-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_3030752-3208743

-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_31312-T1
Valid prediction for GlimmerHMM_glimmerT_31328-T1
Valid prediction for GlimmerHMM_glimmerT_31324-T1
Valid prediction for snap_scaffold_13-snap.586-T1
Valid prediction for snap_scaffold_13-snap.576-T1
Valid prediction for HiQ_model.g20808.t1
Valid prediction for GlimmerHMM_glimmerT_31304-T1
Couldn't classify 161581, 161581
Sorry, prediction CodingQuarry_transcript_12930-T1 fails validation.
(AGT)	 TT	161581-161581	GT	TAG
(TGT)	 AG	161700-161768	GT	GGG
(GTG)	 AG	161862-162050	GT	AGG
(TTC)	 AG	162130-162204	GT	TGG
(GCT)	 AG	162298-162421	GT	CGG
(GAA)	 AG	162654-162781	GT	ATG
(CAA)	 AG	162913-163039	GT	GGG
(AAT)	 AG	163162-163301	GT	AGG
(CTG)	 AG	163403-163532	GT	GGG
(ATT)	 AG	163647-163780	GT	CGG
(TCG)	 AG	163968-164094	GT	GGG
(ATT)	 AG	164171-164379	GT	AGG
(ATA)	 AG	164524-164591	TC	GAT
-recovered CodingQuarry_transcript_12930-T1, terminal, 164524, 164591
-recovered CodingQuarry_transcript_12930-T1, internal, 161700, 161768
-recovered CodingQuarry_transcript_12930-T1, internal, 161862, 162050
-recovered CodingQuarry_transcript_12930-T1, internal, 162130, 162204
-recovered CodingQuarry_transcript_12930-T1, internal, 162298, 162421
-recovered CodingQuarry_transcript_12930-T1, internal, 162654, 162781
-recovered CodingQuarry_transcript_12930-T1, internal, 162913, 163039
-recovered CodingQuarry_transcript_12930-T1, internal, 163162, 163301
-recovered CodingQuarry_transcript_12930-T1, internal, 163403, 163532
-recovered CodingQuarry_transcript_12930-T1, internal, 163647, 163780
-recovered CodingQuarry_transcript_12930-T1, internal, 163968, 164094
-recovered CodingQuarry_transcript_12930-T1, internal, 164171, 164379
Valid prediction for pasa_asmbl_10667.p1
Valid prediction for GlimmerHMM_glimmerT_31313-T1
Valid prediction for CodingQuarry_transcript_12918-T1
Valid prediction for snap_scaffold_13-snap.585-T1
Valid prediction for GlimmerHMM_glimmerT_31327-T1
Valid prediction for snap_scaffold_13-snap.575-T1
Valid prediction for snap_scaffold_13-snap.577-T1
Valid prediction for HiQ_model.g20801.t1
Valid prediction for Augustus_model.g20802.t1
Valid prediction for Augustus_model.g20793.t1
Valid prediction for GlimmerHMM_glimmerT_31297-T1
Valid prediction for Augustus_model.g20809.t1
Valid prediction for GlimmerHMM_glimmerT_31315-T1
Valid prediction for GlimmerHMM_glimmerT_31325-T1
Valid prediction for snap_scaffold_13-snap.564-T1
Valid prediction for CodingQuarry_transcript_12919-T1
Valid prediction for GlimmerHMM_glimmerT_31316-T1
Valid prediction for CodingQuarry_transcript_12921-T1
Valid prediction for pasa_asmbl_10664.p1
Valid prediction for CodingQuarry_transcript_12920-T1
Valid prediction for Augustus_model.g20800.t1
Valid prediction for GlimmerHMM_glimmerT_31318-T1
Valid prediction for snap_scaffold_13-snap.570-T1
Valid prediction for GlimmerHMM_glimmerT_31301-T1
Valid prediction for snap_scaffold_13-snap.562-T1
Valid prediction for Augustus_model.g20795.t1
Couldn't classify 2021, 2070
Sorry, prediction pasa_asmbl_10651.p1 fails validation.
(GAC)	 AG	2021-2070	GT	CGG
(CGG)	 AG	3088-3200	GT	CGG
(GTG)	 AG	3893-4026	GT	AGG
(GGA)	 AG	4198-4344	GT	TAG
(GAC)	 AG	4522-4651	GT	AGG
(AAA)	 AG	4768-5049	GT	AGG
(AGA)	 AG	5374-5507	AG	AAA
-recovered pasa_asmbl_10651.p1, terminal, 5374, 5507
-recovered pasa_asmbl_10651.p1, internal, 2021, 2070
-recovered pasa_asmbl_10651.p1, internal, 3088, 3200
-recovered pasa_asmbl_10651.p1, internal, 3893, 4026
-recovered pasa_asmbl_10651.p1, internal, 4198, 4344
-recovered pasa_asmbl_10651.p1, internal, 4522, 4651
-recovered pasa_asmbl_10651.p1, internal, 4768, 5049
Valid prediction for CodingQuarry_transcript_12928-T1
Valid prediction for Augustus_model.g20798.t1
Valid prediction for CodingQuarry_transcript_12924-T1
Valid prediction for GlimmerHMM_glimmerT_31323-T1
Valid prediction for pasa_asmbl_10657.p1
Valid prediction for GlimmerHMM_glimmerT_31326-T1
Valid prediction for GlimmerHMM_glimmerT_31317-T1
Couldn't classify 64130, 64223
Sorry, prediction pasa_asmbl_11601.p1 fails validation.
(AAA)	 AC	64130-64223	GT	AGG
(GCA)	 AG	65394-65557	GT	GGG
(ATG)	 AG	65777-65902	CA	GAC
-recovered pasa_asmbl_11601.p1, terminal, 65777, 65902
-recovered pasa_asmbl_11601.p1, internal, 65394, 65557
Valid prediction for GlimmerHMM_glimmerT_31314-T1
Valid prediction for snap_scaffold_13-snap.557-T1
Valid prediction for GlimmerHMM_glimmerT_31306-T1
Couldn't classify 114263, 114318
Sorry, prediction pasa_asmbl_10662.p1 fails validation.
(TGT)	 GC	114263-114318	GT	AGG
(TGG)	 AG	114402-114471	GT	AGG
(AGC)	 AG	114555-114689	GT	AGG
(TGT)	 AG	114871-114992	GT	ACG
(TGG)	 AG	115430-115508	GT	AGG
(GCT)	 AG	115626-115700	GT	AGG
(CCA)	 AG	115902-115985	TC	GAT
-recovered pasa_asmbl_10662.p1, terminal, 115902, 115985
-recovered pasa_asmbl_10662.p1, internal, 114402, 114471
-recovered pasa_asmbl_10662.p1, internal, 114555, 114689
-recovered pasa_asmbl_10662.p1, internal, 114871, 114992
-recovered pasa_asmbl_10662.p1, internal, 115430, 115508
-recovered pasa_asmbl_10662.p1, internal, 115626, 115700
Valid prediction for HiQ_model.g20804.t1
Valid prediction for Augustus_model.g20799.t1
Valid prediction for CodingQuarry_transcript_12922-T1
Valid prediction for HiQ_model.g20790.t1
Valid prediction for snap_scaffold_13-snap.580-T1
Valid prediction for snap_scaffold_13-snap.578-T1
Valid prediction for snap_scaffold_13-snap.563-T1
Valid prediction for snap_scaffold_13-snap.574-T1
Valid prediction for snap_scaffold_13-snap.568-T1
Valid prediction for HiQ_model.g20786.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_31320-T1
Valid prediction for CodingQuarry_transcript_12916-T1
Valid prediction for GlimmerHMM_glimmerT_31298-T1
Valid prediction for GlimmerHMM_glimmerT_31307-T1
Valid prediction for snap_scaffold_13-snap.566-T1
Valid prediction for snap_scaffold_13-snap.573-T1
Valid prediction for Augustus_model.g20791.t1
Valid prediction for GlimmerHMM_glimmerT_31321-T1
Valid prediction for GlimmerHMM_glimmerT_31310-T1
Valid prediction for CodingQuarry_transcript_12923-T1
Valid prediction for pasa_asmbl_9521.p1
Valid prediction for GlimmerHMM_glimmerT_31322-T1
Valid prediction for GlimmerHMM_glimmerT_31319-T1
Couldn't classify 151579, 151821
Sorry, prediction pasa_asmbl_9510.p1 fails validation.
(GAG)	 CA	151579-151821	GT	AGG
(GTG)	 AG	152046-152131	GT	AAG
(ATT)	 AG	152481-152619	GT	AGG
(ACG)	 AG	152838-152935	GT	TGG
(GAA)	 AG	153299-153456	GT	AGG
(GTA)	 AG	153703-153929	GG	GAG
-recovered pasa_asmbl_9510.p1, terminal, 152046, 152131
-recovered pasa_asmbl_9510.p1, terminal, 153703, 153929
-recovered pasa_asmbl_9510.p1, internal, 152046, 152131
-recovered pasa_asmbl_9510.p1, internal, 152481, 152619
-recovered pasa_asmbl_9510.p1, internal, 152838, 152935
-recovered pasa_asmbl_9510.p1, internal, 153299, 153456
Valid prediction for HiQ_model.g20797.t1
Valid prediction for snap_scaffold_13-snap.569-T1
Valid prediction for GlimmerHMM_glimmerT_31305-T1
Valid prediction for Augustus_model.g20794.t1
Valid prediction for GlimmerHMM_glimmerT_31303-T1
Valid prediction for snap_scaffold_13-snap.558-T1
Valid prediction for Augustus_model.g20803.t1
Valid prediction for HiQ_model.g20787.t1
Valid prediction for GlimmerHMM_glimmerT_31311-T1
Valid prediction for Augustus_model.g20806.t1
Valid prediction for Augustus_model.g20792.t1
Valid prediction for GlimmerHMM_glimmerT_31309-T1
Valid prediction for HiQ_model.g20807.t1
Valid prediction for Augustus_model.g20805.t1
Valid prediction for Augustus_model.g20789.t1
Valid prediction for CodingQuarry_transcript_12925-T1
Valid prediction for snap_scaffold_13-snap.572-T1
Valid prediction for HiQ_model.g20796.t1
Valid prediction for snap_scaffold_13-snap.567-T1
Valid prediction for CodingQuarry_transcript_12926-T1
Couldn't classify 106124, 106438
Sorry, prediction pasa_asmbl_9520.p1 fails validation.
(CTA)	 TC	106124-106438	GT	AGG
(ATC)	 AG	106720-106912	GT	TGG
(GTG)	 AG	107075-107139	GT	AGG
(GCC)	 AG	107274-107374	GT	AAG
(ACA)	 AG	107478-107548	GT	GAG
(ATA)	 AG	107677-107761	GT	TGG
(CCA)	 AG	107947-108045	GT	ATG
(ATA)	 AG	108133-108202	GT	CTG
(GGG)	 AG	108288-108383	GT	AAG
(GAT)	 AG	108493-108621	GT	TGG
(GTG)	 AG	108760-108867	GG	GAG
-recovered pasa_asmbl_9520.p1, terminal, 108760, 108867
-recovered pasa_asmbl_9520.p1, internal, 106720, 106912
-recovered pasa_asmbl_9520.p1, internal, 107075, 107139
-recovered pasa_asmbl_9520.p1, internal, 107274, 107374
-recovered pasa_asmbl_9520.p1, internal, 107478, 107548
-recovered pasa_asmbl_9520.p1, internal, 107677, 107761
-recovered pasa_asmbl_9520.p1, internal, 107947, 108045
-recovered pasa_asmbl_9520.p1, internal, 108133, 108202
-recovered pasa_asmbl_9520.p1, internal, 108288, 108383
-recovered pasa_asmbl_9520.p1, internal, 108493, 108621
Valid prediction for snap_scaffold_13-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_31300-T1
Couldn't classify 160464, 160770
Sorry, prediction pasa_asmbl_9509.p1 fails validation.
(CTC)	 CT	160464-160770	GT	AGG
(AAT)	 AG	163043-163197	GT	AGG
(GAT)	 AG	164758-164887	GT	GGG
(CCA)	 AG	164978-165123	GT	AGG
(GCT)	 AG	165302-165515	GT	AGG
(GTA)	 AG	165654-165839	GT	CAG
(ATG)	 AG	165991-166100	GT	GGG
(TCT)	 AG	166208-166351	GT	AGG
(GTC)	 AG	166501-166576	GT	AGG
(GGA)	 AG	166700-166856	GT	AGG
(TGA)	 AG	167065-167191	GT	AGG
(GAC)	 AG	167427-167563	GT	AGG
(GGA)	 AG	167677-167752	GT	AGG
(GTT)	 AG	167859-167950	GT	AGG
(CCT)	 AG	168039-168215	GT	ATG
(ATT)	 AG	168501-168563	GT	AGG
(GGA)	 AG	168675-168751	GT	GGG
(GGA)	 AG	168903-169045	GT	AGG
(TCC)	 AG	169221-169328	GT	GGG
(CTT)	 AG	169498-169578	GT	GGG
(AAT)	 AG	169693-169896	CC	AGC
add_exon() Sorry, pasa_asmbl_9509.p1 165991-166100-initial-1 is invalid.
-recovered pasa_asmbl_9509.p1, initial, 165991, 166100
-recovered pasa_asmbl_9509.p1, terminal, 169693, 169896
-recovered pasa_asmbl_9509.p1, internal, 163043, 163197
-recovered pasa_asmbl_9509.p1, internal, 164758, 164887
-recovered pasa_asmbl_9509.p1, internal, 164978, 165123
-recovered pasa_asmbl_9509.p1, internal, 165302, 165515
-recovered pasa_asmbl_9509.p1, internal, 165654, 165839
-recovered pasa_asmbl_9509.p1, internal, 165991, 166100
-recovered pasa_asmbl_9509.p1, internal, 166208, 166351
-recovered pasa_asmbl_9509.p1, internal, 166501, 166576
-recovered pasa_asmbl_9509.p1, internal, 166700, 166856
-recovered pasa_asmbl_9509.p1, internal, 167065, 167191
-recovered pasa_asmbl_9509.p1, internal, 167427, 167563
-recovered pasa_asmbl_9509.p1, internal, 167677, 167752
-recovered pasa_asmbl_9509.p1, internal, 167859, 167950
-recovered pasa_asmbl_9509.p1, internal, 168039, 168215
-recovered pasa_asmbl_9509.p1, internal, 168501, 168563
-recovered pasa_asmbl_9509.p1, internal, 168675, 168751
-recovered pasa_asmbl_9509.p1, internal, 168903, 169045
-recovered pasa_asmbl_9509.p1, internal, 169221, 169328
-recovered pasa_asmbl_9509.p1, internal, 169498, 169578
Valid prediction for snap_scaffold_13-snap.571-T1
Valid prediction for snap_scaffold_13-snap.560-T1
Valid prediction for snap_scaffold_13-snap.582-T1
Valid prediction for GlimmerHMM_glimmerT_31299-T1
Valid prediction for Augustus_model.g20788.t1
Valid prediction for snap_scaffold_13-snap.561-T1
Valid prediction for CodingQuarry_transcript_12927-T1
Valid prediction for GlimmerHMM_glimmerT_31308-T1
Valid prediction for snap_scaffold_13-snap.559-T1
Valid prediction for GlimmerHMM_glimmerT_31302-T1
Valid prediction for snap_scaffold_13-snap.579-T1
Valid prediction for CodingQuarry_transcript_12929-T1
Valid prediction for pasa_asmbl_9515.p1
Valid prediction for snap_scaffold_13-snap.581-T1
Valid prediction for snap_scaffold_13-snap.584-T1
Valid prediction for pasa_asmbl_9516.p1
Valid prediction for snap_scaffold_13-snap.565-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 115985, rend_intergenic: 111680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177992
-exon list size: 511


building trellis

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88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 115985, rend_intergenic: 111680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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