-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_15514709-15714599

-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_4-snap.3136-T1
Valid prediction for GeneMark_model.17832_t
Valid prediction for GeneMark_model.17830_t
Valid prediction for snap_scaffold_4-snap.3143-T1
Valid prediction for GeneMark_model.17857_t
Valid prediction for GeneMark_model.17846_t
Valid prediction for GlimmerHMM_glimmerT_10998-T1
Valid prediction for GeneMark_model.17851_t
Valid prediction for GeneMark_model.17848_t
Valid prediction for snap_scaffold_4-snap.3164-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.17835_t
Valid prediction for GeneMark_model.17841_t
Valid prediction for snap_scaffold_4-snap.3139-T1
Valid prediction for Augustus_model.g7273.t1
Valid prediction for GlimmerHMM_glimmerT_10985-T1
Valid prediction for GeneMark_model.17839_t
Valid prediction for GeneMark_model.17873_t
Valid prediction for GlimmerHMM_glimmerT_10991-T1
Valid prediction for snap_scaffold_4-snap.3146-T1
Valid prediction for GeneMark_model.17875_t
Valid prediction for snap_scaffold_4-snap.3135-T1
Valid prediction for Augustus_model.g7271.t1
Valid prediction for snap_scaffold_4-snap.3142-T1
Valid prediction for GeneMark_model.17878_t
Valid prediction for GlimmerHMM_glimmerT_11001-T1
Valid prediction for GlimmerHMM_glimmerT_10984-T1
Valid prediction for GeneMark_model.17820_t
Valid prediction for snap_scaffold_4-snap.3137-T1
Valid prediction for GeneMark_model.17823_t
Valid prediction for GeneMark_model.17842_t
Valid prediction for Augustus_model.g7268.t1
Valid prediction for GeneMark_model.17871_t
Valid prediction for GeneMark_model.17859_t
Valid prediction for snap_scaffold_4-snap.3150-T1
Valid prediction for GeneMark_model.17838_t
Valid prediction for GlimmerHMM_glimmerT_10987-T1
Valid prediction for snap_scaffold_4-snap.3166-T1
Valid prediction for GeneMark_model.17867_t
Valid prediction for GlimmerHMM_glimmerT_11003-T1
Valid prediction for snap_scaffold_4-snap.3170-T1
Valid prediction for snap_scaffold_4-snap.3154-T1
Valid prediction for GeneMark_model.17822_t
Valid prediction for GeneMark_model.17825_t
Valid prediction for snap_scaffold_4-snap.3160-T1
Valid prediction for GeneMark_model.17833_t
Valid prediction for Augustus_model.g7270.t1
Valid prediction for snap_scaffold_4-snap.3141-T1
Valid prediction for GeneMark_model.17837_t
Valid prediction for GeneMark_model.17827_t
Valid prediction for snap_scaffold_4-snap.3151-T1
Valid prediction for GeneMark_model.17863_t
Valid prediction for GeneMark_model.17869_t
Valid prediction for snap_scaffold_4-snap.3163-T1
Valid prediction for GeneMark_model.17855_t
Valid prediction for GeneMark_model.17865_t
Valid prediction for snap_scaffold_4-snap.3148-T1
Valid prediction for GeneMark_model.17853_t
Valid prediction for snap_scaffold_4-snap.3172-T1
Valid prediction for snap_scaffold_4-snap.3169-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 GeneMark_model.17844_t
Valid prediction for CodingQuarry_transcript_49159-T1
Valid prediction for snap_scaffold_4-snap.3171-T1
Valid prediction for GeneMark_model.17877_t
Valid prediction for GlimmerHMM_glimmerT_10990-T1
Valid prediction for GeneMark_model.17856_t
Valid prediction for snap_scaffold_4-snap.3144-T1
Valid prediction for Augustus_model.g7265.t1
Valid prediction for GeneMark_model.17826_t
Valid prediction for Augustus_model.g7266.t1
Valid prediction for snap_scaffold_4-snap.3155-T1
Valid prediction for Augustus_model.g7260.t1
Valid prediction for Augustus_model.g7262.t1
Valid prediction for GlimmerHMM_glimmerT_10980-T1
Valid prediction for GeneMark_model.17874_t
Valid prediction for GeneMark_model.17828_t
Valid prediction for GlimmerHMM_glimmerT_10999-T1
Valid prediction for GeneMark_model.17854_t
Valid prediction for GeneMark_model.17870_t
Valid prediction for GeneMark_model.17858_t
Valid prediction for GeneMark_model.17868_t
Valid prediction for snap_scaffold_4-snap.3156-T1
Couldn't classify 42667, 42709
Couldn't classify 44078, 44170
Sorry, prediction pasa_asmbl_41859.p1 fails validation.
(TTC)	 CT	42667-42709	GT	CGG
(GTG)	 AG	43416-43526	GT	TAG
(GAG)	 AG	43714-43865	GT	GGG
(GAC)	 AG	44078-44170	AA	CAA
-recovered pasa_asmbl_41859.p1, internal, 43416, 43526
-recovered pasa_asmbl_41859.p1, internal, 43714, 43865
Valid prediction for GlimmerHMM_glimmerT_11000-T1
Valid prediction for snap_scaffold_4-snap.3159-T1
Valid prediction for GlimmerHMM_glimmerT_10996-T1
Valid prediction for GeneMark_model.17840_t
Valid prediction for GlimmerHMM_glimmerT_10981-T1
Valid prediction for GeneMark_model.17852_t
Couldn't classify 184587, 184829
Sorry, prediction pasa_asmbl_41850.p1 fails validation.
(GTG)	 CA	184587-184829	GT	AGG
(GTG)	 AG	185289-185573	GT	AGG
(TTC)	 AG	186117-186207	GT	AGG
(GCG)	 AG	187338-187483	GT	CGG
(AGT)	 AG	187646-187831	GT	AGG
(GAC)	 AG	188366-188518	GT	AGG
(CCC)	 AG	190431-190575	GT	GGG
(GCT)	 AG	191864-192091	GT	AGG
(GTG)	 AG	192519-192674	GT	AGG
(ACT)	 AG	192804-193021	GT	CGG
(CCG)	 AG	193222-193488	GT	TGG
(GCC)	 AG	193894-194289	AT	AGA
-recovered pasa_asmbl_41850.p1, terminal, 186117, 186207
-recovered pasa_asmbl_41850.p1, terminal, 193894, 194289
-recovered pasa_asmbl_41850.p1, internal, 185289, 185573
-recovered pasa_asmbl_41850.p1, internal, 186117, 186207
-recovered pasa_asmbl_41850.p1, internal, 187338, 187483
-recovered pasa_asmbl_41850.p1, internal, 187646, 187831
-recovered pasa_asmbl_41850.p1, internal, 188366, 188518
-recovered pasa_asmbl_41850.p1, internal, 190431, 190575
-recovered pasa_asmbl_41850.p1, internal, 191864, 192091
-recovered pasa_asmbl_41850.p1, internal, 192519, 192674
-recovered pasa_asmbl_41850.p1, internal, 192804, 193021
-recovered pasa_asmbl_41850.p1, internal, 193222, 193488
Couldn't classify 53110, 53300
Couldn't classify 54998, 55008
Sorry, prediction pasa_asmbl_41857.p1 fails validation.
(GCC)	 TG	53110-53300	GT	AGG
(GAC)	 AG	53508-53634	GT	AGG
(CTG)	 AG	54634-54844	GT	GGG
(GTG)	 AG	54998-55008	CG	GGC
-recovered pasa_asmbl_41857.p1, internal, 53508, 53634
-recovered pasa_asmbl_41857.p1, internal, 54634, 54844
Couldn't classify 58590, 59684
Sorry, prediction pasa_asmbl_41855.p1 fails validation.
(GCC)	 TG	58590-59684	AG	AGA
Valid prediction for snap_scaffold_4-snap.3138-T1
Valid prediction for GeneMark_model.17849_t
Valid prediction for CodingQuarry_transcript_49160-T1
Couldn't classify 64970, 65611
Sorry, prediction pasa_asmbl_41853.p1 fails validation.
(AAG)	 GA	64970-65611	GT	GAG
Valid prediction for GlimmerHMM_glimmerT_11002-T1
Valid prediction for GeneMark_model.17834_t
Valid prediction for GeneMark_model.17861_t
Valid prediction for GeneMark_model.17866_t
Valid prediction for snap_scaffold_4-snap.3149-T1
Valid prediction for GeneMark_model.17829_t
Valid prediction for snap_scaffold_4-snap.3145-T1
Valid prediction for GlimmerHMM_glimmerT_10992-T1
Valid prediction for snap_scaffold_4-snap.3152-T1
Valid prediction for Augustus_model.g7261.t1
Valid prediction for GeneMark_model.17821_t
Valid prediction for GlimmerHMM_glimmerT_10995-T1
Valid prediction for GeneMark_model.17860_t
Valid prediction for snap_scaffold_4-snap.3157-T1
Valid prediction for GeneMark_model.17831_t
Valid prediction for GeneMark_model.17872_t
Valid prediction for GeneMark_model.17850_t
Valid prediction for GeneMark_model.17819_t
Valid prediction for GlimmerHMM_glimmerT_10983-T1
Couldn't classify 55156, 55212
Couldn't classify 55944, 56050
Sorry, prediction pasa_asmbl_42277.p2 fails validation.
(TCC)	 AC	55156-55212	GT	AGG
(TGC)	 AG	55361-55556	GT	TGG
(GTG)	 AG	55944-56050	GA	AGG
-recovered pasa_asmbl_42277.p2, internal, 55361, 55556
Valid prediction for snap_scaffold_4-snap.3147-T1
Valid prediction for GeneMark_model.17845_t
Valid prediction for GlimmerHMM_glimmerT_10988-T1
Valid prediction for pasa_asmbl_41861.p1
Valid prediction for GlimmerHMM_glimmerT_10986-T1
Valid prediction for snap_scaffold_4-snap.3134-T1
Valid prediction for snap_scaffold_4-snap.3168-T1
Valid prediction for snap_scaffold_4-snap.3165-T1
Valid prediction for Augustus_model.g7263.t1
Valid prediction for snap_scaffold_4-snap.3153-T1
Couldn't classify 56904, 56996
Couldn't classify 58191, 58535
Sorry, prediction pasa_asmbl_41856.p1 fails validation.
(TTC)	 AG	56904-56996	GT	GGG
(ATC)	 AG	57379-57509	GT	AAG
(GTG)	 AG	57794-57926	GT	AGG
(TGC)	 AG	58191-58535	AG	GCA
-recovered pasa_asmbl_41856.p1, internal, 56904, 56996
-recovered pasa_asmbl_41856.p1, internal, 57379, 57509
-recovered pasa_asmbl_41856.p1, internal, 57794, 57926
Valid prediction for GeneMark_model.17862_t
Valid prediction for GlimmerHMM_glimmerT_10993-T1
Valid prediction for GeneMark_model.17864_t
Valid prediction for GlimmerHMM_glimmerT_10997-T1
Valid prediction for CodingQuarry_transcript_49161-T1
Valid prediction for snap_scaffold_4-snap.3161-T1
Valid prediction for pasa_asmbl_41865.p1
Valid prediction for GlimmerHMM_glimmerT_10979-T1
Valid prediction for GeneMark_model.17847_t
Valid prediction for snap_scaffold_4-snap.3167-T1
Valid prediction for GeneMark_model.17824_t
Couldn't classify 21197, 22054
Sorry, prediction pasa_asmbl_41867.p1 fails validation.
(TCC)	 TC	21197-22054	AA	GAA
Valid prediction for GeneMark_model.17843_t
Valid prediction for Augustus_model.g7264.t1
Valid prediction for GlimmerHMM_glimmerT_10989-T1
Valid prediction for Augustus_model.g7269.t1
Valid prediction for snap_scaffold_4-snap.3140-T1
Valid prediction for snap_scaffold_4-snap.3158-T1
Valid prediction for GeneMark_model.17836_t
Valid prediction for GlimmerHMM_glimmerT_10994-T1
Valid prediction for snap_scaffold_4-snap.3162-T1
Couldn't classify 51638, 51679
Couldn't classify 52630, 52755
Sorry, prediction pasa_asmbl_41858.p1 fails validation.
(TGG)	 CG	51638-51679	GT	AGG
(AGC)	 AG	51770-51941	GT	TGG
(GGC)	 AG	52159-52322	GT	AGG
(CCC)	 AG	52630-52755	AT	GGA
-recovered pasa_asmbl_41858.p1, internal, 51770, 51941
-recovered pasa_asmbl_41858.p1, internal, 52159, 52322
Valid prediction for Augustus_model.g7272.t1
Valid prediction for GlimmerHMM_glimmerT_10982-T1
Valid prediction for Augustus_model.g7267.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 111641, rend_intergenic: 111638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20843, rend_intergenic: 7175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31599, rend_intergenic: 31290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44584, rend_intergenic: 31982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51802, rend_intergenic: 44936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61548, rend_intergenic: 56349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69359, rend_intergenic: 68445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70616, rend_intergenic: 70463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74913, rend_intergenic: 71247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78261, rend_intergenic: 76662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88938, rend_intergenic: 85666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95208, rend_intergenic: 90308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160469, rend_intergenic: 144617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199891
-exon list size: 744


building trellis

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73.6    
73.7    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 28 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 111641, rend_intergenic: 111638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20843, rend_intergenic: 7175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31599, rend_intergenic: 31290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44584, rend_intergenic: 31982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51802, rend_intergenic: 44936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61548, rend_intergenic: 56349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69359, rend_intergenic: 68445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70616, rend_intergenic: 70463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74913, rend_intergenic: 71247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78261, rend_intergenic: 76662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88938, rend_intergenic: 85666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95208, rend_intergenic: 90308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160469, rend_intergenic: 144617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support