-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_4400064-4608045

-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.g21589.t1
Valid prediction for Augustus_model.g21594.t1
Couldn't classify 117011, 117034
Sorry, prediction pasa_asmbl_10789.p1 fails validation.
(AAT)	 TG	117011-117034	GT	AGG
(GGC)	 AG	117384-117511	GT	TGG
(GTG)	 AG	118558-118672	GT	TGG
(GTC)	 AG	119391-119609	GT	CCG
(TCT)	 AG	119903-120016	GT	AGG
(GTC)	 AG	121238-121309	GT	AGG
(ACA)	 AG	121607-121719	GT	TGG
(GAT)	 AG	122577-122674	GT	GGG
(GCG)	 AG	122792-122958	GT	AGG
(AGT)	 AG	123340-123552	CC	AAC
-recovered pasa_asmbl_10789.p1, terminal, 123340, 123552
-recovered pasa_asmbl_10789.p1, internal, 117384, 117511
-recovered pasa_asmbl_10789.p1, internal, 118558, 118672
-recovered pasa_asmbl_10789.p1, internal, 119391, 119609
-recovered pasa_asmbl_10789.p1, internal, 119903, 120016
-recovered pasa_asmbl_10789.p1, internal, 121238, 121309
-recovered pasa_asmbl_10789.p1, internal, 121607, 121719
-recovered pasa_asmbl_10789.p1, internal, 122577, 122674
-recovered pasa_asmbl_10789.p1, internal, 122792, 122958
Valid prediction for snap_scaffold_13-snap.840-T1
Valid prediction for snap_scaffold_13-snap.835-T1
Valid prediction for Augustus_model.g21597.t1
Valid prediction for GeneMark_model.55158_t
Valid prediction for GlimmerHMM_glimmerT_32259-T1
Valid prediction for GeneMark_model.55187_t
Valid prediction for GeneMark_model.55157_t
Valid prediction for GeneMark_model.55173_t
Valid prediction for GeneMark_model.55162_t
Couldn't classify 105856, 105924
Sorry, prediction pasa_asmbl_10787.p1 fails validation.
(AAA)	 GC	105856-105924	GT	AGG
(CAC)	 AG	106082-106274	GT	GGG
(ATC)	 AG	106425-106553	GT	GGG
(AGT)	 AG	106688-106793	GT	AGG
(AGT)	 AG	107541-107672	GT	TTG
(GTG)	 AG	107938-108061	GT	CGG
(ATC)	 AG	108287-108375	GT	AAG
(AGA)	 AG	108653-108777	GT	AGG
(GAG)	 AG	109092-109378	TG	AAT
-recovered pasa_asmbl_10787.p1, terminal, 109092, 109378
-recovered pasa_asmbl_10787.p1, internal, 106082, 106274
-recovered pasa_asmbl_10787.p1, internal, 106425, 106553
-recovered pasa_asmbl_10787.p1, internal, 106688, 106793
-recovered pasa_asmbl_10787.p1, internal, 107541, 107672
-recovered pasa_asmbl_10787.p1, internal, 107938, 108061
-recovered pasa_asmbl_10787.p1, internal, 108287, 108375
-recovered pasa_asmbl_10787.p1, internal, 108653, 108777
Valid prediction for snap_scaffold_13-snap.839-T1
Valid prediction for GeneMark_model.55163_t
Couldn't classify 138805, 139305
Sorry, prediction pasa_asmbl_10793.p2 fails validation.
(CTG)	 CG	138805-139305	GG	GGG
Valid prediction for GeneMark_model.55148_t
Valid prediction for GlimmerHMM_glimmerT_32235-T1
Valid prediction for GlimmerHMM_glimmerT_32234-T1
Valid prediction for GlimmerHMM_glimmerT_32265-T1
Valid prediction for HiQ_model.g21592.t1
Valid prediction for snap_scaffold_13-snap.844-T1
Valid prediction for GeneMark_model.55155_t
Valid prediction for snap_scaffold_13-snap.852-T1
Valid prediction for snap_scaffold_13-snap.843-T1
Valid prediction for snap_scaffold_13-snap.841-T1
Valid prediction for GlimmerHMM_glimmerT_32264-T1
Valid prediction for snap_scaffold_13-snap.831-T1
Valid prediction for GlimmerHMM_glimmerT_32249-T1
Couldn't classify 189577, 189615
Sorry, prediction pasa_asmbl_10797.p1 fails validation.
(AAA)	 GC	189577-189615	GT	CGG
(GAT)	 AG	189969-190059	GT	GGG
(CTA)	 AG	190153-190224	GT	CGG
(ACC)	 AG	190409-190551	AT	AGA
-recovered pasa_asmbl_10797.p1, terminal, 190409, 190551
-recovered pasa_asmbl_10797.p1, internal, 189969, 190059
-recovered pasa_asmbl_10797.p1, internal, 190153, 190224
Valid prediction for CodingQuarry_transcript_12972-T1
Valid prediction for GlimmerHMM_glimmerT_32243-T1
Valid prediction for snap_scaffold_13-snap.855-T1
Valid prediction for GlimmerHMM_glimmerT_32245-T1
Valid prediction for snap_scaffold_13-snap.848-T1
Valid prediction for GlimmerHMM_glimmerT_32244-T1
Valid prediction for GeneMark_model.55164_t
Valid prediction for snap_scaffold_13-snap.837-T1
Valid prediction for Augustus_model.g21591.t1
Valid prediction for GeneMark_model.55156_t
Valid prediction for snap_scaffold_13-snap.827-T1
Valid prediction for GeneMark_model.55180_t
Valid prediction for Augustus_model.g21596.t1
Couldn't classify 150390, 150637
Sorry, prediction pasa_asmbl_10794.p1 fails validation.
(CTG)	 GC	150390-150637	GT	TCG
(GCT)	 AG	153426-153565	GT	AAG
(ACA)	 AG	153891-154035	GT	GGG
(TAA)	 AG	154243-154457	GT	GTG
(GTG)	 AG	154803-154929	GT	TCG
(GCC)	 AG	155357-155607	GT	AAG
(AGC)	 AG	156568-156735	GT	GGG
(GGA)	 AG	157279-157477	GT	AAG
(AAC)	 AG	157954-158243	GT	GGG
(ACA)	 AG	158446-158585	GT	AGG
(GAG)	 AG	159251-159410	GT	CCG
(GAG)	 AG	159670-159772	GT	AAG
(GCA)	 AG	159889-159956	GT	CGG
(TGT)	 AG	160253-160482	GT	TGG
(GTG)	 AG	160950-161060	GT	AGG
(AAC)	 AG	161253-161412	GT	AGG
(ACT)	 AG	161567-161696	GT	TGG
(GTC)	 AG	162156-162290	GT	CTG
(ACA)	 AG	162667-163027	CA	AAC
-recovered pasa_asmbl_10794.p1, terminal, 162667, 163027
-recovered pasa_asmbl_10794.p1, internal, 153426, 153565
-recovered pasa_asmbl_10794.p1, internal, 153891, 154035
-recovered pasa_asmbl_10794.p1, internal, 154243, 154457
-recovered pasa_asmbl_10794.p1, internal, 154803, 154929
-recovered pasa_asmbl_10794.p1, internal, 155357, 155607
-recovered pasa_asmbl_10794.p1, internal, 156568, 156735
-recovered pasa_asmbl_10794.p1, internal, 157279, 157477
-recovered pasa_asmbl_10794.p1, internal, 157954, 158243
-recovered pasa_asmbl_10794.p1, internal, 158446, 158585
-recovered pasa_asmbl_10794.p1, internal, 159251, 159410
-recovered pasa_asmbl_10794.p1, internal, 159670, 159772
-recovered pasa_asmbl_10794.p1, internal, 159889, 159956
-recovered pasa_asmbl_10794.p1, internal, 160253, 160482
-recovered pasa_asmbl_10794.p1, internal, 160950, 161060
-recovered pasa_asmbl_10794.p1, internal, 161253, 161412
-recovered pasa_asmbl_10794.p1, internal, 161567, 161696
-recovered pasa_asmbl_10794.p1, internal, 162156, 162290
Valid prediction for GlimmerHMM_glimmerT_32248-T1
Valid prediction for HiQ_model.g21588.t1
Valid prediction for snap_scaffold_13-snap.836-T1
Valid prediction for GlimmerHMM_glimmerT_32262-T1
Valid prediction for snap_scaffold_13-snap.847-T1
Valid prediction for GlimmerHMM_glimmerT_32242-T1
Valid prediction for snap_scaffold_13-snap.857-T1
Valid prediction for snap_scaffold_13-snap.834-T1
Valid prediction for GeneMark_model.55152_t
Valid prediction for CodingQuarry_transcript_12968-T1
Valid prediction for GlimmerHMM_glimmerT_32254-T1
Valid prediction for Augustus_model.g21583.t1
Valid prediction for GlimmerHMM_glimmerT_32250-T1
Valid prediction for Augustus_model.g21587.t1
Valid prediction for GlimmerHMM_glimmerT_32261-T1
Valid prediction for snap_scaffold_13-snap.838-T1
Valid prediction for HiQ_model.g21593.t1
Valid prediction for CodingQuarry_transcript_12971-T1
Valid prediction for GlimmerHMM_glimmerT_32241-T1
Valid prediction for pasa_asmbl_10798.p1
Valid prediction for GeneMark_model.55185_t
Valid prediction for snap_scaffold_13-snap.854-T1
Valid prediction for pasa_asmbl_10775.p1
Valid prediction for snap_scaffold_13-snap.850-T1
Couldn't classify 101460, 101521
Couldn't classify 105420, 105446
Sorry, prediction pasa_asmbl_10785.p1 fails validation.
(TCG)	 AC	101460-101521	GT	AAG
(GAA)	 AG	101677-101758	GT	AGG
(CCA)	 AG	103297-103382	GT	AAG
(AAC)	 AG	103647-103747	GT	AGG
(TCA)	 AG	104317-104498	GT	AGG
(GTG)	 AG	104872-104979	GT	CCG
(AAG)	 AG	105130-105303	GT	AGG
(GCC)	 AG	105420-105446	AA	GGA
-recovered pasa_asmbl_10785.p1, internal, 101677, 101758
-recovered pasa_asmbl_10785.p1, internal, 103297, 103382
-recovered pasa_asmbl_10785.p1, internal, 103647, 103747
-recovered pasa_asmbl_10785.p1, internal, 104317, 104498
-recovered pasa_asmbl_10785.p1, internal, 104872, 104979
-recovered pasa_asmbl_10785.p1, internal, 105130, 105303
Valid prediction for HiQ_model.g21602.t1
Valid prediction for GeneMark_model.55184_t
Valid prediction for GlimmerHMM_glimmerT_32257-T1
Valid prediction for GlimmerHMM_glimmerT_32252-T1
Couldn't classify 100780, 100910
Couldn't classify 101039, 101336
Sorry, prediction pasa_asmbl_10784.p2 fails validation.
(AAG)	 TA	100780-100910	GT	AGG
(TCA)	 AG	101039-101336	GA	TGG
Valid prediction for GeneMark_model.55182_t
Valid prediction for GeneMark_model.55172_t
Valid prediction for GlimmerHMM_glimmerT_32236-T1
Valid prediction for GlimmerHMM_glimmerT_32247-T1
Valid prediction for HiQ_model.g21601.t1
Valid prediction for GeneMark_model.55149_t
Valid prediction for GeneMark_model.55168_t
Valid prediction for Augustus_model.g21599.t1
Valid prediction for GlimmerHMM_glimmerT_32258-T1
Valid prediction for GeneMark_model.55174_t
Valid prediction for GeneMark_model.55166_t
Valid prediction for GeneMark_model.55178_t

-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 CodingQuarry_transcript_12969-T1
Valid prediction for GlimmerHMM_glimmerT_32238-T1
Valid prediction for GeneMark_model.55153_t
Valid prediction for Augustus_model.g21598.t1
Valid prediction for GeneMark_model.55179_t
Valid prediction for snap_scaffold_13-snap.829-T1
Valid prediction for GlimmerHMM_glimmerT_32253-T1
Valid prediction for GeneMark_model.55161_t
Valid prediction for snap_scaffold_13-snap.826-T1
Valid prediction for GeneMark_model.55159_t
Valid prediction for GlimmerHMM_glimmerT_32263-T1
Valid prediction for Augustus_model.g21585.t1
Valid prediction for GlimmerHMM_glimmerT_32239-T1
Valid prediction for GeneMark_model.55183_t
Valid prediction for GeneMark_model.55154_t
Valid prediction for GlimmerHMM_glimmerT_32260-T1
Valid prediction for GeneMark_model.55167_t
Valid prediction for GlimmerHMM_glimmerT_32240-T1
Valid prediction for GlimmerHMM_glimmerT_32256-T1
Valid prediction for CodingQuarry_transcript_12970-T1
Valid prediction for GeneMark_model.55176_t
Valid prediction for snap_scaffold_13-snap.846-T1
Valid prediction for pasa_asmbl_9600.p1
Valid prediction for snap_scaffold_13-snap.833-T1
Valid prediction for GeneMark_model.55165_t
Valid prediction for GeneMark_model.55160_t
Valid prediction for snap_scaffold_13-snap.842-T1
Valid prediction for snap_scaffold_13-snap.828-T1
Valid prediction for GeneMark_model.55151_t
Valid prediction for snap_scaffold_13-snap.849-T1
Valid prediction for GlimmerHMM_glimmerT_32255-T1
Valid prediction for snap_scaffold_13-snap.856-T1
Valid prediction for GlimmerHMM_glimmerT_32237-T1
Valid prediction for GlimmerHMM_glimmerT_32246-T1
Valid prediction for HiQ_model.g21590.t1
Valid prediction for Augustus_model.g21586.t1
Valid prediction for GeneMark_model.55171_t
Valid prediction for GeneMark_model.55177_t
Valid prediction for GlimmerHMM_glimmerT_32251-T1
Valid prediction for snap_scaffold_13-snap.830-T1
Valid prediction for snap_scaffold_13-snap.851-T1
Valid prediction for Augustus_model.g21584.t1
Valid prediction for HiQ_model.g21600.t1
Valid prediction for Augustus_model.g21595.t1
Valid prediction for GeneMark_model.55181_t
Valid prediction for snap_scaffold_13-snap.832-T1
Valid prediction for snap_scaffold_13-snap.845-T1
Valid prediction for snap_scaffold_13-snap.853-T1
Valid prediction for pasa_asmbl_9598.p1
Valid prediction for GeneMark_model.55170_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 102383, rend_intergenic: 95105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124277, rend_intergenic: 122311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163027, rend_intergenic: 160476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205504, rend_intergenic: 204156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 139428, rend_intergenic: 139425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207982
-exon list size: 583


building trellis

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85.6    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 102383, rend_intergenic: 95105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124277, rend_intergenic: 122311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163027, rend_intergenic: 160476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205504, rend_intergenic: 204156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 139428, rend_intergenic: 139425  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