-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_5741528-5929384

-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 GeneMark_model.90672_t
Valid prediction for HiQ_model.g35194.t1
Valid prediction for snap_scaffold_23-snap.1037-T1
Valid prediction for GlimmerHMM_glimmerT_52304-T1
Valid prediction for GeneMark_model.90708_t
Valid prediction for pasa_asmbl_30900.p1
Valid prediction for GeneMark_model.90688_t
Valid prediction for snap_scaffold_23-snap.1064-T1
Valid prediction for GlimmerHMM_glimmerT_52324-T1
Valid prediction for CodingQuarry_transcript_35611-T1
Valid prediction for GeneMark_model.90694_t
Couldn't classify 114453, 114555
Sorry, prediction pasa_asmbl_30898.p1 fails validation.
(GTA)	 AG	114453-114555	GT	AGG
(CTA)	 AG	114681-114715	GT	AAG
(GAA)	 AG	114793-114843	GT	AGG
(TTA)	 AG	114963-115074	GT	CGG
(GAG)	 AG	115229-115289	GT	CTG
(AGA)	 AG	115454-115564	GT	TCG
(TCA)	 AG	115749-115912	GT	TGG
(AGG)	 AG	116006-116088	GT	AGG
(AGC)	 AG	116183-116296	GC	AGG
(CTC)	 AG	116392-116511	AA	AGA
-recovered pasa_asmbl_30898.p1, terminal, 116392, 116511
-recovered pasa_asmbl_30898.p1, internal, 114453, 114555
-recovered pasa_asmbl_30898.p1, internal, 114681, 114715
-recovered pasa_asmbl_30898.p1, internal, 114793, 114843
-recovered pasa_asmbl_30898.p1, internal, 114963, 115074
-recovered pasa_asmbl_30898.p1, internal, 115229, 115289
-recovered pasa_asmbl_30898.p1, internal, 115454, 115564
-recovered pasa_asmbl_30898.p1, internal, 115749, 115912
-recovered pasa_asmbl_30898.p1, internal, 116006, 116088
-recovered pasa_asmbl_30898.p1, internal, 116183, 116296
Valid prediction for GeneMark_model.90682_t
Valid prediction for Augustus_model.g35184.t1
Valid prediction for snap_scaffold_23-snap.1058-T1
Valid prediction for snap_scaffold_23-snap.1047-T1
Valid prediction for CodingQuarry_transcript_35606-T1
Valid prediction for GeneMark_model.90700_t
Valid prediction for GeneMark_model.90680_t
Valid prediction for snap_scaffold_23-snap.1041-T1
Valid prediction for snap_scaffold_23-snap.1061-T1
Valid prediction for HiQ_model.g35199.t1
Valid prediction for snap_scaffold_23-snap.1050-T1
Valid prediction for GlimmerHMM_glimmerT_52313-T1
Valid prediction for GlimmerHMM_glimmerT_52315-T1
Valid prediction for GeneMark_model.90697_t
Valid prediction for GlimmerHMM_glimmerT_52314-T1
Valid prediction for GlimmerHMM_glimmerT_52296-T1
Valid prediction for snap_scaffold_23-snap.1034-T1
Valid prediction for GlimmerHMM_glimmerT_52303-T1
Valid prediction for GlimmerHMM_glimmerT_52299-T1
Valid prediction for snap_scaffold_23-snap.1049-T1
Couldn't classify 113452, 113524
Couldn't classify 113980, 114237
Sorry, prediction pasa_asmbl_30897.p1 fails validation.
(CTT)	 AA	113452-113524	GC	TGG
(GTT)	 AG	113745-113851	GT	AGG
(GAG)	 AG	113980-114237	GT	GGG
-recovered pasa_asmbl_30897.p1, internal, 113745, 113851
-recovered pasa_asmbl_30897.p1, internal, 113980, 114237
Valid prediction for GlimmerHMM_glimmerT_52318-T1
Valid prediction for GeneMark_model.90710_t
Valid prediction for snap_scaffold_23-snap.1056-T1
Valid prediction for CodingQuarry_transcript_35608-T1
Valid prediction for GeneMark_model.90673_t
Valid prediction for Augustus_model.g35191.t1
Valid prediction for Augustus_model.g35195.t1
Valid prediction for GeneMark_model.90690_t
Valid prediction for HiQ_model.g35196.t1
Valid prediction for snap_scaffold_23-snap.1051-T1
Valid prediction for CodingQuarry_transcript_35607-T1
Valid prediction for HiQ_model.g35198.t1
Valid prediction for GlimmerHMM_glimmerT_52309-T1
Valid prediction for snap_scaffold_23-snap.1059-T1
Valid prediction for CodingQuarry_transcript_35610-T1
Valid prediction for GeneMark_model.90675_t
Valid prediction for GlimmerHMM_glimmerT_52317-T1
Valid prediction for pasa_asmbl_30901.p1
Valid prediction for Augustus_model.g35188.t1
Valid prediction for pasa_asmbl_30902.p1
Valid prediction for GeneMark_model.90683_t
Valid prediction for GlimmerHMM_glimmerT_52327-T1
Couldn't classify 14527, 14611
Sorry, prediction pasa_asmbl_30892.p1 fails validation.
(TCC)	 CC	14527-14611	GT	AGG
(GCA)	 AG	14708-14842	GT	AGG
(ACA)	 AG	14931-14994	GT	AGG
(GTG)	 AG	15081-15147	GT	TGG
(CCC)	 AG	15314-15474	GT	ACG
(CGG)	 AG	15752-15918	GT	GGG
(ACG)	 AG	16163-16261	GT	CGG
(GGG)	 AG	16413-16549	AG	AGA
-recovered pasa_asmbl_30892.p1, terminal, 16413, 16549
-recovered pasa_asmbl_30892.p1, internal, 14708, 14842
-recovered pasa_asmbl_30892.p1, internal, 14931, 14994
-recovered pasa_asmbl_30892.p1, internal, 15081, 15147
-recovered pasa_asmbl_30892.p1, internal, 15314, 15474
-recovered pasa_asmbl_30892.p1, internal, 15752, 15918
-recovered pasa_asmbl_30892.p1, internal, 16163, 16261
Valid prediction for GeneMark_model.90693_t
Valid prediction for Augustus_model.g35187.t1
Valid prediction for GeneMark_model.90686_t
Valid prediction for snap_scaffold_23-snap.1036-T1
Valid prediction for GeneMark_model.90702_t
Valid prediction for snap_scaffold_23-snap.1048-T1
Valid prediction for GlimmerHMM_glimmerT_52297-T1
Valid prediction for snap_scaffold_23-snap.1032-T1
Valid prediction for GeneMark_model.90677_t
Valid prediction for GeneMark_model.90704_t
Valid prediction for pasa_asmbl_30896.p1

-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 snap_scaffold_23-snap.1055-T1
Valid prediction for Augustus_model.g35183.t1
Valid prediction for HiQ_model.g35193.t1
Valid prediction for snap_scaffold_23-snap.1057-T1
Valid prediction for GeneMark_model.90706_t
Valid prediction for Augustus_model.g35204.t1
Valid prediction for snap_scaffold_23-snap.1038-T1
Valid prediction for Augustus_model.g35201.t1
Valid prediction for GeneMark_model.90687_t
Valid prediction for GeneMark_model.90676_t
Valid prediction for GeneMark_model.90691_t
Valid prediction for snap_scaffold_23-snap.1054-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_52310-T1
Valid prediction for GeneMark_model.90695_t
Valid prediction for GlimmerHMM_glimmerT_52322-T1
Valid prediction for Augustus_model.g35206.t1
Valid prediction for Augustus_model.g35189.t1
Valid prediction for GlimmerHMM_glimmerT_52298-T1
Valid prediction for GlimmerHMM_glimmerT_52307-T1
Valid prediction for snap_scaffold_23-snap.1042-T1
Valid prediction for GlimmerHMM_glimmerT_52321-T1
Valid prediction for GlimmerHMM_glimmerT_52295-T1
Valid prediction for GlimmerHMM_glimmerT_52325-T1
Valid prediction for GlimmerHMM_glimmerT_52326-T1
Valid prediction for HiQ_model.g35200.t1
Valid prediction for pasa_asmbl_31675.p1
Valid prediction for CodingQuarry_transcript_35602-T1
Valid prediction for CodingQuarry_transcript_35604-T1
Valid prediction for GeneMark_model.90685_t
Valid prediction for snap_scaffold_23-snap.1039-T1
Valid prediction for Augustus_model.g35202.t1
Valid prediction for pasa_asmbl_31669.p1
Valid prediction for snap_scaffold_23-snap.1040-T1
Couldn't classify 181192, 181249
Sorry, prediction pasa_asmbl_31660.p1 fails validation.
(ATG)	 AT	180601-180911	GT	AGG
(GTA)	 AG	181192-181249	CT	ACC
-recovered pasa_asmbl_31660.p1, initial, 180601, 180911
Valid prediction for GeneMark_model.90701_t
Valid prediction for GlimmerHMM_glimmerT_52320-T1
Valid prediction for GlimmerHMM_glimmerT_52319-T1
Valid prediction for snap_scaffold_23-snap.1044-T1
Valid prediction for GlimmerHMM_glimmerT_52311-T1
Valid prediction for snap_scaffold_23-snap.1052-T1
Valid prediction for GeneMark_model.90698_t
Couldn't classify 104199, 104299
Couldn't classify 104665, 104839
Sorry, prediction pasa_asmbl_31915.p1 fails validation.
(ATC)	 GC	104199-104299	GT	AGG
(AAA)	 AG	104394-104510	GT	AAG
(GTT)	 AG	104665-104839	GT	AGG
-recovered pasa_asmbl_31915.p1, internal, 104394, 104510
-recovered pasa_asmbl_31915.p1, internal, 104665, 104839
Valid prediction for Augustus_model.g35192.t1
Valid prediction for GlimmerHMM_glimmerT_52306-T1
Valid prediction for GeneMark_model.90689_t
Valid prediction for HiQ_model.g35197.t1
Valid prediction for snap_scaffold_23-snap.1060-T1
Valid prediction for Augustus_model.g35185.t1
Couldn't classify 84440, 84514
Sorry, prediction pasa_asmbl_31666.p2 fails validation.
(CAT)	 GG	84440-84514	GT	AGG
(CGA)	 AG	84637-84752	GT	CGG
(CAT)	 AG	85087-85186	GT	AGG
(GTC)	 AG	85569-85595	AC	AGA
-recovered pasa_asmbl_31666.p2, terminal, 85569, 85595
-recovered pasa_asmbl_31666.p2, internal, 84637, 84752
-recovered pasa_asmbl_31666.p2, internal, 85087, 85186
Valid prediction for GlimmerHMM_glimmerT_52301-T1
Valid prediction for snap_scaffold_23-snap.1053-T1
Valid prediction for GlimmerHMM_glimmerT_52308-T1
Valid prediction for CodingQuarry_transcript_35601-T1
Valid prediction for GlimmerHMM_glimmerT_52302-T1
Valid prediction for GlimmerHMM_glimmerT_52300-T1
Valid prediction for pasa_asmbl_31671.p1
Valid prediction for snap_scaffold_23-snap.1063-T1
Valid prediction for GlimmerHMM_glimmerT_52305-T1
Valid prediction for CodingQuarry_transcript_35609-T1
Valid prediction for CodingQuarry_transcript_35612-T1
Valid prediction for GeneMark_model.90705_t
Valid prediction for GeneMark_model.90674_t
Valid prediction for GeneMark_model.90707_t
Couldn't classify 82260, 82419
Couldn't classify 84046, 84240
Sorry, prediction pasa_asmbl_31667.p1 fails validation.
(GCG)	 GC	82260-82419	GT	TGG
(CGG)	 AG	82898-83013	GT	AGG
(GAG)	 AG	84046-84240	TA	GGT
-recovered pasa_asmbl_31667.p1, internal, 82898, 83013
Valid prediction for Augustus_model.g35207.t1
Valid prediction for Augustus_model.g35203.t1
Valid prediction for snap_scaffold_23-snap.1045-T1
Valid prediction for snap_scaffold_23-snap.1062-T1
Valid prediction for GlimmerHMM_glimmerT_52316-T1
Valid prediction for GlimmerHMM_glimmerT_52312-T1
Valid prediction for snap_scaffold_23-snap.1043-T1
Valid prediction for GeneMark_model.90709_t
Valid prediction for CodingQuarry_transcript_35600-T1
Valid prediction for GeneMark_model.90699_t
Valid prediction for GeneMark_model.90681_t
Valid prediction for pasa_asmbl_31663.p1
Valid prediction for GeneMark_model.90692_t
Valid prediction for GeneMark_model.90703_t
Valid prediction for GlimmerHMM_glimmerT_52323-T1
Valid prediction for snap_scaffold_23-snap.1046-T1
Valid prediction for GeneMark_model.90684_t
Couldn't classify 30811, 30850
Couldn't classify 33167, 33447
Sorry, prediction pasa_asmbl_31679.p1 fails validation.
(TAC)	 TC	30811-30850	GT	AGG
(GTC)	 AG	31563-31820	GT	TGG
(GCT)	 AG	33167-33447	AG	CCA
-recovered pasa_asmbl_31679.p1, internal, 31563, 31820
Valid prediction for GeneMark_model.90679_t
Valid prediction for Augustus_model.g35190.t1
Valid prediction for Augustus_model.g35205.t1
Valid prediction for CodingQuarry_transcript_35605-T1
Valid prediction for CodingQuarry_transcript_35603-T1
Valid prediction for GeneMark_model.90696_t
Valid prediction for snap_scaffold_23-snap.1035-T1
Couldn't classify 50299, 50374
Couldn't classify 52447, 52490
Sorry, prediction pasa_asmbl_31677.p1 fails validation.
(GGC)	 TT	50299-50374	GT	AGG
(CTC)	 AG	50628-50875	GT	GAG
(ACT)	 AG	50993-51183	GT	AGG
(GTC)	 AG	51309-51424	GT	AGG
(CGC)	 AG	52125-52250	GT	CGG
(GCT)	 AG	52447-52490	CA	GAC
add_exon() Sorry, pasa_asmbl_31677.p1 51309-51424-terminal-2 is invalid.
-recovered pasa_asmbl_31677.p1, terminal, 51309, 51424
-recovered pasa_asmbl_31677.p1, internal, 50628, 50875
-recovered pasa_asmbl_31677.p1, internal, 50993, 51183
-recovered pasa_asmbl_31677.p1, internal, 51309, 51424
-recovered pasa_asmbl_31677.p1, internal, 52125, 52250
Valid prediction for snap_scaffold_23-snap.1033-T1
Valid prediction for HiQ_model.g35186.t1
Valid prediction for GeneMark_model.90678_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 80303, rend_intergenic: 75733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167405, rend_intergenic: 154577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173287, rend_intergenic: 169135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180380, rend_intergenic: 177955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187857
-exon list size: 627


building trellis

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81.9    
82.0    
82.2    
82.4    
82.5    
82.7    
82.8    
83.0    
83.1    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.3    
84.4    
84.6    
84.7    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 80303, rend_intergenic: 75733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167405, rend_intergenic: 154577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173287, rend_intergenic: 169135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180380, rend_intergenic: 177955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support