-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_2340920-2613627

-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_51867-T1
Valid prediction for snap_scaffold_23-snap.466-T1
Valid prediction for snap_scaffold_23-snap.454-T1
Valid prediction for pasa_asmbl_30700.p1
Valid prediction for GeneMark_model.90091_t
Couldn't classify 32594, 36562
Sorry, prediction pasa_asmbl_30699.p1 fails validation.
(GTT)	 AT	32594-36562	GT	GAG
Valid prediction for GlimmerHMM_glimmerT_51857-T1
Valid prediction for CodingQuarry_transcript_35520-T1
Valid prediction for pasa_asmbl_30704.p1
Valid prediction for snap_scaffold_23-snap.453-T1
Valid prediction for GlimmerHMM_glimmerT_51855-T1
Valid prediction for Augustus_model.g34850.t1
Valid prediction for snap_scaffold_23-snap.445-T1
Valid prediction for GlimmerHMM_glimmerT_51865-T1
Valid prediction for GeneMark_model.90112_t
Valid prediction for snap_scaffold_23-snap.473-T1
Valid prediction for snap_scaffold_23-snap.446-T1
Valid prediction for HiQ_model.g34844.t1
Valid prediction for snap_scaffold_23-snap.444-T1
Valid prediction for snap_scaffold_23-snap.460-T1
Valid prediction for GeneMark_model.90085_t
Valid prediction for snap_scaffold_23-snap.452-T1
Valid prediction for GeneMark_model.90097_t
Valid prediction for snap_scaffold_23-snap.448-T1
Valid prediction for CodingQuarry_transcript_35517-T1
Valid prediction for Augustus_model.g34854.t1
Valid prediction for GeneMark_model.90126_t
Valid prediction for snap_scaffold_23-snap.469-T1
Valid prediction for Augustus_model.g34848.t1
Valid prediction for snap_scaffold_23-snap.476-T1
Valid prediction for GeneMark_model.90094_t
Valid prediction for HiQ_model.g34849.t1
Valid prediction for GlimmerHMM_glimmerT_51872-T1
Valid prediction for snap_scaffold_23-snap.478-T1
Valid prediction for GlimmerHMM_glimmerT_51856-T1
Valid prediction for Augustus_model.g34847.t1
Valid prediction for GeneMark_model.90099_t
Valid prediction for snap_scaffold_23-snap.462-T1
Valid prediction for GeneMark_model.90113_t
Valid prediction for GeneMark_model.90110_t
Valid prediction for CodingQuarry_transcript_35518-T1
Valid prediction for Augustus_model.g34853.t1
Valid prediction for GlimmerHMM_glimmerT_51862-T1
Valid prediction for GeneMark_model.90087_t
Valid prediction for GeneMark_model.90116_t
Valid prediction for snap_scaffold_23-snap.459-T1
Valid prediction for GeneMark_model.90118_t
Valid prediction for GlimmerHMM_glimmerT_51850-T1
Valid prediction for GlimmerHMM_glimmerT_51851-T1
Valid prediction for GeneMark_model.90102_t
Couldn't classify 30374, 32311
Sorry, prediction pasa_asmbl_30698.p1 fails validation.
(AAA)	 CG	30374-32311	CC	CCC
Valid prediction for snap_scaffold_23-snap.441-T1
Valid prediction for snap_scaffold_23-snap.461-T1
Valid prediction for GlimmerHMM_glimmerT_51854-T1
Valid prediction for snap_scaffold_23-snap.468-T1
Valid prediction for GeneMark_model.90103_t
Valid prediction for snap_scaffold_23-snap.442-T1
Valid prediction for GeneMark_model.90089_t
Valid prediction for GeneMark_model.90101_t
Valid prediction for Augustus_model.g34841.t1
Valid prediction for pasa_asmbl_30702.p1
Valid prediction for HiQ_model.g34857.t1
Valid prediction for Augustus_model.g34843.t1
Valid prediction for snap_scaffold_23-snap.457-T1
Valid prediction for pasa_asmbl_30709.p1
Valid prediction for GlimmerHMM_glimmerT_51863-T1
Valid prediction for GeneMark_model.90119_t
Valid prediction for GlimmerHMM_glimmerT_51873-T1
Couldn't classify 29167, 29172
Couldn't classify 29926, 30087
Sorry, prediction pasa_asmbl_30697.p1 fails validation.
(AAT)	 CT	29167-29172	GT	AGG
(GCC)	 AG	29273-29350	GT	AGG
(GTC)	 AG	29641-29757	GT	AGG
(GAA)	 AG	29926-30087	GG	GGG
-recovered pasa_asmbl_30697.p1, internal, 29273, 29350
-recovered pasa_asmbl_30697.p1, internal, 29641, 29757
Valid prediction for GeneMark_model.90106_t
Valid prediction for GeneMark_model.90123_t
Valid prediction for GlimmerHMM_glimmerT_51860-T1
Valid prediction for snap_scaffold_23-snap.470-T1
Valid prediction for GlimmerHMM_glimmerT_51858-T1
Valid prediction for GlimmerHMM_glimmerT_51844-T1
Valid prediction for GeneMark_model.90121_t
Valid prediction for GlimmerHMM_glimmerT_51864-T1
Valid prediction for snap_scaffold_23-snap.465-T1
Valid prediction for snap_scaffold_23-snap.477-T1
Valid prediction for GeneMark_model.90093_t
Valid prediction for snap_scaffold_23-snap.467-T1
Valid prediction for snap_scaffold_23-snap.443-T1
Valid prediction for CodingQuarry_transcript_35519-T1
Valid prediction for Augustus_model.g34852.t1
Valid prediction for Augustus_model.g34856.t1
Valid prediction for snap_scaffold_23-snap.456-T1
Valid prediction for GlimmerHMM_glimmerT_51861-T1
Valid prediction for Augustus_model.g34851.t1
Valid prediction for GlimmerHMM_glimmerT_51871-T1
Valid prediction for snap_scaffold_23-snap.463-T1
Valid prediction for GeneMark_model.90108_t
Valid prediction for snap_scaffold_23-snap.447-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 Augustus_model.g34858.t1
Valid prediction for GlimmerHMM_glimmerT_51877-T1
Valid prediction for CodingQuarry_transcript_35524-T1
Valid prediction for snap_scaffold_23-snap.484-T1
Valid prediction for GlimmerHMM_glimmerT_51859-T1
Couldn't classify 20152, 20297
Sorry, prediction pasa_asmbl_31970.p1 fails validation.
(CCA)	 TC	20152-20297	GT	TCG
(GTA)	 AG	20474-20756	TG	GAT
-recovered pasa_asmbl_31970.p1, terminal, 20474, 20756
Valid prediction for GeneMark_model.90114_t
Valid prediction for GlimmerHMM_glimmerT_51852-T1
Valid prediction for GlimmerHMM_glimmerT_51849-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.451-T1
Valid prediction for CodingQuarry_transcript_35523-T1
Valid prediction for snap_scaffold_23-snap.455-T1
Valid prediction for Augustus_model.g34846.t1
Valid prediction for GeneMark_model.90090_t
Valid prediction for snap_scaffold_23-snap.485-T1
Valid prediction for snap_scaffold_23-snap.440-T1
Valid prediction for GlimmerHMM_glimmerT_51876-T1
Valid prediction for GlimmerHMM_glimmerT_51853-T1
Valid prediction for GlimmerHMM_glimmerT_51870-T1
Valid prediction for GeneMark_model.90128_t
Valid prediction for GlimmerHMM_glimmerT_51846-T1
Valid prediction for snap_scaffold_23-snap.483-T1
Couldn't classify 49712, 49792
Sorry, prediction pasa_asmbl_31458.p1 fails validation.
(ATG)	 AG	46760-46843	GT	CGG
(CCG)	 AG	48053-48151	GT	CAG
(GTT)	 AG	48644-48706	GT	AGG
(GGT)	 AG	48867-48994	GT	TGG
(GTG)	 AG	49223-49337	GT	TGG
(GTG)	 AG	49712-49792	GT	TGG
-recovered pasa_asmbl_31458.p1, initial, 46760, 46843
-recovered pasa_asmbl_31458.p1, internal, 46760, 46843
-recovered pasa_asmbl_31458.p1, internal, 48053, 48151
-recovered pasa_asmbl_31458.p1, internal, 48644, 48706
-recovered pasa_asmbl_31458.p1, internal, 48867, 48994
-recovered pasa_asmbl_31458.p1, internal, 49223, 49337
-recovered pasa_asmbl_31458.p1, internal, 49712, 49792
Valid prediction for GeneMark_model.90098_t
Valid prediction for snap_scaffold_23-snap.458-T1
Valid prediction for GlimmerHMM_glimmerT_51866-T1
Valid prediction for snap_scaffold_23-snap.449-T1
Valid prediction for CodingQuarry_transcript_35521-T1
Valid prediction for GlimmerHMM_glimmerT_51875-T1
Valid prediction for pasa_asmbl_31461.p1
Valid prediction for snap_scaffold_23-snap.482-T1
Valid prediction for GeneMark_model.90124_t
Valid prediction for snap_scaffold_23-snap.481-T1
Valid prediction for snap_scaffold_23-snap.479-T1
Valid prediction for GeneMark_model.90111_t
Valid prediction for CodingQuarry_transcript_35522-T1
Valid prediction for GlimmerHMM_glimmerT_51874-T1
Valid prediction for GeneMark_model.90092_t
Valid prediction for GlimmerHMM_glimmerT_51868-T1
Valid prediction for GlimmerHMM_glimmerT_51843-T1
Valid prediction for GeneMark_model.90117_t
Valid prediction for GeneMark_model.90125_t
Valid prediction for GeneMark_model.90122_t
Valid prediction for Augustus_model.g34845.t1
Valid prediction for GeneMark_model.90100_t
Couldn't classify 17251, 17440
Sorry, prediction pasa_asmbl_31966.p1 fails validation.
(ATG)	 CA	16212-16346	GT	CAG
(GAA)	 AG	16445-16576	GT	AGG
(GTG)	 AG	16663-16750	GT	GGG
(GAC)	 AG	16855-17074	GT	TCG
(GTA)	 AG	17251-17440	AT	TAA
-recovered pasa_asmbl_31966.p1, initial, 16212, 16346
-recovered pasa_asmbl_31966.p1, internal, 16445, 16576
-recovered pasa_asmbl_31966.p1, internal, 16663, 16750
-recovered pasa_asmbl_31966.p1, internal, 16855, 17074
Couldn't classify 50042, 50131
Sorry, prediction pasa_asmbl_31457.p1 fails validation.
(TCC)	 AC	50042-50131	GT	AGG
(GTC)	 AG	50630-50701	GT	AGG
(ACT)	 AG	50930-51042	GT	TGG
(GAT)	 AG	51285-51382	GT	GGG
(GTG)	 AG	51642-51805	GT	AGG
(AGA)	 AG	52030-52275	CC	GAC
-recovered pasa_asmbl_31457.p1, terminal, 52030, 52275
-recovered pasa_asmbl_31457.p1, internal, 50630, 50701
-recovered pasa_asmbl_31457.p1, internal, 50930, 51042
-recovered pasa_asmbl_31457.p1, internal, 51285, 51382
-recovered pasa_asmbl_31457.p1, internal, 51642, 51805
Valid prediction for Augustus_model.g34842.t1
Valid prediction for snap_scaffold_23-snap.464-T1
Valid prediction for GeneMark_model.90115_t
Valid prediction for GeneMark_model.90088_t
Couldn't classify 12539, 12550
Couldn't classify 13465, 13717
Sorry, prediction pasa_asmbl_31466.p1 fails validation.
(CCG)	 AG	12539-12550	GT	CAG
(GAA)	 AG	12651-12782	GT	AGG
(GTA)	 AG	12868-12955	GT	AGG
(GCC)	 AG	13069-13288	GT	TCG
(GTA)	 AG	13465-13717	AA	GGA
-recovered pasa_asmbl_31466.p1, terminal, 12868, 12955
-recovered pasa_asmbl_31466.p1, internal, 12539, 12550
-recovered pasa_asmbl_31466.p1, internal, 12651, 12782
-recovered pasa_asmbl_31466.p1, internal, 12868, 12955
-recovered pasa_asmbl_31466.p1, internal, 13069, 13288
Valid prediction for snap_scaffold_23-snap.474-T1
Valid prediction for GlimmerHMM_glimmerT_51869-T1
Valid prediction for GeneMark_model.90086_t
Valid prediction for GeneMark_model.90096_t
Valid prediction for snap_scaffold_23-snap.450-T1
Valid prediction for GlimmerHMM_glimmerT_51845-T1
Valid prediction for GlimmerHMM_glimmerT_51847-T1
Valid prediction for GlimmerHMM_glimmerT_51848-T1
Valid prediction for GeneMark_model.90127_t
Valid prediction for GeneMark_model.90095_t
Valid prediction for GeneMark_model.90107_t
Valid prediction for GeneMark_model.90104_t
Valid prediction for HiQ_model.g34855.t1
Valid prediction for snap_scaffold_23-snap.475-T1
Couldn't classify 7353, 7502
Sorry, prediction pasa_asmbl_31467.p1 fails validation.
(TTC)	 TG	7353-7502	GT	ACG
(CCT)	 AG	7605-7882	GT	AGG
(GCC)	 AG	7983-8115	GT	AGG
(ATG)	 AG	8234-8363	GT	AGG
(GCT)	 AG	8702-8835	GT	AGG
(GTT)	 AG	9028-9152	GT	AAG
(GTA)	 AG	9312-9525	GC	GAG
-recovered pasa_asmbl_31467.p1, initial, 8234, 8363
add_exon() Sorry, pasa_asmbl_31467.p1 8234-8363-terminal-3 is invalid.
-recovered pasa_asmbl_31467.p1, terminal, 8234, 8363
-recovered pasa_asmbl_31467.p1, terminal, 9312, 9525
-recovered pasa_asmbl_31467.p1, internal, 7605, 7882
-recovered pasa_asmbl_31467.p1, internal, 7983, 8115
-recovered pasa_asmbl_31467.p1, internal, 8234, 8363
-recovered pasa_asmbl_31467.p1, internal, 8702, 8835
-recovered pasa_asmbl_31467.p1, internal, 9028, 9152
-recovered pasa_asmbl_31467.p1, internal, 9312, 9525
Valid prediction for Augustus_model.g34860.t1
Valid prediction for GeneMark_model.90109_t
Valid prediction for GeneMark_model.90120_t
Valid prediction for snap_scaffold_23-snap.472-T1
Valid prediction for snap_scaffold_23-snap.471-T1
Valid prediction for snap_scaffold_23-snap.480-T1
Valid prediction for Augustus_model.g34859.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 48068, rend_intergenic: 42931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84232, rend_intergenic: 83357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156414, rend_intergenic: 153436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203547, rend_intergenic: 200829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 272708
-exon list size: 571


building trellis

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91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 48068, rend_intergenic: 42931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84232, rend_intergenic: 83357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156414, rend_intergenic: 153436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203547, rend_intergenic: 200829  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

-building DP trellis

-building trellis in range 1 - 12997
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11781
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11658
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support