-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_8938671-9197327

-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_28-snap.2051-T1
Valid prediction for GeneMark_model.105943_t
Valid prediction for HiQ_model.g40465.t1
Valid prediction for GeneMark_model.105938_t
Valid prediction for GlimmerHMM_glimmerT_60802-T1
Valid prediction for GeneMark_model.105925_t
Valid prediction for GlimmerHMM_glimmerT_60785-T1
Valid prediction for snap_scaffold_28-snap.2057-T1
Valid prediction for snap_scaffold_28-snap.2050-T1
Valid prediction for snap_scaffold_28-snap.2066-T1
Valid prediction for snap_scaffold_28-snap.2056-T1
Valid prediction for GeneMark_model.105917_t
Valid prediction for snap_scaffold_28-snap.2045-T1
Valid prediction for snap_scaffold_28-snap.2053-T1
Valid prediction for snap_scaffold_28-snap.2071-T1
Valid prediction for snap_scaffold_28-snap.2065-T1
Valid prediction for GeneMark_model.105935_t
Valid prediction for GlimmerHMM_glimmerT_60793-T1
Valid prediction for GeneMark_model.105944_t
Valid prediction for CodingQuarry_transcript_43653-T1
Valid prediction for GeneMark_model.105939_t
Valid prediction for GeneMark_model.105945_t
Valid prediction for GeneMark_model.105913_t
Valid prediction for GlimmerHMM_glimmerT_60790-T1
Valid prediction for snap_scaffold_28-snap.2046-T1
Valid prediction for GlimmerHMM_glimmerT_60805-T1
Valid prediction for GeneMark_model.105949_t
Valid prediction for GeneMark_model.105941_t
Valid prediction for GlimmerHMM_glimmerT_60798-T1
Valid prediction for GeneMark_model.105921_t
Valid prediction for GlimmerHMM_glimmerT_60791-T1
Valid prediction for GlimmerHMM_glimmerT_60804-T1
Valid prediction for snap_scaffold_28-snap.2068-T1
Valid prediction for GeneMark_model.105951_t
Valid prediction for snap_scaffold_28-snap.2073-T1
Valid prediction for snap_scaffold_28-snap.2048-T1
Valid prediction for GeneMark_model.105930_t
Valid prediction for GlimmerHMM_glimmerT_60800-T1
Valid prediction for CodingQuarry_transcript_43655-T1
Valid prediction for GlimmerHMM_glimmerT_60803-T1
Valid prediction for GeneMark_model.105953_t
Valid prediction for snap_scaffold_28-snap.2059-T1
Valid prediction for GeneMark_model.105932_t
Valid prediction for snap_scaffold_28-snap.2055-T1
Valid prediction for GlimmerHMM_glimmerT_60795-T1
Valid prediction for snap_scaffold_28-snap.2042-T1
Couldn't classify 173692, 174300
Sorry, prediction pasa_asmbl_38465.p1 fails validation.
(GTG)	 CG	173692-174300	GT	AGG
(GAG)	 AG	174534-174751	GT	TGG
(CTA)	 AG	175312-175381	CC	GAC
-recovered pasa_asmbl_38465.p1, terminal, 175312, 175381
-recovered pasa_asmbl_38465.p1, internal, 174534, 174751
Valid prediction for GeneMark_model.105919_t
Valid prediction for GlimmerHMM_glimmerT_60797-T1
Valid prediction for snap_scaffold_28-snap.2069-T1
Valid prediction for snap_scaffold_28-snap.2063-T1
Valid prediction for GeneMark_model.105928_t
Valid prediction for GeneMark_model.105937_t
Valid prediction for GeneMark_model.105916_t
Valid prediction for GlimmerHMM_glimmerT_60788-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.g40466.t1
Valid prediction for GeneMark_model.105911_t
Valid prediction for GlimmerHMM_glimmerT_60792-T1
Valid prediction for GlimmerHMM_glimmerT_60801-T1
Valid prediction for GlimmerHMM_glimmerT_60796-T1
Valid prediction for GeneMark_model.105931_t
Valid prediction for GeneMark_model.105927_t
Valid prediction for snap_scaffold_28-snap.2041-T1
Valid prediction for GeneMark_model.105924_t
Couldn't classify 32930, 33573
Couldn't classify 34798, 34911
Sorry, prediction pasa_asmbl_37824.p1 fails validation.
(CCG)	 AG	32930-33573	GT	AGG
(TTT)	 AG	33815-33932	GT	AGG
(GTG)	 AG	34279-34380	GT	CGG
(GTC)	 AG	34798-34911	CT	CTC
-recovered pasa_asmbl_37824.p1, internal, 32930, 33573
-recovered pasa_asmbl_37824.p1, internal, 33815, 33932
-recovered pasa_asmbl_37824.p1, internal, 34279, 34380
Valid prediction for snap_scaffold_28-snap.2067-T1
Valid prediction for GeneMark_model.105923_t
Valid prediction for snap_scaffold_28-snap.2062-T1
Valid prediction for Augustus_model.g40469.t1
Couldn't classify 75133, 75168
Sorry, prediction pasa_asmbl_37820.p1 fails validation.
(AAT)	 TG	75133-75168	GT	AGG
(GTG)	 AG	75966-76091	GT	GGG
(AAA)	 AG	76618-76683	GT	AGG
(GCG)	 AG	77733-77800	GT	TGG
(GGT)	 AG	78350-78398	GT	GAG
(CAA)	 AG	78778-78890	GT	CAG
(CGG)	 AG	79036-79108	GT	AGG
(CTA)	 AG	79285-79354	GT	AGG
(GGA)	 AG	79628-79704	GT	AGG
(TCA)	 AG	79795-79864	GT	AGG
(TCA)	 AG	80048-80132	GT	GTG
(CTA)	 AG	80541-80643	AG	AAA
-recovered pasa_asmbl_37820.p1, terminal, 80541, 80643
-recovered pasa_asmbl_37820.p1, internal, 75966, 76091
-recovered pasa_asmbl_37820.p1, internal, 76618, 76683
-recovered pasa_asmbl_37820.p1, internal, 77733, 77800
-recovered pasa_asmbl_37820.p1, internal, 78350, 78398
-recovered pasa_asmbl_37820.p1, internal, 78778, 78890
-recovered pasa_asmbl_37820.p1, internal, 79036, 79108
-recovered pasa_asmbl_37820.p1, internal, 79285, 79354
-recovered pasa_asmbl_37820.p1, internal, 79628, 79704
-recovered pasa_asmbl_37820.p1, internal, 79795, 79864
-recovered pasa_asmbl_37820.p1, internal, 80048, 80132
Valid prediction for snap_scaffold_28-snap.2049-T1
Valid prediction for GeneMark_model.105920_t
Valid prediction for GeneMark_model.105926_t
Valid prediction for GeneMark_model.105929_t
Valid prediction for snap_scaffold_28-snap.2047-T1
Valid prediction for GlimmerHMM_glimmerT_60794-T1
Valid prediction for GeneMark_model.105914_t
Valid prediction for snap_scaffold_28-snap.2044-T1
Valid prediction for snap_scaffold_28-snap.2052-T1
Valid prediction for snap_scaffold_28-snap.2054-T1
Valid prediction for GeneMark_model.105915_t
Valid prediction for snap_scaffold_28-snap.2043-T1
Valid prediction for GeneMark_model.105936_t
Valid prediction for GeneMark_model.105946_t
Valid prediction for GeneMark_model.105954_t
Valid prediction for GeneMark_model.105948_t
Valid prediction for GeneMark_model.105940_t
Valid prediction for GeneMark_model.105947_t
Valid prediction for GlimmerHMM_glimmerT_60783-T1
Valid prediction for GeneMark_model.105922_t
Valid prediction for GeneMark_model.105918_t
Valid prediction for GeneMark_model.105934_t
Valid prediction for CodingQuarry_transcript_43654-T1
Couldn't classify 31940, 32656
Sorry, prediction pasa_asmbl_37825.p1 fails validation.
(CTG)	 AA	31940-32656	AC	ACA
Valid prediction for GeneMark_model.105952_t
Valid prediction for GeneMark_model.105942_t
Valid prediction for Augustus_model.g40464.t1
Valid prediction for Augustus_model.g40467.t1
Valid prediction for snap_scaffold_28-snap.2070-T1
Valid prediction for snap_scaffold_28-snap.2064-T1
Valid prediction for Augustus_model.g40468.t1
Valid prediction for GlimmerHMM_glimmerT_60786-T1
Valid prediction for GlimmerHMM_glimmerT_60787-T1
Valid prediction for snap_scaffold_28-snap.2072-T1
Valid prediction for GeneMark_model.105910_t
Valid prediction for GeneMark_model.105912_t
Couldn't classify 28724, 28840
Couldn't classify 30624, 30796
Sorry, prediction pasa_asmbl_37902.p1 fails validation.
(GAC)	 CC	28724-28840	GT	GGG
(GAG)	 AG	28971-29115	GT	AGG
(CTG)	 AG	30624-30796	AC	TCA
-recovered pasa_asmbl_37902.p1, internal, 28971, 29115
Valid prediction for GlimmerHMM_glimmerT_60799-T1
Valid prediction for HiQ_model.g40463.t1
Valid prediction for GlimmerHMM_glimmerT_60789-T1
Valid prediction for GlimmerHMM_glimmerT_60784-T1
Valid prediction for snap_scaffold_28-snap.2060-T1
Valid prediction for snap_scaffold_28-snap.2061-T1
Valid prediction for GeneMark_model.105933_t
Valid prediction for GeneMark_model.105950_t
Valid prediction for snap_scaffold_28-snap.2058-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 35250, rend_intergenic: 32957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133582, rend_intergenic: 124927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143423, rend_intergenic: 142264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149253, rend_intergenic: 146448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184138, rend_intergenic: 181225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192676, rend_intergenic: 185404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232228, rend_intergenic: 230985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239318, rend_intergenic: 233423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253615, rend_intergenic: 241191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 258657
-exon list size: 601


building trellis

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98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 35250, rend_intergenic: 32957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133582, rend_intergenic: 124927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143423, rend_intergenic: 142264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149253, rend_intergenic: 146448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184138, rend_intergenic: 181225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192676, rend_intergenic: 185404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232228, rend_intergenic: 230985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239318, rend_intergenic: 233423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253615, rend_intergenic: 241191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support