-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_12644181-12889894

-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 GeneMark_model.22113_t
Valid prediction for Augustus_model.g8746.t1
Valid prediction for snap_scaffold_5-snap.2370-T1
Valid prediction for GlimmerHMM_glimmerT_13120-T1
Valid prediction for pasa_asmbl_44502.p1
Valid prediction for GeneMark_model.22122_t
Valid prediction for CodingQuarry_transcript_52160-T1
Valid prediction for GeneMark_model.22153_t
Valid prediction for snap_scaffold_5-snap.2392-T1
Valid prediction for GeneMark_model.22150_t
Valid prediction for GlimmerHMM_glimmerT_13127-T1
Valid prediction for snap_scaffold_5-snap.2384-T1
Valid prediction for snap_scaffold_5-snap.2367-T1
Valid prediction for Augustus_model.g8757.t1
Couldn't classify 173194, 173997
Sorry, prediction pasa_asmbl_44494.p1 fails validation.
(ATG)	 TT	171276-171302	GT	AGG
(AGA)	 AG	171884-171905	GT	AGG
(TGC)	 AG	172717-172796	GT	AGG
(AAC)	 AG	173194-173997	CC	CCC
-recovered pasa_asmbl_44494.p1, initial, 171276, 171302
-recovered pasa_asmbl_44494.p1, internal, 171884, 171905
-recovered pasa_asmbl_44494.p1, internal, 172717, 172796
Valid prediction for Augustus_model.g8748.t1
Valid prediction for snap_scaffold_5-snap.2360-T1
Valid prediction for GeneMark_model.22117_t
Valid prediction for CodingQuarry_transcript_52164-T1
Valid prediction for snap_scaffold_5-snap.2372-T1
Valid prediction for GlimmerHMM_glimmerT_13123-T1
Valid prediction for snap_scaffold_5-snap.2398-T1
Valid prediction for GlimmerHMM_glimmerT_13111-T1
Valid prediction for GlimmerHMM_glimmerT_13131-T1
Valid prediction for GeneMark_model.22143_t
Valid prediction for GlimmerHMM_glimmerT_13110-T1
Valid prediction for snap_scaffold_5-snap.2365-T1
Valid prediction for HiQ_model.g8758.t1
Valid prediction for Augustus_model.g8760.t1
Valid prediction for snap_scaffold_5-snap.2377-T1
Valid prediction for GeneMark_model.22155_t
Valid prediction for GlimmerHMM_glimmerT_13130-T1
Valid prediction for snap_scaffold_5-snap.2390-T1
Valid prediction for GlimmerHMM_glimmerT_13106-T1
Valid prediction for GlimmerHMM_glimmerT_13134-T1
Valid prediction for pasa_asmbl_44496.p1
Valid prediction for CodingQuarry_transcript_52165-T1
Valid prediction for GeneMark_model.22142_t
Valid prediction for HiQ_model.g8744.t1
Valid prediction for snap_scaffold_5-snap.2399-T1
Valid prediction for GeneMark_model.22118_t
Valid prediction for snap_scaffold_5-snap.2393-T1
Valid prediction for GeneMark_model.22130_t
Valid prediction for snap_scaffold_5-snap.2374-T1
Valid prediction for snap_scaffold_5-snap.2358-T1
Valid prediction for GeneMark_model.22129_t
Valid prediction for snap_scaffold_5-snap.2375-T1
Valid prediction for HiQ_model.g8761.t1
Valid prediction for snap_scaffold_5-snap.2359-T1
Valid prediction for GeneMark_model.22112_t
Valid prediction for pasa_asmbl_44482.p1
Valid prediction for snap_scaffold_5-snap.2388-T1
Valid prediction for snap_scaffold_5-snap.2389-T1
Valid prediction for GlimmerHMM_glimmerT_13112-T1
Valid prediction for GeneMark_model.22124_t
Valid prediction for pasa_asmbl_44495.p1
Valid prediction for snap_scaffold_5-snap.2363-T1
Valid prediction for GeneMark_model.22157_t
Valid prediction for HiQ_model.g8754.t1
Valid prediction for GeneMark_model.22140_t
Valid prediction for GeneMark_model.22159_t
Valid prediction for GeneMark_model.22128_t
Valid prediction for GlimmerHMM_glimmerT_13125-T1
Valid prediction for snap_scaffold_5-snap.2379-T1
Valid prediction for GeneMark_model.22146_t
Valid prediction for GeneMark_model.22144_t
Valid prediction for GeneMark_model.22134_t
Valid prediction for GeneMark_model.22138_t
Valid prediction for GlimmerHMM_glimmerT_13136-T1
Valid prediction for GlimmerHMM_glimmerT_13116-T1
Valid prediction for GeneMark_model.22147_t
Valid prediction for snap_scaffold_5-snap.2397-T1
Valid prediction for snap_scaffold_5-snap.2366-T1
Valid prediction for snap_scaffold_5-snap.2381-T1
Valid prediction for Augustus_model.g8752.t1
Valid prediction for GeneMark_model.22156_t
Couldn't classify 48502, 48639
Sorry, prediction pasa_asmbl_44999.p1 fails validation.
(ATG)	 AG	48068-48253	GT	AGG
(GTG)	 AG	48502-48639	AT	TGA
-recovered pasa_asmbl_44999.p1, initial, 48068, 48253
-recovered pasa_asmbl_44999.p1, internal, 48068, 48253
Valid prediction for GlimmerHMM_glimmerT_13129-T1
Valid prediction for GlimmerHMM_glimmerT_13135-T1
Valid prediction for Augustus_model.g8747.t1
Valid prediction for GeneMark_model.22160_t
Valid prediction for Augustus_model.g8756.t1
Valid prediction for snap_scaffold_5-snap.2378-T1
Valid prediction for GlimmerHMM_glimmerT_13124-T1
Valid prediction for CodingQuarry_transcript_52166-T1
Valid prediction for snap_scaffold_5-snap.2386-T1
Valid prediction for GeneMark_model.22162_t
Valid prediction for snap_scaffold_5-snap.2396-T1
Valid prediction for GeneMark_model.22148_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: -)Couldn't classify 133191, 133250
Sorry, prediction pasa_asmbl_45863.p1 fails validation.
(GCC)	 AT	133191-133250	GT	TTG
(GTG)	 AG	134009-134557	CC	AGC
-recovered pasa_asmbl_45863.p1, terminal, 134009, 134557
Valid prediction for snap_scaffold_5-snap.2382-T1
Valid prediction for GeneMark_model.22125_t
Valid prediction for Augustus_model.g8751.t1
Valid prediction for snap_scaffold_5-snap.2387-T1
Valid prediction for GeneMark_model.22154_t
Valid prediction for GeneMark_model.22121_t
Valid prediction for snap_scaffold_5-snap.2385-T1
Valid prediction for GeneMark_model.22151_t
Valid prediction for GlimmerHMM_glimmerT_13128-T1
Valid prediction for GeneMark_model.22116_t
Valid prediction for GlimmerHMM_glimmerT_13122-T1
Valid prediction for GeneMark_model.22114_t
Valid prediction for GlimmerHMM_glimmerT_13107-T1
Valid prediction for GeneMark_model.22139_t
Valid prediction for CodingQuarry_transcript_52162-T1
Valid prediction for GeneMark_model.22149_t
Valid prediction for snap_scaffold_5-snap.2376-T1
Valid prediction for GeneMark_model.22123_t
Valid prediction for GeneMark_model.22133_t
Valid prediction for snap_scaffold_5-snap.2369-T1
Valid prediction for GeneMark_model.22145_t
Valid prediction for GeneMark_model.22132_t
Valid prediction for GeneMark_model.22136_t
Valid prediction for GlimmerHMM_glimmerT_13126-T1
Valid prediction for snap_scaffold_5-snap.2380-T1
Valid prediction for snap_scaffold_5-snap.2364-T1
Valid prediction for GlimmerHMM_glimmerT_13113-T1
Valid prediction for GeneMark_model.22135_t
Couldn't classify 139316, 139561
Sorry, prediction pasa_asmbl_45860.p1 fails validation.
(ATG)	 CA	138271-138552	GT	AAG
(ACC)	 AG	139316-139561	TA	GGT
-recovered pasa_asmbl_45860.p1, initial, 138271, 138552
Valid prediction for GeneMark_model.22131_t
Valid prediction for GeneMark_model.22141_t
Valid prediction for GeneMark_model.22127_t
Valid prediction for GeneMark_model.22161_t
Valid prediction for snap_scaffold_5-snap.2362-T1
Valid prediction for Augustus_model.g8745.t1
Valid prediction for GeneMark_model.22119_t
Valid prediction for GlimmerHMM_glimmerT_13108-T1
Valid prediction for GeneMark_model.22158_t
Valid prediction for GlimmerHMM_glimmerT_13105-T1
Valid prediction for HiQ_model.g8750.t1
Valid prediction for GlimmerHMM_glimmerT_13132-T1
Valid prediction for snap_scaffold_5-snap.2368-T1
Valid prediction for Augustus_model.g8759.t1
Valid prediction for GlimmerHMM_glimmerT_13115-T1
Couldn't classify 156187, 156325
Sorry, prediction pasa_asmbl_45856.p1 fails validation.
(GAG)	 TG	156187-156325	GT	AGG
(CTG)	 AG	157460-157704	GT	AGG
(AAC)	 AG	159739-159839	GT	GGG
(GCG)	 AG	160450-160729	GT	AGG
(GCC)	 AG	161204-161314	GT	CGG
(GGT)	 AG	161885-162012	GT	AGG
(GAA)	 AG	162155-162266	AC	AAA
-recovered pasa_asmbl_45856.p1, terminal, 162155, 162266
-recovered pasa_asmbl_45856.p1, internal, 157460, 157704
-recovered pasa_asmbl_45856.p1, internal, 159739, 159839
-recovered pasa_asmbl_45856.p1, internal, 160450, 160729
-recovered pasa_asmbl_45856.p1, internal, 161204, 161314
-recovered pasa_asmbl_45856.p1, internal, 161885, 162012
Valid prediction for GlimmerHMM_glimmerT_13118-T1
Valid prediction for snap_scaffold_5-snap.2394-T1
Valid prediction for GlimmerHMM_glimmerT_13121-T1
Valid prediction for GlimmerHMM_glimmerT_13119-T1
Valid prediction for GlimmerHMM_glimmerT_13109-T1
Valid prediction for HiQ_model.g8755.t1
Valid prediction for GeneMark_model.22126_t
Valid prediction for GlimmerHMM_glimmerT_13133-T1
Valid prediction for snap_scaffold_5-snap.2373-T1
Valid prediction for CodingQuarry_transcript_52161-T1
Valid prediction for GlimmerHMM_glimmerT_13117-T1
Valid prediction for snap_scaffold_5-snap.2391-T1
Valid prediction for GeneMark_model.22115_t
Valid prediction for Augustus_model.g8753.t1
Valid prediction for snap_scaffold_5-snap.2395-T1
Valid prediction for GeneMark_model.22111_t
Valid prediction for snap_scaffold_5-snap.2361-T1
Valid prediction for GeneMark_model.22152_t
Valid prediction for pasa_asmbl_45869.p1
Valid prediction for GeneMark_model.22120_t
Valid prediction for GlimmerHMM_glimmerT_13114-T1
Valid prediction for CodingQuarry_transcript_52163-T1
Valid prediction for HiQ_model.g8749.t1
Valid prediction for snap_scaffold_5-snap.2383-T1
Valid prediction for snap_scaffold_5-snap.2371-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32487, rend_intergenic: 28501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38394, rend_intergenic: 35811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42690, rend_intergenic: 39387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51323, rend_intergenic: 43735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70955, rend_intergenic: 53728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94619, rend_intergenic: 89175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106288, rend_intergenic: 103223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113835, rend_intergenic: 110242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123894, rend_intergenic: 122163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144589, rend_intergenic: 140030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149259, rend_intergenic: 146304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152327, rend_intergenic: 149798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161971, rend_intergenic: 153703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219288, rend_intergenic: 216118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 245714
-exon list size: 677


building trellis

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90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 32487, rend_intergenic: 28501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38394, rend_intergenic: 35811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42690, rend_intergenic: 39387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51323, rend_intergenic: 43735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70955, rend_intergenic: 53728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94619, rend_intergenic: 89175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106288, rend_intergenic: 103223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113835, rend_intergenic: 110242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123894, rend_intergenic: 122163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144589, rend_intergenic: 140030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149259, rend_intergenic: 146304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152327, rend_intergenic: 149798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161971, rend_intergenic: 153703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219288, rend_intergenic: 216118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support