-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_15474143-15746241

-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 Augustus_model.g10845.t1
Valid prediction for snap_scaffold_6-snap.3297-T1
Valid prediction for snap_scaffold_6-snap.3302-T1
Valid prediction for GlimmerHMM_glimmerT_16131-T1
Couldn't classify 237119, 237211
Sorry, prediction pasa_asmbl_47670.p1 fails validation.
(CAG)	 TG	237119-237211	GT	AGG
(ACC)	 AG	237371-237480	GT	CAG
(GCT)	 AG	238040-238481	GT	AGG
(GTG)	 AG	239508-239724	GT	AGG
(TGA)	 AG	239913-240021	GT	CAG
(GGC)	 AG	240624-240783	GT	AGG
(GAT)	 AG	241187-241306	GT	AGG
(GTC)	 AG	241504-241590	GT	CAG
(GAG)	 AG	241752-241913	GC	GAG
-recovered pasa_asmbl_47670.p1, terminal, 241752, 241913
-recovered pasa_asmbl_47670.p1, internal, 237371, 237480
-recovered pasa_asmbl_47670.p1, internal, 238040, 238481
-recovered pasa_asmbl_47670.p1, internal, 239508, 239724
-recovered pasa_asmbl_47670.p1, internal, 239913, 240021
-recovered pasa_asmbl_47670.p1, internal, 240624, 240783
-recovered pasa_asmbl_47670.p1, internal, 241187, 241306
-recovered pasa_asmbl_47670.p1, internal, 241504, 241590
-recovered pasa_asmbl_47670.p1, internal, 241752, 241913
Valid prediction for snap_scaffold_6-snap.3276-T1
Valid prediction for Augustus_model.g10846.t1
Valid prediction for snap_scaffold_6-snap.3275-T1
Valid prediction for GlimmerHMM_glimmerT_16141-T1
Valid prediction for GlimmerHMM_glimmerT_16133-T1
Valid prediction for snap_scaffold_6-snap.3262-T1
Valid prediction for GlimmerHMM_glimmerT_16115-T1
Valid prediction for Augustus_model.g10836.t1
Valid prediction for snap_scaffold_6-snap.3268-T1
Valid prediction for snap_scaffold_6-snap.3290-T1
Valid prediction for snap_scaffold_6-snap.3282-T1
Valid prediction for snap_scaffold_6-snap.3295-T1
Valid prediction for snap_scaffold_6-snap.3270-T1
Valid prediction for GlimmerHMM_glimmerT_16122-T1
Valid prediction for GlimmerHMM_glimmerT_16130-T1
Valid prediction for snap_scaffold_6-snap.3287-T1
Valid prediction for CodingQuarry_transcript_55366-T1
Valid prediction for GlimmerHMM_glimmerT_16123-T1
Valid prediction for snap_scaffold_6-snap.3306-T1
Valid prediction for GlimmerHMM_glimmerT_16145-T1
Valid prediction for snap_scaffold_6-snap.3308-T1
Valid prediction for GlimmerHMM_glimmerT_16137-T1
Valid prediction for GlimmerHMM_glimmerT_16139-T1
Valid prediction for Augustus_model.g10832.t1
Valid prediction for Augustus_model.g10838.t1
Valid prediction for GlimmerHMM_glimmerT_16128-T1
Valid prediction for GlimmerHMM_glimmerT_16143-T1
Valid prediction for snap_scaffold_6-snap.3296-T1
Valid prediction for snap_scaffold_6-snap.3258-T1
Valid prediction for Augustus_model.g10840.t1
Valid prediction for snap_scaffold_6-snap.3291-T1
Valid prediction for GlimmerHMM_glimmerT_16126-T1
Valid prediction for snap_scaffold_6-snap.3294-T1
Valid prediction for snap_scaffold_6-snap.3264-T1
Valid prediction for Augustus_model.g10839.t1
Valid prediction for Augustus_model.g10841.t1
Valid prediction for HiQ_model.g10844.t1
Valid prediction for Augustus_model.g10828.t1
Valid prediction for GlimmerHMM_glimmerT_16136-T1
Valid prediction for GlimmerHMM_glimmerT_16119-T1
Couldn't classify 222458, 222624
Sorry, prediction pasa_asmbl_47669.p1 fails validation.
(GTC)	 AC	222458-222624	GT	CAG
(GGA)	 AG	222920-223025	GT	AGG
(AGA)	 AG	223201-223249	GT	CGG
(ACG)	 AG	223441-223586	GT	AGG
(TTG)	 AG	223837-223931	GT	AAG
(GAT)	 AG	224092-224317	GA	GAG
-recovered pasa_asmbl_47669.p1, terminal, 224092, 224317
-recovered pasa_asmbl_47669.p1, internal, 222920, 223025
-recovered pasa_asmbl_47669.p1, internal, 223201, 223249
-recovered pasa_asmbl_47669.p1, internal, 223441, 223586
-recovered pasa_asmbl_47669.p1, internal, 223837, 223931
Valid prediction for snap_scaffold_6-snap.3284-T1
Valid prediction for snap_scaffold_6-snap.3280-T1
Valid prediction for GlimmerHMM_glimmerT_16142-T1
Valid prediction for snap_scaffold_6-snap.3259-T1
Valid prediction for snap_scaffold_6-snap.3303-T1
Valid prediction for GlimmerHMM_glimmerT_16144-T1
Valid prediction for snap_scaffold_6-snap.3286-T1
Valid prediction for snap_scaffold_6-snap.3300-T1
Valid prediction for snap_scaffold_6-snap.3299-T1
Valid prediction for GlimmerHMM_glimmerT_16132-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.g10837.t1
Valid prediction for CodingQuarry_transcript_55363-T1
Valid prediction for snap_scaffold_6-snap.3269-T1
Valid prediction for snap_scaffold_6-snap.3278-T1
Valid prediction for GlimmerHMM_glimmerT_16124-T1
Valid prediction for pasa_asmbl_49075.p1
Valid prediction for snap_scaffold_6-snap.3288-T1
Valid prediction for snap_scaffold_6-snap.3309-T1
Valid prediction for snap_scaffold_6-snap.3293-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.3292-T1
Valid prediction for snap_scaffold_6-snap.3298-T1
Valid prediction for snap_scaffold_6-snap.3277-T1
Valid prediction for GlimmerHMM_glimmerT_16147-T1
Valid prediction for Augustus_model.g10831.t1
Valid prediction for snap_scaffold_6-snap.3279-T1
Valid prediction for GlimmerHMM_glimmerT_16114-T1
Valid prediction for Augustus_model.g10847.t1
Valid prediction for GlimmerHMM_glimmerT_16129-T1
Valid prediction for GlimmerHMM_glimmerT_16135-T1
Valid prediction for snap_scaffold_6-snap.3272-T1
Valid prediction for snap_scaffold_6-snap.3273-T1
Valid prediction for snap_scaffold_6-snap.3307-T1
Valid prediction for Augustus_model.g10830.t1
Valid prediction for Augustus_model.g10835.t1
Valid prediction for GlimmerHMM_glimmerT_16134-T1
Valid prediction for GlimmerHMM_glimmerT_16116-T1
Valid prediction for Augustus_model.g10842.t1
Valid prediction for GlimmerHMM_glimmerT_16146-T1
Valid prediction for snap_scaffold_6-snap.3256-T1
Valid prediction for snap_scaffold_6-snap.3285-T1
Valid prediction for snap_scaffold_6-snap.3281-T1
Valid prediction for snap_scaffold_6-snap.3260-T1
Valid prediction for Augustus_model.g10843.t1
Couldn't classify 252088, 252246
Couldn't classify 254398, 254502
Sorry, prediction pasa_asmbl_49445.p1 fails validation.
(AAT)	 CG	252088-252246	GT	AGG
(GCA)	 AG	252617-252715	GT	AGG
(GAG)	 AG	253355-253525	GT	AGG
(ATC)	 AG	254398-254502	AC	ACA
-recovered pasa_asmbl_49445.p1, internal, 252617, 252715
-recovered pasa_asmbl_49445.p1, internal, 253355, 253525
Valid prediction for snap_scaffold_6-snap.3267-T1
Valid prediction for snap_scaffold_6-snap.3257-T1
Valid prediction for GlimmerHMM_glimmerT_16120-T1
Valid prediction for snap_scaffold_6-snap.3305-T1
Valid prediction for GlimmerHMM_glimmerT_16138-T1
Valid prediction for Augustus_model.g10829.t1
Valid prediction for Augustus_model.g10834.t1
Valid prediction for GlimmerHMM_glimmerT_16125-T1
Valid prediction for snap_scaffold_6-snap.3266-T1
Valid prediction for snap_scaffold_6-snap.3304-T1
Valid prediction for GlimmerHMM_glimmerT_16140-T1
Valid prediction for snap_scaffold_6-snap.3283-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_16127-T1
Valid prediction for HiQ_model.g10833.t1
Valid prediction for GlimmerHMM_glimmerT_16113-T1
Valid prediction for GlimmerHMM_glimmerT_16117-T1
Valid prediction for CodingQuarry_transcript_55364-T1
Valid prediction for snap_scaffold_6-snap.3274-T1
Valid prediction for GlimmerHMM_glimmerT_16118-T1
Valid prediction for snap_scaffold_6-snap.3265-T1
Valid prediction for snap_scaffold_6-snap.3289-T1
Valid prediction for snap_scaffold_6-snap.3301-T1
Valid prediction for snap_scaffold_6-snap.3261-T1
Valid prediction for snap_scaffold_6-snap.3263-T1
Valid prediction for snap_scaffold_6-snap.3271-T1
Couldn't classify 202800, 202835
Sorry, prediction pasa_asmbl_49078.p1 fails validation.
(ATA)	 CC	202800-202835	GT	GGG
(AAA)	 AG	203122-203257	GT	AGG
(TGA)	 AG	203767-203858	GT	AGG
(TTG)	 AG	203958-204044	GT	GGG
(GAT)	 AG	204202-204210	TG	AGT
-recovered pasa_asmbl_49078.p1, terminal, 204202, 204210
-recovered pasa_asmbl_49078.p1, internal, 203122, 203257
-recovered pasa_asmbl_49078.p1, internal, 203767, 203858
-recovered pasa_asmbl_49078.p1, internal, 203958, 204044
Valid prediction for GlimmerHMM_glimmerT_16121-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11412, rend_intergenic: 5381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44127, rend_intergenic: 33155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50971, rend_intergenic: 44797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57499, rend_intergenic: 51129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94876, rend_intergenic: 81803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113707, rend_intergenic: 97977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118388, rend_intergenic: 114732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119355, rend_intergenic: 118905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121718, rend_intergenic: 120195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125692, rend_intergenic: 123586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141173, rend_intergenic: 127396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141366, rend_intergenic: 141243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152619, rend_intergenic: 141437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157103, rend_intergenic: 154436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190790, rend_intergenic: 159233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195297, rend_intergenic: 191658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221870, rend_intergenic: 195320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242186, rend_intergenic: 237367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254098, rend_intergenic: 252702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266371, rend_intergenic: 254236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 272099
-exon list size: 530


building trellis

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-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 11412, rend_intergenic: 5381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44127, rend_intergenic: 33155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50971, rend_intergenic: 44797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57499, rend_intergenic: 51129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94876, rend_intergenic: 81803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113707, rend_intergenic: 97977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118388, rend_intergenic: 114732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119355, rend_intergenic: 118905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121718, rend_intergenic: 120195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125692, rend_intergenic: 123586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141173, rend_intergenic: 127396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141366, rend_intergenic: 141243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152619, rend_intergenic: 141437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157103, rend_intergenic: 154436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190790, rend_intergenic: 159233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195297, rend_intergenic: 191658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221870, rend_intergenic: 195320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242186, rend_intergenic: 237367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254098, rend_intergenic: 252702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266371, rend_intergenic: 254236  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