-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_16280886-16449967

-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_13661-T1
Valid prediction for GeneMark_model.22915_t
Valid prediction for GeneMark_model.22930_t
Valid prediction for snap_scaffold_5-snap.3062-T1
Valid prediction for HiQ_model.g9131.t1
Valid prediction for GlimmerHMM_glimmerT_13647-T1
Valid prediction for snap_scaffold_5-snap.3055-T1
Valid prediction for pasa_asmbl_44737.p1
Valid prediction for HiQ_model.g9128.t1
Valid prediction for GeneMark_model.22908_t
Couldn't classify 9321, 9362
Sorry, prediction pasa_asmbl_44741.p1 fails validation.
(CCG)	 CC	9321-9362	GT	CGG
(TCA)	 AG	10350-10446	GT	GGG
(ATG)	 AG	10555-10704	GT	GGG
(TGC)	 AG	11331-11576	GT	TGG
(AGA)	 AG	11734-11851	GT	AAG
(GTA)	 AG	11959-12099	GT	CTG
(GTA)	 AG	12309-12596	GT	AGG
(GTA)	 AG	12790-12895	GT	AGG
(GTT)	 AG	13044-13161	GT	AGG
(GTG)	 AG	13323-13504	GT	AGG
(ATC)	 AG	13613-13803	GT	TGG
(CTT)	 AG	14025-14127	AC	AGA
add_exon() Sorry, pasa_asmbl_44741.p1 10555-10704-initial-1 is invalid.
-recovered pasa_asmbl_44741.p1, initial, 10555, 10704
-recovered pasa_asmbl_44741.p1, terminal, 14025, 14127
-recovered pasa_asmbl_44741.p1, internal, 10350, 10446
-recovered pasa_asmbl_44741.p1, internal, 10555, 10704
-recovered pasa_asmbl_44741.p1, internal, 11331, 11576
-recovered pasa_asmbl_44741.p1, internal, 11734, 11851
-recovered pasa_asmbl_44741.p1, internal, 11959, 12099
-recovered pasa_asmbl_44741.p1, internal, 12309, 12596
-recovered pasa_asmbl_44741.p1, internal, 12790, 12895
-recovered pasa_asmbl_44741.p1, internal, 13044, 13161
-recovered pasa_asmbl_44741.p1, internal, 13323, 13504
-recovered pasa_asmbl_44741.p1, internal, 13613, 13803
Valid prediction for snap_scaffold_5-snap.3065-T1
Valid prediction for snap_scaffold_5-snap.3045-T1
Valid prediction for snap_scaffold_5-snap.3043-T1
Valid prediction for snap_scaffold_5-snap.3040-T1
Valid prediction for GeneMark_model.22907_t
Valid prediction for GlimmerHMM_glimmerT_13643-T1
Valid prediction for snap_scaffold_5-snap.3035-T1
Couldn't classify 46409, 46513
Sorry, prediction pasa_asmbl_44749.p1 fails validation.
(ATG)	 GC	44590-44638	GT	AGG
(TGG)	 AG	44771-44858	GT	AGG
(GGA)	 AG	45092-45228	GT	ATG
(CCT)	 AG	45377-45480	GT	AGG
(GAA)	 AG	45637-45747	GT	AGG
(GCA)	 AG	45867-45920	GT	TGG
(GCA)	 AG	46014-46223	GT	TGG
(GCG)	 AG	46409-46513	TA	GGT
-recovered pasa_asmbl_44749.p1, initial, 44590, 44638
add_exon() Sorry, pasa_asmbl_44749.p1 44771-44858-terminal-3 is invalid.
-recovered pasa_asmbl_44749.p1, terminal, 44771, 44858
-recovered pasa_asmbl_44749.p1, internal, 44771, 44858
-recovered pasa_asmbl_44749.p1, internal, 45092, 45228
-recovered pasa_asmbl_44749.p1, internal, 45377, 45480
-recovered pasa_asmbl_44749.p1, internal, 45637, 45747
-recovered pasa_asmbl_44749.p1, internal, 45867, 45920
-recovered pasa_asmbl_44749.p1, internal, 46014, 46223
Valid prediction for snap_scaffold_5-snap.3046-T1
Valid prediction for GeneMark_model.22925_t
Valid prediction for HiQ_model.g9133.t1
Valid prediction for Augustus_model.g9132.t1
Valid prediction for snap_scaffold_5-snap.3052-T1
Valid prediction for snap_scaffold_5-snap.3064-T1
Valid prediction for snap_scaffold_5-snap.3048-T1
Valid prediction for snap_scaffold_5-snap.3060-T1
Valid prediction for Augustus_model.g9143.t1
Valid prediction for Augustus_model.g9142.t1
Valid prediction for GlimmerHMM_glimmerT_13651-T1
Valid prediction for Augustus_model.g9130.t1
Couldn't classify 98547, 98631
Couldn't classify 100206, 100406
Sorry, prediction pasa_asmbl_44758.p1 fails validation.
(CTG)	 GC	98547-98631	GT	AGG
(CTC)	 AG	98854-98990	GT	AGG
(GTC)	 AG	99106-99186	GT	CAG
(GGC)	 AG	99606-99733	GT	AGG
(GAT)	 AG	99853-99967	GT	AGG
(GCC)	 AG	100206-100406	GG	CCG
-recovered pasa_asmbl_44758.p1, internal, 98854, 98990
-recovered pasa_asmbl_44758.p1, internal, 99106, 99186
-recovered pasa_asmbl_44758.p1, internal, 99606, 99733
-recovered pasa_asmbl_44758.p1, internal, 99853, 99967
Valid prediction for snap_scaffold_5-snap.3066-T1
Valid prediction for GlimmerHMM_glimmerT_13657-T1
Valid prediction for GlimmerHMM_glimmerT_13649-T1
Valid prediction for GeneMark_model.22910_t
Valid prediction for Augustus_model.g9127.t1
Couldn't classify 62728, 62949
Sorry, prediction pasa_asmbl_44755.p1 fails validation.
(GGT)	 TA	62728-62949	GT	AGG
(CGG)	 AG	65918-66014	GT	AGG
(ACC)	 AG	66324-66454	GT	CTG
(CTC)	 AG	66640-66804	GT	AGG
(GAC)	 AG	67044-67201	GT	GGG
(GTC)	 AG	67355-67430	GT	CTG
(CTG)	 AG	67897-68016	GT	TGG
(AGA)	 AG	68531-68680	GT	AGG
(GTG)	 AG	68816-69004	GT	CGG
(AAT)	 AG	69194-69299	GT	TGG
(CAG)	 AG	69545-69801	TG	GAT
-recovered pasa_asmbl_44755.p1, terminal, 69545, 69801
-recovered pasa_asmbl_44755.p1, internal, 65918, 66014
-recovered pasa_asmbl_44755.p1, internal, 66324, 66454
-recovered pasa_asmbl_44755.p1, internal, 66640, 66804
-recovered pasa_asmbl_44755.p1, internal, 67044, 67201
-recovered pasa_asmbl_44755.p1, internal, 67355, 67430
-recovered pasa_asmbl_44755.p1, internal, 67897, 68016
-recovered pasa_asmbl_44755.p1, internal, 68531, 68680
-recovered pasa_asmbl_44755.p1, internal, 68816, 69004
-recovered pasa_asmbl_44755.p1, internal, 69194, 69299
Valid prediction for GlimmerHMM_glimmerT_13658-T1
Valid prediction for snap_scaffold_5-snap.3041-T1
Couldn't classify 105273, 105281
Sorry, prediction pasa_asmbl_44760.p1 fails validation.
(TCA)	 AG	105273-105281	GT	CTG
(ATT)	 AG	105413-105487	GT	AGG
(ATC)	 AG	105621-105795	GT	AGG
(ACC)	 AG	105897-106020	GT	AGG
(CGC)	 AG	106410-106662	AG	GAA
-recovered pasa_asmbl_44760.p1, terminal, 106410, 106662
-recovered pasa_asmbl_44760.p1, internal, 105273, 105281
-recovered pasa_asmbl_44760.p1, internal, 105413, 105487
-recovered pasa_asmbl_44760.p1, internal, 105621, 105795
-recovered pasa_asmbl_44760.p1, internal, 105897, 106020
Valid prediction for Augustus_model.g9137.t1
Valid prediction for snap_scaffold_5-snap.3059-T1
Valid prediction for Augustus_model.g9134.t1
Valid prediction for GeneMark_model.22921_t
Couldn't classify 50331, 50339
Couldn't classify 50454, 50834
Sorry, prediction pasa_asmbl_44752.p1 fails validation.
(CCT)	 TC	50331-50339	GT	TGG
(GAG)	 AG	50454-50834	CC	CCC
Valid prediction for pasa_asmbl_44743.p1
Valid prediction for GeneMark_model.22927_t
Valid prediction for snap_scaffold_5-snap.3042-T1
Valid prediction for snap_scaffold_5-snap.3039-T1
Valid prediction for GlimmerHMM_glimmerT_13652-T1
Valid prediction for GlimmerHMM_glimmerT_13659-T1
Valid prediction for GlimmerHMM_glimmerT_13645-T1
Valid prediction for Augustus_model.g9139.t1
Valid prediction for GlimmerHMM_glimmerT_13646-T1
Valid prediction for GlimmerHMM_glimmerT_13662-T1
Valid prediction for snap_scaffold_5-snap.3056-T1
Valid prediction for GeneMark_model.22906_t
Couldn't classify 53406, 53460
Sorry, prediction pasa_asmbl_44754.p1 fails validation.
(GAC)	 CA	53406-53460	GT	CGG
(TCC)	 AG	54224-54426	GT	GAG
(GGA)	 AG	54541-54645	GT	AGG
(GTA)	 AG	54787-55422	GA	GAG
-recovered pasa_asmbl_44754.p1, terminal, 54787, 55422
-recovered pasa_asmbl_44754.p1, internal, 54224, 54426
-recovered pasa_asmbl_44754.p1, internal, 54541, 54645
Valid prediction for CodingQuarry_transcript_52288-T1
Valid prediction for snap_scaffold_5-snap.3044-T1
Valid prediction for GlimmerHMM_glimmerT_13654-T1
Valid prediction for GeneMark_model.22905_t
Valid prediction for GeneMark_model.22928_t
Valid prediction for GeneMark_model.22917_t
Valid prediction for snap_scaffold_5-snap.3063-T1
Couldn't classify 103943, 104089
Couldn't classify 105224, 105242
Sorry, prediction pasa_asmbl_44759.p1 fails validation.
(ATC)	 CA	103943-104089	GT	AGG
(GCG)	 AG	104609-104779	GT	AGG
(GGT)	 AG	105057-105118	GT	AGG
(GGT)	 AG	105224-105242	GG	GGG
-recovered pasa_asmbl_44759.p1, internal, 104609, 104779
-recovered pasa_asmbl_44759.p1, internal, 105057, 105118
Valid prediction for Augustus_model.g9141.t1
Valid prediction for Augustus_model.g9138.t1
Valid prediction for GeneMark_model.22919_t
Valid prediction for Augustus_model.g9129.t1
Valid prediction for GeneMark_model.22912_t
Couldn't classify 48493, 48695
Couldn't classify 49791, 49916
Sorry, prediction pasa_asmbl_44750.p1 fails validation.
(AAC)	 CA	48493-48695	GT	AGG
(GAG)	 AG	49079-49130	GT	CGG
(AGA)	 AG	49280-49438	GT	AGG
(CAG)	 AG	49791-49916	CC	CCC
-recovered pasa_asmbl_44750.p1, internal, 49079, 49130
-recovered pasa_asmbl_44750.p1, internal, 49280, 49438

-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 Augustus_model.g9126.t1
Valid prediction for GlimmerHMM_glimmerT_13650-T1
Valid prediction for snap_scaffold_5-snap.3058-T1
Valid prediction for GlimmerHMM_glimmerT_13660-T1
Valid prediction for GlimmerHMM_glimmerT_13648-T1
Valid prediction for Augustus_model.g9136.t1
Valid prediction for GeneMark_model.22914_t
Valid prediction for GlimmerHMM_glimmerT_13653-T1
Valid prediction for GeneMark_model.22911_t
Valid prediction for GeneMark_model.22904_t
Valid prediction for snap_scaffold_5-snap.3051-T1
Valid prediction for snap_scaffold_5-snap.3036-T1
Valid prediction for GlimmerHMM_glimmerT_13655-T1
Valid prediction for GeneMark_model.22931_t
Valid prediction for GeneMark_model.22916_t
Valid prediction for GeneMark_model.22923_t
Valid prediction for GeneMark_model.22918_t
Valid prediction for GlimmerHMM_glimmerT_13644-T1
Valid prediction for Augustus_model.g9140.t1
Valid prediction for Augustus_model.g9135.t1
Valid prediction for GeneMark_model.22929_t
Valid prediction for snap_scaffold_5-snap.3061-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3047-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3053-T1
Valid prediction for snap_scaffold_5-snap.3038-T1
Valid prediction for snap_scaffold_5-snap.3037-T1
Valid prediction for GeneMark_model.22909_t
Valid prediction for GlimmerHMM_glimmerT_13656-T1
Valid prediction for GeneMark_model.22920_t
Valid prediction for snap_scaffold_5-snap.3054-T1
Valid prediction for snap_scaffold_5-snap.3050-T1
Valid prediction for snap_scaffold_5-snap.3034-T1
Valid prediction for GeneMark_model.22926_t
Valid prediction for GeneMark_model.22913_t
Valid prediction for snap_scaffold_5-snap.3049-T1
Valid prediction for GeneMark_model.22924_t
Valid prediction for snap_scaffold_5-snap.3057-T1
Valid prediction for GlimmerHMM_glimmerT_13663-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5639, rend_intergenic: 3950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14127, rend_intergenic: 5688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70400, rend_intergenic: 66595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90356, rend_intergenic: 88834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107603, rend_intergenic: 92924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142759, rend_intergenic: 138275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 169082
-exon list size: 625


building trellis

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85.2    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.7    
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    
97.4    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 5639, rend_intergenic: 3950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14127, rend_intergenic: 5688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70400, rend_intergenic: 66595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90356, rend_intergenic: 88834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107603, rend_intergenic: 92924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142759, rend_intergenic: 138275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support