-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_12560955-12827922

-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_15-snap.2590-T1
Valid prediction for HiQ_model.g24743.t1
Valid prediction for GlimmerHMM_glimmerT_37150-T1
Valid prediction for snap_scaffold_15-snap.2588-T1
Valid prediction for GlimmerHMM_glimmerT_37156-T1
Valid prediction for snap_scaffold_15-snap.2587-T1
Valid prediction for Augustus_model.g24739.t1
Valid prediction for snap_scaffold_15-snap.2564-T1
Valid prediction for CodingQuarry_transcript_18189-T1
Couldn't classify 227913, 227929
Sorry, prediction pasa_asmbl_15608.p1 fails validation.
(TTC)	 CA	227913-227929	GT	AGG
(AGG)	 AG	230121-230165	GT	AGG
(TCG)	 AG	231133-231523	GG	AGG
-recovered pasa_asmbl_15608.p1, terminal, 231133, 231523
-recovered pasa_asmbl_15608.p1, internal, 230121, 230165
Valid prediction for Augustus_model.g24750.t1
Valid prediction for snap_scaffold_15-snap.2549-T1
Valid prediction for snap_scaffold_15-snap.2574-T1
Valid prediction for GlimmerHMM_glimmerT_37171-T1
Valid prediction for GlimmerHMM_glimmerT_37170-T1
Valid prediction for pasa_asmbl_15585.p1
Valid prediction for snap_scaffold_15-snap.2586-T1
Valid prediction for GlimmerHMM_glimmerT_37146-T1
Valid prediction for pasa_asmbl_15599.p1
Valid prediction for HiQ_model.g24737.t1
Valid prediction for GlimmerHMM_glimmerT_37158-T1
Valid prediction for CodingQuarry_transcript_18187-T1
Couldn't classify 69746, 70402
Sorry, prediction pasa_asmbl_15593.p1 fails validation.
(AGG)	 TC	69746-70402	CT	GAC
Couldn't classify 215398, 215464
Couldn't classify 226544, 226595
Sorry, prediction pasa_asmbl_15605.p1 fails validation.
(GTC)	 CA	215398-215464	GT	AGG
(GGG)	 AG	215683-215753	GT	AGG
(ATT)	 AG	218434-218490	GT	AGG
(GCA)	 AG	219231-219467	GT	AGG
(GAG)	 AG	220009-220128	GT	AGG
(CAA)	 AG	220839-220938	GT	AGG
(ACA)	 AG	221942-222054	GT	AGG
(CTG)	 AG	222718-222868	GT	AGG
(CCG)	 AG	223056-223255	GT	CGG
(AGT)	 AG	223797-223900	GT	AGG
(CAC)	 AG	226544-226595	AT	GCA
add_exon() Sorry, pasa_asmbl_15605.p1 220839-220938-terminal-3 is invalid.
-recovered pasa_asmbl_15605.p1, terminal, 220839, 220938
-recovered pasa_asmbl_15605.p1, internal, 215683, 215753
-recovered pasa_asmbl_15605.p1, internal, 218434, 218490
-recovered pasa_asmbl_15605.p1, internal, 219231, 219467
-recovered pasa_asmbl_15605.p1, internal, 220009, 220128
-recovered pasa_asmbl_15605.p1, internal, 220839, 220938
-recovered pasa_asmbl_15605.p1, internal, 221942, 222054
-recovered pasa_asmbl_15605.p1, internal, 222718, 222868
-recovered pasa_asmbl_15605.p1, internal, 223056, 223255
-recovered pasa_asmbl_15605.p1, internal, 223797, 223900
Valid prediction for snap_scaffold_15-snap.2600-T1
Valid prediction for Augustus_model.g24744.t1
Valid prediction for snap_scaffold_15-snap.2601-T1
Valid prediction for Augustus_model.g24738.t1
Valid prediction for snap_scaffold_15-snap.2580-T1
Valid prediction for snap_scaffold_15-snap.2557-T1
Valid prediction for GlimmerHMM_glimmerT_37157-T1
Valid prediction for GlimmerHMM_glimmerT_37165-T1
Valid prediction for snap_scaffold_15-snap.2594-T1
Valid prediction for GlimmerHMM_glimmerT_37162-T1
Valid prediction for Augustus_model.g24745.t1
Valid prediction for snap_scaffold_15-snap.2558-T1
Valid prediction for snap_scaffold_15-snap.2581-T1
Valid prediction for Augustus_model.g24748.t1
Valid prediction for CodingQuarry_transcript_18188-T1
Valid prediction for snap_scaffold_15-snap.2559-T1
Valid prediction for GlimmerHMM_glimmerT_37161-T1
Valid prediction for snap_scaffold_15-snap.2569-T1
Valid prediction for snap_scaffold_15-snap.2562-T1
Valid prediction for HiQ_model.g24746.t1
Valid prediction for snap_scaffold_15-snap.2593-T1
Valid prediction for snap_scaffold_15-snap.2563-T1
Valid prediction for snap_scaffold_15-snap.2584-T1
Valid prediction for GlimmerHMM_glimmerT_37143-T1
Valid prediction for snap_scaffold_15-snap.2598-T1
Valid prediction for GlimmerHMM_glimmerT_37166-T1
Valid prediction for CodingQuarry_transcript_18186-T1
Valid prediction for GlimmerHMM_glimmerT_37160-T1
Valid prediction for Augustus_model.g24753.t1
Valid prediction for Augustus_model.g24740.t1
Valid prediction for HiQ_model.g24747.t1
Valid prediction for pasa_asmbl_15597.p1
Valid prediction for snap_scaffold_15-snap.2585-T1
Valid prediction for snap_scaffold_15-snap.2579-T1
Valid prediction for snap_scaffold_15-snap.2561-T1
Valid prediction for snap_scaffold_15-snap.2575-T1
Valid prediction for snap_scaffold_15-snap.2597-T1
Valid prediction for GlimmerHMM_glimmerT_37145-T1
Valid prediction for snap_scaffold_15-snap.2577-T1
Valid prediction for GlimmerHMM_glimmerT_37142-T1
Valid prediction for GlimmerHMM_glimmerT_37144-T1
Valid prediction for snap_scaffold_15-snap.2599-T1
Valid prediction for Augustus_model.g24751.t1
Valid prediction for GlimmerHMM_glimmerT_37147-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: -)Couldn't classify 181800, 181808
Couldn't classify 183610, 183624
Sorry, prediction pasa_asmbl_14597.p1 fails validation.
(ATT)	 GC	181800-181808	GT	GGG
(GTG)	 AG	182215-182431	GT	GGG
(ATC)	 AG	182667-182729	GT	CGG
(TGA)	 AG	183149-183390	GT	AGG
(GTG)	 AG	183610-183624	AT	AGA
-recovered pasa_asmbl_14597.p1, internal, 182215, 182431
-recovered pasa_asmbl_14597.p1, internal, 182667, 182729
-recovered pasa_asmbl_14597.p1, internal, 183149, 183390
Valid prediction for snap_scaffold_15-snap.2552-T1
Valid prediction for GlimmerHMM_glimmerT_37159-T1
Valid prediction for pasa_asmbl_14599.p1
Valid prediction for snap_scaffold_15-snap.2565-T1
Valid prediction for CodingQuarry_transcript_18185-T1
Valid prediction for snap_scaffold_15-snap.2550-T1
Valid prediction for snap_scaffold_15-snap.2596-T1
Valid prediction for snap_scaffold_15-snap.2567-T1
Valid prediction for GlimmerHMM_glimmerT_37152-T1
Valid prediction for snap_scaffold_15-snap.2571-T1
Couldn't classify 32328, 32478
Sorry, prediction pasa_asmbl_14602.p1 fails validation.
(TGG)	 TG	32328-32478	GT	GGG
(GTG)	 AG	32817-32995	AA	GAA
-recovered pasa_asmbl_14602.p1, terminal, 32817, 32995
Valid prediction for Augustus_model.g24742.t1
Valid prediction for Augustus_model.g24734.t1
Valid prediction for CodingQuarry_transcript_18183-T1
Valid prediction for HiQ_model.g24735.t1
Valid prediction for HiQ_model.g24752.t1
Valid prediction for GlimmerHMM_glimmerT_37141-T1
Valid prediction for GlimmerHMM_glimmerT_37167-T1
Valid prediction for snap_scaffold_15-snap.2554-T1
Valid prediction for snap_scaffold_15-snap.2573-T1
Valid prediction for GlimmerHMM_glimmerT_37163-T1
Valid prediction for pasa_asmbl_14851.p1
Valid prediction for GlimmerHMM_glimmerT_37148-T1
Couldn't classify 183856, 183964
Couldn't classify 187229, 187330
Sorry, prediction pasa_asmbl_14594.p1 fails validation.
(TCG)	 GC	183856-183964	GT	CAG
(GTT)	 AG	184333-184430	GT	AGG
(ATA)	 AG	184558-184642	GT	AGG
(AAG)	 AG	184832-184949	GT	AGG
(GGA)	 AG	185246-185363	GT	TGG
(GGC)	 AG	187229-187330	TC	CCT
-recovered pasa_asmbl_14594.p1, internal, 184333, 184430
-recovered pasa_asmbl_14594.p1, internal, 184558, 184642
-recovered pasa_asmbl_14594.p1, internal, 184832, 184949
-recovered pasa_asmbl_14594.p1, internal, 185246, 185363
Valid prediction for Augustus_model.g24754.t1
Valid prediction for snap_scaffold_15-snap.2583-T1
Valid prediction for CodingQuarry_transcript_18182-T1
Valid prediction for GlimmerHMM_glimmerT_37153-T1
Valid prediction for GlimmerHMM_glimmerT_37168-T1
Valid prediction for Augustus_model.g24733.t1
Valid prediction for snap_scaffold_15-snap.2553-T1
Valid prediction for snap_scaffold_15-snap.2595-T1
Valid prediction for snap_scaffold_15-snap.2570-T1
Valid prediction for snap_scaffold_15-snap.2572-T1
Valid prediction for snap_scaffold_15-snap.2589-T1
Valid prediction for snap_scaffold_15-snap.2555-T1
Valid prediction for snap_scaffold_15-snap.2566-T1
Valid prediction for snap_scaffold_15-snap.2582-T1
Valid prediction for snap_scaffold_15-snap.2556-T1
Valid prediction for snap_scaffold_15-snap.2578-T1
Valid prediction for Augustus_model.g24741.t1
Valid prediction for snap_scaffold_15-snap.2560-T1
Couldn't classify 176390, 176481
Couldn't classify 180317, 180346
Sorry, prediction pasa_asmbl_14598.p1 fails validation.
(CTG)	 AG	176390-176481	GT	AGG
(CAA)	 AG	176835-176932	GT	AGG
(GTC)	 AG	177202-177281	GT	GAG
(ACC)	 AG	179804-179887	GT	ATG
(GAG)	 AG	180317-180346	AC	CCA
-recovered pasa_asmbl_14598.p1, internal, 176390, 176481
-recovered pasa_asmbl_14598.p1, internal, 176835, 176932
-recovered pasa_asmbl_14598.p1, internal, 177202, 177281
-recovered pasa_asmbl_14598.p1, internal, 179804, 179887
Couldn't classify 232959, 233097
Couldn't classify 233776, 233789
Sorry, prediction CodingQuarry_transcript_18184-T1 fails validation.
(ATG)	 AA	232292-232379	GT	TGG
(ATG)	 AG	232584-232621	GT	AGG
(TCC)	 AG	232959-233097	TG	TCT
(CTC)	 TC	233776-233789	CG	AAC
-recovered CodingQuarry_transcript_18184-T1, initial, 232292, 232379
add_exon() Sorry, CodingQuarry_transcript_18184-T1 232584-232621-initial-1 is invalid.
-recovered CodingQuarry_transcript_18184-T1, initial, 232584, 232621
-recovered CodingQuarry_transcript_18184-T1, internal, 232584, 232621
Valid prediction for GlimmerHMM_glimmerT_37154-T1
Valid prediction for Augustus_model.g24749.t1
Valid prediction for Augustus_model.g24732.t1
Valid prediction for snap_scaffold_15-snap.2548-T1
Valid prediction for snap_scaffold_15-snap.2568-T1
Valid prediction for GlimmerHMM_glimmerT_37139-T1
Valid prediction for HiQ_model.g24736.t1
Valid prediction for snap_scaffold_15-snap.2592-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_37149-T1
Valid prediction for snap_scaffold_15-snap.2591-T1
Valid prediction for GlimmerHMM_glimmerT_37138-T1
Valid prediction for GlimmerHMM_glimmerT_37155-T1
Valid prediction for GlimmerHMM_glimmerT_37164-T1
Valid prediction for GlimmerHMM_glimmerT_37151-T1
Valid prediction for GlimmerHMM_glimmerT_37169-T1
Valid prediction for pasa_asmbl_14586.p1
Valid prediction for snap_scaffold_15-snap.2576-T1
Valid prediction for GlimmerHMM_glimmerT_37140-T1
Valid prediction for snap_scaffold_15-snap.2551-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 95968, rend_intergenic: 92517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109100, rend_intergenic: 106241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116418, rend_intergenic: 110217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213638, rend_intergenic: 206821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224153, rend_intergenic: 213638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 266968
-exon list size: 464


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 95968, rend_intergenic: 92517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109100, rend_intergenic: 106241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116418, rend_intergenic: 110217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213638, rend_intergenic: 206821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224153, rend_intergenic: 213638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support