-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_5340910-5492357

-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_24-snap.1075-T1
Valid prediction for GlimmerHMM_glimmerT_53796-T1
Valid prediction for snap_scaffold_24-snap.1068-T1
Valid prediction for GlimmerHMM_glimmerT_53786-T1
Valid prediction for GlimmerHMM_glimmerT_53790-T1
Valid prediction for GlimmerHMM_glimmerT_53788-T1
Couldn't classify 124265, 124351
Sorry, prediction pasa_asmbl_32235.p1 fails validation.
(TTC)	 AG	124265-124351	GT	TGG
(GCT)	 AG	124651-125166	AG	AAA
-recovered pasa_asmbl_32235.p1, terminal, 124651, 125166
-recovered pasa_asmbl_32235.p1, internal, 124265, 124351
Valid prediction for Augustus_model.g36019.t1
Valid prediction for CodingQuarry_transcript_37240-T1
Valid prediction for GlimmerHMM_glimmerT_53794-T1
Valid prediction for GlimmerHMM_glimmerT_53799-T1
Valid prediction for Augustus_model.g36021.t1
Valid prediction for GeneMark_model.93811_t
Valid prediction for snap_scaffold_24-snap.1077-T1
Valid prediction for GeneMark_model.93820_t
Valid prediction for GeneMark_model.93824_t
Couldn't classify 85841, 85987
Sorry, prediction pasa_asmbl_32229.p1 fails validation.
(TGC)	 AC	85841-85987	GT	AGG
(GTG)	 AG	86240-86377	GT	AGG
(TAC)	 AG	86601-86739	GT	TGG
(CTG)	 AG	86912-87063	GT	CGG
(AGG)	 AG	87212-87310	GT	GGG
(GAA)	 AG	87492-87638	TA	GAT
-recovered pasa_asmbl_32229.p1, terminal, 87492, 87638
-recovered pasa_asmbl_32229.p1, internal, 86240, 86377
-recovered pasa_asmbl_32229.p1, internal, 86601, 86739
-recovered pasa_asmbl_32229.p1, internal, 86912, 87063
-recovered pasa_asmbl_32229.p1, internal, 87212, 87310
Valid prediction for GlimmerHMM_glimmerT_53804-T1
Valid prediction for snap_scaffold_24-snap.1064-T1
Valid prediction for GlimmerHMM_glimmerT_53803-T1
Valid prediction for GlimmerHMM_glimmerT_53782-T1
Valid prediction for Augustus_model.g36017.t1
Valid prediction for GeneMark_model.93822_t
Valid prediction for GlimmerHMM_glimmerT_53797-T1
Valid prediction for GeneMark_model.93823_t
Valid prediction for Augustus_model.g36010.t1
Valid prediction for GeneMark_model.93813_t
Valid prediction for GeneMark_model.93807_t
Valid prediction for HiQ_model.g36011.t1
Valid prediction for snap_scaffold_24-snap.1055-T1
Valid prediction for Augustus_model.g36014.t1
Valid prediction for GeneMark_model.93830_t
Valid prediction for Augustus_model.g36018.t1
Valid prediction for snap_scaffold_24-snap.1076-T1
Couldn't classify 33005, 33073
Couldn't classify 39149, 39248
Sorry, prediction pasa_asmbl_32664.p1 fails validation.
(AGG)	 TC	33005-33073	GT	AGG
(GGC)	 AG	33346-33461	GT	AGG
(GAC)	 AG	35230-35299	GT	GGG
(AAA)	 AG	35564-35656	GT	AGG
(GAG)	 AG	35965-36057	GC	AGG
(GAG)	 AG	36751-36876	GT	AGG
(GGG)	 AG	37136-37357	GT	AGG
(ATG)	 AG	38030-38122	GT	AGG
(GCT)	 AG	38806-38884	GT	AGG
(AAG)	 AG	38983-39037	GT	AGG
(GAA)	 AG	39149-39248	GA	GTG
-recovered pasa_asmbl_32664.p1, initial, 38030, 38122
-recovered pasa_asmbl_32664.p1, internal, 33346, 33461
-recovered pasa_asmbl_32664.p1, internal, 35230, 35299
-recovered pasa_asmbl_32664.p1, internal, 35564, 35656
-recovered pasa_asmbl_32664.p1, internal, 35965, 36057
-recovered pasa_asmbl_32664.p1, internal, 36751, 36876
-recovered pasa_asmbl_32664.p1, internal, 37136, 37357
-recovered pasa_asmbl_32664.p1, internal, 38030, 38122
-recovered pasa_asmbl_32664.p1, internal, 38806, 38884
-recovered pasa_asmbl_32664.p1, internal, 38983, 39037
Valid prediction for GlimmerHMM_glimmerT_53787-T1
Valid prediction for snap_scaffold_24-snap.1080-T1
Valid prediction for GeneMark_model.93809_t
Valid prediction for snap_scaffold_24-snap.1073-T1
Valid prediction for snap_scaffold_24-snap.1061-T1
Valid prediction for GeneMark_model.93815_t
Couldn't classify 114153, 114314
Sorry, prediction pasa_asmbl_32233.p1 fails validation.
(GAG)	 CA	114153-114314	GT	AGG
(TTC)	 AG	114579-114777	GT	CAG
(GCT)	 AG	117258-117334	GT	CGG
(GAA)	 AG	117428-117483	GT	AGG
(GTG)	 AG	117810-117918	GT	TGG
(TAT)	 AG	118896-118964	AC	AGA
-recovered pasa_asmbl_32233.p1, terminal, 118896, 118964
-recovered pasa_asmbl_32233.p1, internal, 114579, 114777
-recovered pasa_asmbl_32233.p1, internal, 117258, 117334
-recovered pasa_asmbl_32233.p1, internal, 117428, 117483
-recovered pasa_asmbl_32233.p1, internal, 117810, 117918
Valid prediction for Augustus_model.g36016.t1
Valid prediction for snap_scaffold_24-snap.1078-T1
Valid prediction for snap_scaffold_24-snap.1056-T1
Valid prediction for Augustus_model.g36009.t1
Valid prediction for GeneMark_model.93828_t
Valid prediction for GlimmerHMM_glimmerT_53784-T1
Valid prediction for snap_scaffold_24-snap.1062-T1
Couldn't classify 44401, 44401
Sorry, prediction CodingQuarry_transcript_37238-T1 fails validation.
(ATG)	 CC	42333-42416	GT	ATG
(GGT)	 AG	42751-42866	GT	TGG
(ATA)	 AG	44401-44401	TA	GAT
-recovered CodingQuarry_transcript_37238-T1, initial, 42333, 42416
-recovered CodingQuarry_transcript_37238-T1, internal, 42751, 42866
Valid prediction for GeneMark_model.93817_t
Valid prediction for Augustus_model.g36004.t1
Valid prediction for GlimmerHMM_glimmerT_53795-T1
Valid prediction for CodingQuarry_transcript_37241-T1
Valid prediction for GeneMark_model.93821_t
Valid prediction for snap_scaffold_24-snap.1083-T1
Valid prediction for pasa_asmbl_32228.p1
Valid prediction for snap_scaffold_24-snap.1058-T1
Valid prediction for GlimmerHMM_glimmerT_53809-T1
Valid prediction for Augustus_model.g36012.t1
Valid prediction for GlimmerHMM_glimmerT_53802-T1
Couldn't classify 91369, 91677
Sorry, prediction pasa_asmbl_32232.p1 fails validation.
(ATG)	 TC	91369-91677	AC	CCA
Valid prediction for Augustus_model.g36006.t1
Couldn't classify 121924, 122004
Couldn't classify 122579, 122635
Sorry, prediction pasa_asmbl_32234.p1 fails validation.
(GCC)	 TC	121924-122004	GT	GGG
(ATG)	 AG	122290-122451	GT	TGG
(AGT)	 AG	122579-122635	AC	ACA
-recovered pasa_asmbl_32234.p1, initial, 122290, 122451
-recovered pasa_asmbl_32234.p1, internal, 122290, 122451
Valid prediction for GlimmerHMM_glimmerT_53800-T1
Valid prediction for GlimmerHMM_glimmerT_53798-T1
Valid prediction for snap_scaffold_24-snap.1067-T1
Valid prediction for Augustus_model.g36008.t1
Valid prediction for GlimmerHMM_glimmerT_53791-T1
Valid prediction for GlimmerHMM_glimmerT_53792-T1
Valid prediction for snap_scaffold_24-snap.1084-T1
Valid prediction for Augustus_model.g36015.t1
Valid prediction for snap_scaffold_24-snap.1074-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 42306, 42416
Sorry, prediction pasa_asmbl_32225.p1 fails validation.
(GGT)	 CA	42306-42416	GT	ATG
(GGT)	 AG	42751-42866	GT	TGG
(GCT)	 AG	43368-43441	GT	AGG
(ATA)	 AG	44401-44492	AC	AGA
-recovered pasa_asmbl_32225.p1, terminal, 44401, 44492
-recovered pasa_asmbl_32225.p1, internal, 42751, 42866
-recovered pasa_asmbl_32225.p1, internal, 43368, 43441
Valid prediction for snap_scaffold_24-snap.1072-T1
Valid prediction for GeneMark_model.93806_t
Couldn't classify 14530, 14593
Couldn't classify 23284, 23451
Sorry, prediction pasa_asmbl_32222.p1 fails validation.
(ATC)	 AG	14530-14593	GT	AGG
(GTG)	 AG	17194-17308	GT	AGG
(CCT)	 AG	18629-18719	GT	CGG
(GGG)	 AG	18970-19083	GT	AGG
(ATC)	 AG	19967-20083	GT	CTG
(GCC)	 AG	20394-20543	GT	GGG
(GAC)	 AG	21025-21149	GT	AGG
(GTT)	 AG	21758-21872	GT	AGG
(GTG)	 AG	22325-22444	GT	AGG
(AGC)	 AG	22559-22750	GT	AGG
(GTG)	 AG	22924-23115	GT	AGG
(GCC)	 AG	23284-23451	GC	CCG
-recovered pasa_asmbl_32222.p1, internal, 14530, 14593
-recovered pasa_asmbl_32222.p1, internal, 17194, 17308
-recovered pasa_asmbl_32222.p1, internal, 18629, 18719
-recovered pasa_asmbl_32222.p1, internal, 18970, 19083
-recovered pasa_asmbl_32222.p1, internal, 19967, 20083
-recovered pasa_asmbl_32222.p1, internal, 20394, 20543
-recovered pasa_asmbl_32222.p1, internal, 21025, 21149
-recovered pasa_asmbl_32222.p1, internal, 21758, 21872
-recovered pasa_asmbl_32222.p1, internal, 22325, 22444
-recovered pasa_asmbl_32222.p1, internal, 22559, 22750
-recovered pasa_asmbl_32222.p1, internal, 22924, 23115
-recovered pasa_asmbl_32222.p1, internal, 23284, 23451
Valid prediction for GeneMark_model.93831_t
Valid prediction for Augustus_model.g36013.t1
Valid prediction for snap_scaffold_24-snap.1071-T1
Valid prediction for CodingQuarry_transcript_37237-T1
Valid prediction for snap_scaffold_24-snap.1069-T1
Valid prediction for GeneMark_model.93833_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 GeneMark_model.93810_t
Valid prediction for GeneMark_model.93829_t
Valid prediction for snap_scaffold_24-snap.1053-T1
Valid prediction for snap_scaffold_24-snap.1054-T1
Valid prediction for snap_scaffold_24-snap.1079-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.1081-T1
Valid prediction for Augustus_model.g36005.t1
Valid prediction for Augustus_model.g36020.t1
Valid prediction for snap_scaffold_24-snap.1066-T1
Valid prediction for GlimmerHMM_glimmerT_53793-T1
Valid prediction for GeneMark_model.93804_t
Valid prediction for GeneMark_model.93819_t
Valid prediction for GeneMark_model.93827_t
Valid prediction for GeneMark_model.93826_t
Valid prediction for GlimmerHMM_glimmerT_53785-T1
Valid prediction for GlimmerHMM_glimmerT_53783-T1
Valid prediction for snap_scaffold_24-snap.1060-T1
Valid prediction for snap_scaffold_24-snap.1059-T1
Valid prediction for GlimmerHMM_glimmerT_53805-T1
Valid prediction for GlimmerHMM_glimmerT_53806-T1
Valid prediction for GeneMark_model.93834_t
Valid prediction for GeneMark_model.93812_t
Valid prediction for GeneMark_model.93802_t
Valid prediction for Augustus_model.g36003.t1
Valid prediction for GlimmerHMM_glimmerT_53807-T1
Valid prediction for GlimmerHMM_glimmerT_53801-T1
Valid prediction for Augustus_model.g36007.t1
Valid prediction for GlimmerHMM_glimmerT_53808-T1
Valid prediction for GlimmerHMM_glimmerT_53789-T1
Valid prediction for snap_scaffold_24-snap.1063-T1
Valid prediction for GeneMark_model.93816_t
Valid prediction for GeneMark_model.93818_t
Valid prediction for snap_scaffold_24-snap.1065-T1
Valid prediction for snap_scaffold_24-snap.1070-T1
Valid prediction for GeneMark_model.93803_t
Valid prediction for snap_scaffold_24-snap.1057-T1
Valid prediction for GlimmerHMM_glimmerT_53810-T1
Valid prediction for GeneMark_model.93808_t
Valid prediction for GeneMark_model.93805_t
Valid prediction for GeneMark_model.93832_t
Valid prediction for snap_scaffold_24-snap.1082-T1
Valid prediction for GeneMark_model.93814_t
Valid prediction for GeneMark_model.93825_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19253, rend_intergenic: 17184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36153, rend_intergenic: 30592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39915, rend_intergenic: 36754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57646, rend_intergenic: 50667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118849, rend_intergenic: 113393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134825, rend_intergenic: 132626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 151448
-exon list size: 566


building trellis

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95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 19253, rend_intergenic: 17184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36153, rend_intergenic: 30592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39915, rend_intergenic: 36754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57646, rend_intergenic: 50667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118849, rend_intergenic: 113393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134825, rend_intergenic: 132626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support