-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_464009-727166

-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_18-snap.93-T1
Valid prediction for GeneMark_model.73633_t
Valid prediction for snap_scaffold_18-snap.83-T1
Valid prediction for GlimmerHMM_glimmerT_42621-T1
Valid prediction for CodingQuarry_transcript_23600-T1
Valid prediction for GeneMark_model.73636_t
Valid prediction for snap_scaffold_18-snap.102-T1
Couldn't classify 183018, 183189
Sorry, prediction pasa_asmbl_20343.p1 fails validation.
(AAA)	 TC	183018-183189	GT	GGG
(GGT)	 AG	183364-183464	GT	TGG
(CAC)	 AG	183798-183897	GT	GGG
(AGG)	 AG	185095-185192	GT	AGG
(ATT)	 AG	185701-185817	GT	AGG
(CAC)	 AG	186175-186261	GT	AGG
(GAC)	 AG	186402-186656	TA	AAT
-recovered pasa_asmbl_20343.p1, terminal, 186402, 186656
-recovered pasa_asmbl_20343.p1, internal, 183364, 183464
-recovered pasa_asmbl_20343.p1, internal, 183798, 183897
-recovered pasa_asmbl_20343.p1, internal, 185095, 185192
-recovered pasa_asmbl_20343.p1, internal, 185701, 185817
-recovered pasa_asmbl_20343.p1, internal, 186175, 186261
Valid prediction for pasa_asmbl_20331.p1
Valid prediction for Augustus_model.g28501.t1
Valid prediction for GeneMark_model.73620_t
Valid prediction for GlimmerHMM_glimmerT_42620-T1
Valid prediction for snap_scaffold_18-snap.108-T1
Valid prediction for GeneMark_model.73655_t
Valid prediction for GlimmerHMM_glimmerT_42614-T1
Valid prediction for pasa_asmbl_20327.p1
Valid prediction for CodingQuarry_transcript_23596-T1
Valid prediction for Augustus_model.g28520.t1
Valid prediction for GeneMark_model.73638_t
Valid prediction for snap_scaffold_18-snap.85-T1
Valid prediction for GeneMark_model.73621_t
Valid prediction for pasa_asmbl_20326.p1
Valid prediction for snap_scaffold_18-snap.101-T1
Valid prediction for HiQ_model.g28513.t1
Valid prediction for GeneMark_model.73611_t
Valid prediction for GlimmerHMM_glimmerT_42609-T1
Valid prediction for Augustus_model.g28518.t1
Valid prediction for snap_scaffold_18-snap.72-T1
Valid prediction for CodingQuarry_transcript_23595-T1
Valid prediction for snap_scaffold_18-snap.123-T1
Valid prediction for snap_scaffold_18-snap.92-T1
Valid prediction for GeneMark_model.73627_t
Valid prediction for GlimmerHMM_glimmerT_42611-T1
Valid prediction for GeneMark_model.73664_t
Valid prediction for snap_scaffold_18-snap.106-T1
Valid prediction for snap_scaffold_18-snap.115-T1
Valid prediction for snap_scaffold_18-snap.94-T1
Valid prediction for GeneMark_model.73617_t
Valid prediction for GeneMark_model.73657_t
Valid prediction for GeneMark_model.73639_t
Valid prediction for snap_scaffold_18-snap.104-T1
Valid prediction for GlimmerHMM_glimmerT_42603-T1
Valid prediction for GlimmerHMM_glimmerT_42618-T1
Valid prediction for snap_scaffold_18-snap.86-T1
Valid prediction for snap_scaffold_18-snap.111-T1
Valid prediction for snap_scaffold_18-snap.100-T1
Valid prediction for Augustus_model.g28494.t1
Valid prediction for GeneMark_model.73623_t
Valid prediction for snap_scaffold_18-snap.113-T1
Valid prediction for Augustus_model.g28515.t1
Valid prediction for Augustus_model.g28509.t1
Valid prediction for snap_scaffold_18-snap.99-T1
Valid prediction for Augustus_model.g28508.t1
Valid prediction for Augustus_model.g28510.t1
Valid prediction for GeneMark_model.73629_t
Valid prediction for Augustus_model.g28512.t1
Valid prediction for GeneMark_model.73628_t
Valid prediction for Augustus_model.g28500.t1
Valid prediction for snap_scaffold_18-snap.119-T1
Valid prediction for pasa_asmbl_20339.p1
Valid prediction for snap_scaffold_18-snap.96-T1
Valid prediction for Augustus_model.g28516.t1
Valid prediction for GeneMark_model.73634_t
Valid prediction for Augustus_model.g28517.t1
Valid prediction for GlimmerHMM_glimmerT_42619-T1
Valid prediction for GlimmerHMM_glimmerT_42616-T1
Valid prediction for snap_scaffold_18-snap.103-T1
Valid prediction for GlimmerHMM_glimmerT_42617-T1
Valid prediction for GlimmerHMM_glimmerT_42622-T1
Couldn't classify 168492, 168557
Sorry, prediction pasa_asmbl_20336.p1 fails validation.
(TTC)	 TC	168492-168557	GT	GGG
(GAC)	 AG	168845-168952	GT	AGG
(GTG)	 AG	169093-169156	GT	AGG
(GAA)	 AG	169603-169657	GT	GGG
(GTA)	 AG	169737-169825	GT	AAG
(GGA)	 AG	169987-170126	CC	AAC
add_exon() Sorry, pasa_asmbl_20336.p1 169093-169156-terminal-3 is invalid.
-recovered pasa_asmbl_20336.p1, terminal, 169093, 169156
-recovered pasa_asmbl_20336.p1, terminal, 169987, 170126
-recovered pasa_asmbl_20336.p1, internal, 168845, 168952
-recovered pasa_asmbl_20336.p1, internal, 169093, 169156
-recovered pasa_asmbl_20336.p1, internal, 169603, 169657
-recovered pasa_asmbl_20336.p1, internal, 169737, 169825
Valid prediction for GlimmerHMM_glimmerT_42608-T1
Valid prediction for GeneMark_model.73613_t
Valid prediction for GeneMark_model.73649_t
Valid prediction for GeneMark_model.73658_t
Valid prediction for CodingQuarry_transcript_23598-T1
Valid prediction for GeneMark_model.73609_t
Valid prediction for Augustus_model.g28498.t1
Valid prediction for GeneMark_model.73616_t
Valid prediction for GeneMark_model.73661_t
Valid prediction for HiQ_model.g28504.t1
Valid prediction for GeneMark_model.73631_t
Valid prediction for Augustus_model.g28521.t1
Valid prediction for GeneMark_model.73645_t
Valid prediction for HiQ_model.g28507.t1
Valid prediction for GlimmerHMM_glimmerT_42606-T1
Valid prediction for snap_scaffold_18-snap.110-T1
Valid prediction for snap_scaffold_18-snap.98-T1
Valid prediction for snap_scaffold_18-snap.90-T1
Valid prediction for HiQ_model.g28502.t1
Valid prediction for HiQ_model.g28505.t1
Valid prediction for GeneMark_model.73651_t
Valid prediction for snap_scaffold_18-snap.74-T1
Valid prediction for snap_scaffold_18-snap.91-T1
Valid prediction for snap_scaffold_18-snap.118-T1
Valid prediction for snap_scaffold_18-snap.73-T1
Valid prediction for Augustus_model.g28493.t1
Valid prediction for GeneMark_model.73653_t
Valid prediction for GeneMark_model.73610_t
Valid prediction for GlimmerHMM_glimmerT_42602-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 GlimmerHMM_glimmerT_42612-T1
Valid prediction for snap_scaffold_18-snap.81-T1
Valid prediction for snap_scaffold_18-snap.88-T1
Valid prediction for GeneMark_model.73635_t
Valid prediction for snap_scaffold_18-snap.105-T1
Valid prediction for GeneMark_model.73662_t
Valid prediction for snap_scaffold_18-snap.121-T1
Valid prediction for GeneMark_model.73640_t
Valid prediction for GeneMark_model.73614_t
Valid prediction for GeneMark_model.73642_t
Valid prediction for GeneMark_model.73647_t
Valid prediction for snap_scaffold_18-snap.107-T1
Couldn't classify 217806, 217842
Couldn't classify 219002, 219042
Sorry, prediction pasa_asmbl_19624.p1 fails validation.
(GAG)	 AC	217806-217842	GT	AGG
(TTC)	 AG	217917-218078	GT	AAG
(ACC)	 AG	218457-218654	GT	TGG
(CTC)	 AG	219002-219042	TA	CGT
-recovered pasa_asmbl_19624.p1, internal, 217917, 218078
-recovered pasa_asmbl_19624.p1, internal, 218457, 218654
Valid prediction for GeneMark_model.73652_t
Valid prediction for Augustus_model.g28497.t1
Valid prediction for snap_scaffold_18-snap.71-T1
Valid prediction for GeneMark_model.73615_t
Valid prediction for GlimmerHMM_glimmerT_42601-T1
Valid prediction for GeneMark_model.73643_t
Valid prediction for GlimmerHMM_glimmerT_42613-T1
Valid prediction for Augustus_model.g28514.t1
Valid prediction for GlimmerHMM_glimmerT_42607-T1
Valid prediction for GeneMark_model.73644_t
Valid prediction for Augustus_model.g28503.t1
Valid prediction for GeneMark_model.73612_t
Valid prediction for Augustus_model.g28496.t1
Valid prediction for snap_scaffold_18-snap.84-T1
Valid prediction for GeneMark_model.73618_t
Valid prediction for GeneMark_model.73660_t
Valid prediction for snap_scaffold_18-snap.80-T1
Valid prediction for snap_scaffold_18-snap.78-T1
Valid prediction for pasa_asmbl_19625.p1
Valid prediction for snap_scaffold_18-snap.117-T1
Valid prediction for GlimmerHMM_glimmerT_42604-T1
Valid prediction for snap_scaffold_18-snap.122-T1
Valid prediction for snap_scaffold_18-snap.89-T1
Valid prediction for snap_scaffold_18-snap.125-T1
Valid prediction for Augustus_model.g28495.t1
Valid prediction for GlimmerHMM_glimmerT_42615-T1
Valid prediction for GeneMark_model.73637_t
Valid prediction for snap_scaffold_18-snap.87-T1
Valid prediction for snap_scaffold_18-snap.79-T1
Valid prediction for GeneMark_model.73650_t
Valid prediction for snap_scaffold_18-snap.75-T1
Valid prediction for GeneMark_model.73632_t
Valid prediction for Augustus_model.g28519.t1
Valid prediction for Augustus_model.g28492.t1
Valid prediction for GeneMark_model.73622_t
Valid prediction for Augustus_model.g28499.t1
Valid prediction for snap_scaffold_18-snap.82-T1
Valid prediction for GeneMark_model.73626_t
Valid prediction for GeneMark_model.73641_t
Valid prediction for GeneMark_model.73656_t
Valid prediction for snap_scaffold_18-snap.120-T1
Valid prediction for GeneMark_model.73659_t
Valid prediction for GlimmerHMM_glimmerT_42610-T1
Valid prediction for GlimmerHMM_glimmerT_42605-T1
Valid prediction for snap_scaffold_18-snap.114-T1
Valid prediction for snap_scaffold_18-snap.109-T1
Valid prediction for snap_scaffold_18-snap.112-T1
Valid prediction for snap_scaffold_18-snap.95-T1
Valid prediction for GeneMark_model.73663_t
Valid prediction for snap_scaffold_18-snap.116-T1
Valid prediction for HiQ_model.g28506.t1
Valid prediction for GeneMark_model.73648_t
Valid prediction for Augustus_model.g28511.t1
Valid prediction for CodingQuarry_transcript_23597-T1
Valid prediction for snap_scaffold_18-snap.77-T1
Valid prediction for snap_scaffold_18-snap.97-T1
Valid prediction for GeneMark_model.73625_t
Valid prediction for snap_scaffold_18-snap.76-T1
Valid prediction for GeneMark_model.73654_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31103, rend_intergenic: 26114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177235, rend_intergenic: 174250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184577, rend_intergenic: 178208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186656, rend_intergenic: 185697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196860, rend_intergenic: 192557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199272, rend_intergenic: 197095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212145, rend_intergenic: 205090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224577, rend_intergenic: 215602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226079, rend_intergenic: 225153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231619, rend_intergenic: 227857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253394, rend_intergenic: 238862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254988, rend_intergenic: 253866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 263158
-exon list size: 716


building trellis

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83.6    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.5    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 31103, rend_intergenic: 26114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177235, rend_intergenic: 174250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184577, rend_intergenic: 178208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186656, rend_intergenic: 185697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196860, rend_intergenic: 192557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199272, rend_intergenic: 197095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212145, rend_intergenic: 205090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224577, rend_intergenic: 215602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226079, rend_intergenic: 225153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231619, rend_intergenic: 227857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253394, rend_intergenic: 238862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254988, rend_intergenic: 253866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support