-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_16651535-16877764

-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_13729-T1
Valid prediction for snap_scaffold_5-snap.3152-T1
Valid prediction for Augustus_model.g9167.t1
Valid prediction for snap_scaffold_5-snap.3126-T1
Valid prediction for GeneMark_model.23009_t
Valid prediction for GeneMark_model.22998_t
Valid prediction for snap_scaffold_5-snap.3143-T1
Valid prediction for snap_scaffold_5-snap.3147-T1
Valid prediction for snap_scaffold_5-snap.3125-T1
Valid prediction for GlimmerHMM_glimmerT_13724-T1
Valid prediction for GeneMark_model.23004_t
Valid prediction for GeneMark_model.22985_t
Valid prediction for GlimmerHMM_glimmerT_13733-T1
Valid prediction for snap_scaffold_5-snap.3144-T1
Valid prediction for GeneMark_model.22997_t
Valid prediction for GlimmerHMM_glimmerT_13726-T1
Valid prediction for snap_scaffold_5-snap.3122-T1
Valid prediction for Augustus_model.g9181.t1
Valid prediction for GlimmerHMM_glimmerT_13731-T1
Valid prediction for GeneMark_model.23002_t
Valid prediction for GeneMark_model.22988_t
Valid prediction for GlimmerHMM_glimmerT_13711-T1
Valid prediction for GeneMark_model.23012_t
Valid prediction for GeneMark_model.22982_t
Valid prediction for GeneMark_model.23006_t
Valid prediction for GlimmerHMM_glimmerT_13716-T1
Valid prediction for snap_scaffold_5-snap.3135-T1
Valid prediction for snap_scaffold_5-snap.3149-T1
Valid prediction for Augustus_model.g9185.t1
Valid prediction for GeneMark_model.22983_t
Valid prediction for GlimmerHMM_glimmerT_13705-T1
Valid prediction for snap_scaffold_5-snap.3139-T1
Valid prediction for GlimmerHMM_glimmerT_13714-T1
Valid prediction for GeneMark_model.22979_t
Valid prediction for GeneMark_model.22992_t
Valid prediction for GlimmerHMM_glimmerT_13707-T1
Valid prediction for GeneMark_model.22993_t
Valid prediction for GlimmerHMM_glimmerT_13710-T1
Valid prediction for GlimmerHMM_glimmerT_13735-T1
Valid prediction for snap_scaffold_5-snap.3150-T1
Valid prediction for snap_scaffold_5-snap.3116-T1
Valid prediction for Augustus_model.g9172.t1
Valid prediction for GeneMark_model.22995_t
Valid prediction for Augustus_model.g9175.t1
Valid prediction for GeneMark_model.23007_t
Valid prediction for GlimmerHMM_glimmerT_13725-T1
Couldn't classify 12377, 12617
Couldn't classify 15374, 15504
Sorry, prediction pasa_asmbl_44781.p1 fails validation.
(GCA)	 CA	12377-12617	GT	CGG
(TGG)	 AG	12735-12971	GT	CGG
(GCC)	 AG	13293-13523	GT	AGG
(ACA)	 AG	13826-13993	GT	GGG
(GAA)	 AG	14527-14683	GT	AGG
(GTA)	 AG	15105-15229	GT	GGG
(GCA)	 AG	15374-15504	GT	AGG
-recovered pasa_asmbl_44781.p1, internal, 12735, 12971
-recovered pasa_asmbl_44781.p1, internal, 13293, 13523
-recovered pasa_asmbl_44781.p1, internal, 13826, 13993
-recovered pasa_asmbl_44781.p1, internal, 14527, 14683
-recovered pasa_asmbl_44781.p1, internal, 15105, 15229
-recovered pasa_asmbl_44781.p1, internal, 15374, 15504
Valid prediction for GeneMark_model.22986_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 Augustus_model.g9177.t1
Valid prediction for GeneMark_model.23010_t
Valid prediction for GeneMark_model.23005_t
Valid prediction for HiQ_model.g9180.t1
Valid prediction for pasa_asmbl_46156.p1
Valid prediction for GeneMark_model.22981_t
Valid prediction for CodingQuarry_transcript_52292-T1
Valid prediction for GlimmerHMM_glimmerT_13717-T1
Valid prediction for GlimmerHMM_glimmerT_13723-T1
Valid prediction for snap_scaffold_5-snap.3115-T1
Valid prediction for Augustus_model.g9170.t1
Valid prediction for GeneMark_model.22999_t
Couldn't classify 119602, 119663
Couldn't classify 122555, 122636
Sorry, prediction pasa_asmbl_46351.p1 fails validation.
(GCA)	 CA	119602-119663	GT	AAG
(ATG)	 AG	119746-119855	GT	AAG
(TGA)	 AG	122155-122199	GT	TGG
(GGA)	 AG	122304-122439	GT	ATG
(GTG)	 AG	122555-122636	GA	TGG
add_exon() Sorry, pasa_asmbl_46351.p1 119746-119855-initial-1 is invalid.
-recovered pasa_asmbl_46351.p1, initial, 119746, 119855
-recovered pasa_asmbl_46351.p1, internal, 119746, 119855
-recovered pasa_asmbl_46351.p1, internal, 122155, 122199
-recovered pasa_asmbl_46351.p1, internal, 122304, 122439
Valid prediction for snap_scaffold_5-snap.3131-T1
Valid prediction for GlimmerHMM_glimmerT_13727-T1
Valid prediction for GlimmerHMM_glimmerT_13713-T1
Valid prediction for GlimmerHMM_glimmerT_13709-T1
Valid prediction for pasa_asmbl_46150.p1
Couldn't classify 174000, 174371
Sorry, prediction pasa_asmbl_46148.p1 fails validation.
(GAA)	 AC	174000-174371	AA	CCA
Valid prediction for GlimmerHMM_glimmerT_13728-T1
Valid prediction for GeneMark_model.22991_t
Valid prediction for snap_scaffold_5-snap.3148-T1
Valid prediction for GeneMark_model.22996_t
Valid prediction for snap_scaffold_5-snap.3129-T1
Valid prediction for snap_scaffold_5-snap.3124-T1
Valid prediction for CodingQuarry_transcript_52291-T1
Valid prediction for Augustus_model.g9176.t1
Valid prediction for GlimmerHMM_glimmerT_13721-T1
Valid prediction for snap_scaffold_5-snap.3130-T1
Valid prediction for snap_scaffold_5-snap.3121-T1
Valid prediction for GeneMark_model.22990_t
Valid prediction for snap_scaffold_5-snap.3145-T1
Valid prediction for Augustus_model.g9169.t1
Valid prediction for snap_scaffold_5-snap.3118-T1
Valid prediction for Augustus_model.g9179.t1
Valid prediction for GlimmerHMM_glimmerT_13732-T1
Valid prediction for GeneMark_model.23003_t
Valid prediction for GeneMark_model.23000_t
Valid prediction for GeneMark_model.23013_t
Valid prediction for GlimmerHMM_glimmerT_13730-T1
Valid prediction for GlimmerHMM_glimmerT_13722-T1
Valid prediction for snap_scaffold_5-snap.3119-T1
Valid prediction for snap_scaffold_5-snap.3133-T1
Valid prediction for snap_scaffold_5-snap.3137-T1
Valid prediction for HiQ_model.g9173.t1
Valid prediction for GeneMark_model.22984_t
Valid prediction for snap_scaffold_5-snap.3146-T1
Valid prediction for snap_scaffold_5-snap.3140-T1
Valid prediction for Augustus_model.g9178.t1
Valid prediction for GeneMark_model.22987_t
Valid prediction for CodingQuarry_transcript_52293-T1
Valid prediction for GlimmerHMM_glimmerT_13718-T1
Couldn't classify 91502, 91544
Sorry, prediction pasa_asmbl_46154.p1 fails validation.
(ACG)	 TG	91502-91544	GT	TGG
(AGA)	 AG	91645-91780	GT	ATG
(GTG)	 AG	91844-91953	GT	AGG
(TGA)	 AG	92021-92037	GA	AGG
add_exon() Sorry, pasa_asmbl_46154.p1 91844-91953-terminal-2 is invalid.
-recovered pasa_asmbl_46154.p1, terminal, 91844, 91953
-recovered pasa_asmbl_46154.p1, terminal, 92021, 92037
-recovered pasa_asmbl_46154.p1, internal, 91645, 91780
-recovered pasa_asmbl_46154.p1, internal, 91844, 91953
Valid prediction for Augustus_model.g9183.t1
Valid prediction for GlimmerHMM_glimmerT_13704-T1
Valid prediction for Augustus_model.g9166.t1
Valid prediction for GlimmerHMM_glimmerT_13719-T1
Couldn't classify 135930, 135975
Couldn't classify 137419, 137420
Sorry, prediction pasa_asmbl_46152.p1 fails validation.
(GGA)	 TT	135930-135975	GT	AAG
(TCA)	 AG	136089-136133	GT	CGG
(GGA)	 AG	136237-136372	GT	ATG
(GTG)	 AG	137241-137341	GT	CTG
(AGT)	 AG	137419-137420	TA	AGT
-recovered pasa_asmbl_46152.p1, internal, 136089, 136133
-recovered pasa_asmbl_46152.p1, internal, 136237, 136372
-recovered pasa_asmbl_46152.p1, internal, 137241, 137341
Valid prediction for snap_scaffold_5-snap.3128-T1
Valid prediction for Augustus_model.g9174.t1
Couldn't classify 184286, 184609
Couldn't classify 184833, 184865
Sorry, prediction pasa_asmbl_46147.p1 fails validation.
(GAG)	 AG	184286-184609	GT	AGG
(GGG)	 AG	184833-184865	CC	GAC
-recovered pasa_asmbl_46147.p1, internal, 184286, 184609
Couldn't classify 199364, 199445
Couldn't classify 200989, 201408
Sorry, prediction pasa_asmbl_46145.p1 fails validation.
(CAC)	 AG	199364-199445	GT	GGG
(ATT)	 AG	199543-199624	GT	AGG
(GAT)	 AG	199829-200004	GT	AAG
(CTT)	 AG	200124-200248	GT	AGG
(AAC)	 AG	200401-200527	GT	AGG
(GTG)	 AG	200637-200770	GT	AGG
(GAG)	 AG	200989-201408	AG	CTA
-recovered pasa_asmbl_46145.p1, internal, 199364, 199445
-recovered pasa_asmbl_46145.p1, internal, 199543, 199624
-recovered pasa_asmbl_46145.p1, internal, 199829, 200004
-recovered pasa_asmbl_46145.p1, internal, 200124, 200248
-recovered pasa_asmbl_46145.p1, internal, 200401, 200527
-recovered pasa_asmbl_46145.p1, internal, 200637, 200770
Valid prediction for snap_scaffold_5-snap.3142-T1
Valid prediction for snap_scaffold_5-snap.3120-T1
Valid prediction for GeneMark_model.23011_t
Valid prediction for pasa_asmbl_46144.p1
Valid prediction for snap_scaffold_5-snap.3123-T1
Valid prediction for GeneMark_model.22978_t
Valid prediction for snap_scaffold_5-snap.3151-T1
Valid prediction for snap_scaffold_5-snap.3132-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_13734-T1
Couldn't classify 119304, 119320
Sorry, prediction pasa_asmbl_46153.p1 fails validation.
(ATG)	 CC	118320-118353	GT	CTG
(TGC)	 AG	118620-118649	GT	AGG
(TGA)	 AG	118735-118779	GT	TGG
(GGA)	 AG	118904-119039	GT	AAG
(GTG)	 AG	119123-119232	GT	AAG
(TTT)	 AG	119304-119320	AT	ACA
-recovered pasa_asmbl_46153.p1, initial, 118320, 118353
-recovered pasa_asmbl_46153.p1, internal, 118620, 118649
-recovered pasa_asmbl_46153.p1, internal, 118735, 118779
-recovered pasa_asmbl_46153.p1, internal, 118904, 119039
-recovered pasa_asmbl_46153.p1, internal, 119123, 119232
Valid prediction for GlimmerHMM_glimmerT_13708-T1
Valid prediction for Augustus_model.g9168.t1
Valid prediction for snap_scaffold_5-snap.3117-T1
Valid prediction for GeneMark_model.23008_t
Valid prediction for GlimmerHMM_glimmerT_13712-T1
Valid prediction for snap_scaffold_5-snap.3138-T1
Valid prediction for GeneMark_model.22980_t
Valid prediction for GlimmerHMM_glimmerT_13720-T1
Valid prediction for snap_scaffold_5-snap.3141-T1
Valid prediction for GlimmerHMM_glimmerT_13706-T1
Valid prediction for GlimmerHMM_glimmerT_13715-T1
Valid prediction for snap_scaffold_5-snap.3136-T1
Valid prediction for Augustus_model.g9182.t1
Valid prediction for Augustus_model.g9171.t1
Valid prediction for snap_scaffold_5-snap.3127-T1
Valid prediction for snap_scaffold_5-snap.3134-T1
Valid prediction for Augustus_model.g9184.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15561, rend_intergenic: 9323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129390, rend_intergenic: 115521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148995, rend_intergenic: 147000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175123, rend_intergenic: 172831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194768, rend_intergenic: 186252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201406, rend_intergenic: 196990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222774, rend_intergenic: 210737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 226230
-exon list size: 690


building trellis

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83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 15561, rend_intergenic: 9323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129390, rend_intergenic: 115521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148995, rend_intergenic: 147000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175123, rend_intergenic: 172831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194768, rend_intergenic: 186252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201406, rend_intergenic: 196990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222774, rend_intergenic: 210737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support