-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_15197539-15425902

-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 CodingQuarry_transcript_28762-T1
Valid prediction for Augustus_model.g3406.t1
Valid prediction for snap_scaffold_2-snap.2935-T1
Valid prediction for snap_scaffold_2-snap.2923-T1
Valid prediction for GlimmerHMM_glimmerT_5055-T1
Valid prediction for snap_scaffold_2-snap.2927-T1
Valid prediction for GlimmerHMM_glimmerT_5041-T1
Valid prediction for pasa_asmbl_25031.p1
Valid prediction for snap_scaffold_2-snap.2941-T1
Valid prediction for snap_scaffold_2-snap.2933-T1
Valid prediction for snap_scaffold_2-snap.2906-T1
Valid prediction for snap_scaffold_2-snap.2909-T1
Valid prediction for pasa_asmbl_25027.p1
Valid prediction for snap_scaffold_2-snap.2942-T1
Valid prediction for snap_scaffold_2-snap.2917-T1
Valid prediction for GlimmerHMM_glimmerT_5054-T1
Valid prediction for Augustus_model.g3392.t1
Valid prediction for snap_scaffold_2-snap.2921-T1
Valid prediction for CodingQuarry_transcript_28751-T1
Valid prediction for GlimmerHMM_glimmerT_5044-T1
Valid prediction for GlimmerHMM_glimmerT_5042-T1
Valid prediction for snap_scaffold_2-snap.2904-T1
Valid prediction for GlimmerHMM_glimmerT_5053-T1
Valid prediction for Augustus_model.g3413.t1
Valid prediction for GlimmerHMM_glimmerT_5051-T1
Valid prediction for GlimmerHMM_glimmerT_5039-T1
Valid prediction for CodingQuarry_transcript_28749-T1
Valid prediction for CodingQuarry_transcript_28752-T1
Valid prediction for snap_scaffold_2-snap.2912-T1
Valid prediction for Augustus_model.g3389.t1
Valid prediction for pasa_asmbl_25035.p1
Valid prediction for HiQ_model.g3404.t1
Valid prediction for snap_scaffold_2-snap.2938-T1
Couldn't classify 30791, 30821
Sorry, prediction pasa_asmbl_24991.p1 fails validation.
(GGG)	 TT	30791-30821	GT	AGG
(GGG)	 AG	30974-31272	GA	GAG
-recovered pasa_asmbl_24991.p1, terminal, 30974, 31272
Valid prediction for snap_scaffold_2-snap.2936-T1
Valid prediction for Augustus_model.g3408.t1
Valid prediction for HiQ_model.g3399.t1
Valid prediction for HiQ_model.g3394.t1
Valid prediction for Augustus_model.g3410.t1
Valid prediction for snap_scaffold_2-snap.2929-T1
Valid prediction for snap_scaffold_2-snap.2924-T1
Valid prediction for GlimmerHMM_glimmerT_5027-T1
Valid prediction for pasa_asmbl_25023.p1
Valid prediction for snap_scaffold_2-snap.2915-T1
Valid prediction for GlimmerHMM_glimmerT_5049-T1
Valid prediction for GlimmerHMM_glimmerT_5026-T1
Valid prediction for pasa_asmbl_24993.p1
Valid prediction for HiQ_model.g3412.t1
Valid prediction for GlimmerHMM_glimmerT_5028-T1
Valid prediction for GlimmerHMM_glimmerT_5046-T1
Valid prediction for HiQ_model.g3396.t1
Valid prediction for Augustus_model.g3401.t1
Valid prediction for snap_scaffold_2-snap.2931-T1
Valid prediction for GlimmerHMM_glimmerT_5031-T1
Valid prediction for CodingQuarry_transcript_28761-T1
Valid prediction for snap_scaffold_2-snap.2907-T1
Valid prediction for snap_scaffold_2-snap.2920-T1
Valid prediction for CodingQuarry_transcript_28750-T1
Valid prediction for snap_scaffold_2-snap.2910-T1
Valid prediction for GlimmerHMM_glimmerT_5058-T1
Valid prediction for CodingQuarry_transcript_28758-T1
Valid prediction for HiQ_model.g3395.t1
Valid prediction for snap_scaffold_2-snap.2916-T1
Valid prediction for GlimmerHMM_glimmerT_5033-T1
Valid prediction for GlimmerHMM_glimmerT_5040-T1
Valid prediction for HiQ_model.g3400.t1
Valid prediction for snap_scaffold_2-snap.2945-T1
Valid prediction for snap_scaffold_2-snap.2940-T1
Couldn't classify 98622, 98654
Sorry, prediction pasa_asmbl_25028.p1 fails validation.
(TTT)	 CC	98622-98654	GC	AGG
(TTC)	 AG	99311-99487	GT	AGG
(GTA)	 AG	101568-101777	GT	CTG
(ATC)	 AG	102956-103169	GT	AGG
(GCT)	 AG	103625-103803	GA	GAG
-recovered pasa_asmbl_25028.p1, terminal, 103625, 103803
-recovered pasa_asmbl_25028.p1, internal, 99311, 99487
-recovered pasa_asmbl_25028.p1, internal, 101568, 101777
-recovered pasa_asmbl_25028.p1, internal, 102956, 103169
Valid prediction for CodingQuarry_transcript_28755-T1
Valid prediction for pasa_asmbl_25010.p1
Couldn't classify 154140, 154330
Sorry, prediction pasa_asmbl_25034.p1 fails validation.
(AGG)	 CC	154140-154330	GT	AGG
(CCC)	 AG	154471-154576	GT	AAG
(GTA)	 AG	154690-154926	GT	GAG
(GTC)	 AG	155116-155415	GT	AGG
(GCT)	 AG	155536-155811	CG	AAC
-recovered pasa_asmbl_25034.p1, terminal, 155536, 155811
-recovered pasa_asmbl_25034.p1, internal, 154471, 154576
-recovered pasa_asmbl_25034.p1, internal, 154690, 154926
-recovered pasa_asmbl_25034.p1, internal, 155116, 155415
Valid prediction for CodingQuarry_transcript_28754-T1
Valid prediction for GlimmerHMM_glimmerT_5030-T1
Valid prediction for pasa_asmbl_24996.p1
Valid prediction for GlimmerHMM_glimmerT_5035-T1
Valid prediction for snap_scaffold_2-snap.2939-T1
Valid prediction for CodingQuarry_transcript_28757-T1
Valid prediction for Augustus_model.g3411.t1
Valid prediction for snap_scaffold_2-snap.2913-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.g3418.t1
Valid prediction for snap_scaffold_2-snap.2930-T1
Valid prediction for GlimmerHMM_glimmerT_5061-T1
Valid prediction for snap_scaffold_2-snap.2934-T1
Valid prediction for Augustus_model.g3415.t1
Couldn't classify 81650, 81710
Sorry, prediction pasa_asmbl_23622.p1 fails validation.
(CTC)	 AT	81650-81710	GT	TGG
(ACA)	 AG	83357-83436	GT	CTG
(AGG)	 AG	83885-84043	GT	CAG
(AGA)	 AG	84129-84161	GA	GAG
-recovered pasa_asmbl_23622.p1, terminal, 84129, 84161
-recovered pasa_asmbl_23622.p1, internal, 83357, 83436
-recovered pasa_asmbl_23622.p1, internal, 83885, 84043
Valid prediction for snap_scaffold_2-snap.2932-T1
Valid prediction for GlimmerHMM_glimmerT_5043-T1
Valid prediction for snap_scaffold_2-snap.2926-T1
Valid prediction for Augustus_model.g3409.t1
Valid prediction for GlimmerHMM_glimmerT_5052-T1
Valid prediction for Augustus_model.g3390.t1
Valid prediction for CodingQuarry_transcript_28753-T1
Couldn't classify 168323, 168766
Sorry, prediction pasa_asmbl_23615.p1 fails validation.
(AAC)	 GC	168323-168766	GT	CGG
(ATG)	 AG	168903-169021	GT	AGG
(GAA)	 AG	169103-169206	GT	TGG
(AGG)	 AG	169305-169482	GT	GGG
(TTG)	 AG	169670-169817	GT	TGG
(ACA)	 AG	169916-170001	GT	GGG
(ATG)	 AG	170086-170177	GT	AGG
(AAA)	 AG	170290-170351	CT	AAC
-recovered pasa_asmbl_23615.p1, initial, 168903, 169021
add_exon() Sorry, pasa_asmbl_23615.p1 170086-170177-initial-1 is invalid.
-recovered pasa_asmbl_23615.p1, initial, 170086, 170177
-recovered pasa_asmbl_23615.p1, terminal, 170290, 170351
-recovered pasa_asmbl_23615.p1, internal, 168903, 169021
-recovered pasa_asmbl_23615.p1, internal, 169103, 169206
-recovered pasa_asmbl_23615.p1, internal, 169305, 169482
-recovered pasa_asmbl_23615.p1, internal, 169670, 169817
-recovered pasa_asmbl_23615.p1, internal, 169916, 170001
-recovered pasa_asmbl_23615.p1, internal, 170086, 170177
Valid prediction for GlimmerHMM_glimmerT_5045-T1
Valid prediction for snap_scaffold_2-snap.2922-T1
Valid prediction for HiQ_model.g3402.t1
Valid prediction for GlimmerHMM_glimmerT_5032-T1
Valid prediction for Augustus_model.g3414.t1
Valid prediction for snap_scaffold_2-snap.2919-T1
Valid prediction for snap_scaffold_2-snap.2950-T1
Valid prediction for GlimmerHMM_glimmerT_5047-T1
Valid prediction for pasa_asmbl_23620.p1
Valid prediction for snap_scaffold_2-snap.2946-T1
Valid prediction for snap_scaffold_2-snap.2925-T1
Valid prediction for GlimmerHMM_glimmerT_5059-T1
Valid prediction for Augustus_model.g3417.t1
Valid prediction for GlimmerHMM_glimmerT_5050-T1
Valid prediction for snap_scaffold_2-snap.2951-T1
Valid prediction for GlimmerHMM_glimmerT_5034-T1
Valid prediction for HiQ_model.g3397.t1
Valid prediction for snap_scaffold_2-snap.2937-T1
Valid prediction for snap_scaffold_2-snap.2944-T1
Valid prediction for Augustus_model.g3405.t1
Couldn't classify 44740, 44857
Couldn't classify 45388, 45477
Sorry, prediction pasa_asmbl_23623.p1 fails validation.
(AAG)	 TG	44740-44857	GT	AGG
(CAG)	 AG	44958-45085	GT	AGG
(GAT)	 AG	45199-45282	GT	AGG
(CTT)	 AG	45388-45477	AC	CCA
-recovered pasa_asmbl_23623.p1, internal, 44958, 45085
-recovered pasa_asmbl_23623.p1, internal, 45199, 45282
Valid prediction for CodingQuarry_transcript_28760-T1
Valid prediction for snap_scaffold_2-snap.2914-T1
Valid prediction for snap_scaffold_2-snap.2949-T1
Valid prediction for Augustus_model.g3398.t1
Valid prediction for GlimmerHMM_glimmerT_5057-T1
Valid prediction for snap_scaffold_2-snap.2918-T1
Valid prediction for snap_scaffold_2-snap.2947-T1
Valid prediction for HiQ_model.g3393.t1
Valid prediction for CodingQuarry_transcript_28748-T1
Valid prediction for snap_scaffold_2-snap.2948-T1
Valid prediction for GlimmerHMM_glimmerT_5056-T1
Valid prediction for GlimmerHMM_glimmerT_5060-T1
Valid prediction for CodingQuarry_transcript_28756-T1
Valid prediction for GlimmerHMM_glimmerT_5029-T1
Valid prediction for Augustus_model.g3416.t1
Valid prediction for GlimmerHMM_glimmerT_5038-T1
Valid prediction for GlimmerHMM_glimmerT_5037-T1
Valid prediction for snap_scaffold_2-snap.2928-T1
Valid prediction for GlimmerHMM_glimmerT_5036-T1
Valid prediction for Augustus_model.g3407.t1
Valid prediction for Augustus_model.g3391.t1
Valid prediction for snap_scaffold_2-snap.2908-T1
Valid prediction for GlimmerHMM_glimmerT_5048-T1
Valid prediction for snap_scaffold_2-snap.2905-T1
Valid prediction for Augustus_model.g3403.t1
Valid prediction for snap_scaffold_2-snap.2943-T1
Valid prediction for pasa_asmbl_23617.p1
Valid prediction for snap_scaffold_2-snap.2911-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16133, rend_intergenic: 9408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38213, rend_intergenic: 34269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103803, rend_intergenic: 97248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129818, rend_intergenic: 128121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132926, rend_intergenic: 130561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152137, rend_intergenic: 144395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161486, rend_intergenic: 157909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 228364
-exon list size: 502


building trellis

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-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 16133, rend_intergenic: 9408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38213, rend_intergenic: 34269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103803, rend_intergenic: 97248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129818, rend_intergenic: 128121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132926, rend_intergenic: 130561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152137, rend_intergenic: 144395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161486, rend_intergenic: 157909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support