmerT_32488-T1
Valid prediction for GlimmerHMM_glimmerT_32484-T1
Valid prediction for snap_scaffold_13-snap.2269-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2250-T1
Valid prediction for snap_scaffold_13-snap.2251-T1
Valid prediction for snap_scaffold_13-snap.2254-T1
Couldn't classify 83274, 83328
Sorry, prediction pasa_asmbl_10121.p1 fails validation.
(ATT)	 TA	83274-83328	GT	GAG
(AGT)	 AG	83604-83743	GC	AGG
(GTG)	 AG	83975-84079	CC	GAC
-recovered pasa_asmbl_10121.p1, terminal, 83975, 84079
-recovered pasa_asmbl_10121.p1, internal, 83604, 83743
Valid prediction for snap_scaffold_13-snap.2265-T1
Valid prediction for snap_scaffold_13-snap.2261-T1
Valid prediction for snap_scaffold_13-snap.2253-T1
Valid prediction for snap_scaffold_13-snap.2243-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10063, rend_intergenic: 6669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12830, rend_intergenic: 10502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55171, rend_intergenic: 48578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71348, rend_intergenic: 65607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74781, rend_intergenic: 71440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84540, rend_intergenic: 74998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91695, rend_intergenic: 84589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111549, rend_intergenic: 102402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142665, rend_intergenic: 137137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144609, rend_intergenic: 143099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155300, rend_intergenic: 146323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182588
-exon list size: 463


building trellis

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-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 10063, rend_intergenic: 6669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12830, rend_intergenic: 10502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55171, rend_intergenic: 48578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71348, rend_intergenic: 65607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74781, rend_intergenic: 71440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84540, rend_intergenic: 74998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91695, rend_intergenic: 84589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111549, rend_intergenic: 102402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142665, rend_intergenic: 137137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144609, rend_intergenic: 143099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155300, rend_intergenic: 146323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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