-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_16309848-16513073

-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 pasa_asmbl_46107.p1
Valid prediction for snap_scaffold_5-snap.3012-T1
Couldn't classify 19531, 19733
Couldn't classify 20829, 20954
Sorry, prediction pasa_asmbl_46088.p1 fails validation.
(AAC)	 CA	19531-19733	GT	AGG
(GAG)	 AG	20117-20168	GT	CGG
(AGA)	 AG	20318-20476	GT	AGG
(CAG)	 AG	20829-20954	CC	CCC
-recovered pasa_asmbl_46088.p1, internal, 20117, 20168
-recovered pasa_asmbl_46088.p1, internal, 20318, 20476
Valid prediction for HiQ_model.g8894.t1
Valid prediction for snap_scaffold_5-snap.3052-T1
Valid prediction for GlimmerHMM_glimmerT_13355-T1
Valid prediction for GlimmerHMM_glimmerT_13364-T1
Valid prediction for CodingQuarry_transcript_52417-T1
Valid prediction for snap_scaffold_5-snap.3022-T1
Valid prediction for Augustus_model.g8885.t1
Valid prediction for Augustus_model.g8884.t1
Valid prediction for snap_scaffold_5-snap.3053-T1
Valid prediction for snap_scaffold_5-snap.3008-T1
Valid prediction for snap_scaffold_5-snap.3021-T1
Valid prediction for GlimmerHMM_glimmerT_13351-T1
Valid prediction for snap_scaffold_5-snap.3033-T1
Valid prediction for GlimmerHMM_glimmerT_13361-T1
Valid prediction for snap_scaffold_5-snap.3024-T1
Valid prediction for Augustus_model.g8888.t1
Valid prediction for snap_scaffold_5-snap.3037-T1
Valid prediction for GlimmerHMM_glimmerT_13356-T1
Valid prediction for snap_scaffold_5-snap.3032-T1
Couldn't classify 17447, 17551
Sorry, prediction pasa_asmbl_46087.p1 fails validation.
(ATG)	 GC	15628-15676	GT	AGG
(TGG)	 AG	15809-15896	GT	AGG
(GGA)	 AG	16130-16266	GT	ATG
(CCT)	 AG	16415-16518	GT	AGG
(GAA)	 AG	16675-16785	GT	AGG
(GCA)	 AG	16905-16958	GT	TGG
(GCA)	 AG	17052-17261	GT	TGG
(GCG)	 AG	17447-17551	TA	GGT
-recovered pasa_asmbl_46087.p1, initial, 15628, 15676
add_exon() Sorry, pasa_asmbl_46087.p1 15809-15896-terminal-3 is invalid.
-recovered pasa_asmbl_46087.p1, terminal, 15809, 15896
-recovered pasa_asmbl_46087.p1, internal, 15809, 15896
-recovered pasa_asmbl_46087.p1, internal, 16130, 16266
-recovered pasa_asmbl_46087.p1, internal, 16415, 16518
-recovered pasa_asmbl_46087.p1, internal, 16675, 16785
-recovered pasa_asmbl_46087.p1, internal, 16905, 16958
-recovered pasa_asmbl_46087.p1, internal, 17052, 17261
Valid prediction for HiQ_model.g8879.t1
Valid prediction for Augustus_model.g8875.t1
Valid prediction for snap_scaffold_5-snap.3042-T1
Valid prediction for snap_scaffold_5-snap.3046-T1
Valid prediction for snap_scaffold_5-snap.3035-T1
Valid prediction for snap_scaffold_5-snap.3007-T1
Valid prediction for snap_scaffold_5-snap.3031-T1
Valid prediction for snap_scaffold_5-snap.3015-T1
Valid prediction for GlimmerHMM_glimmerT_13358-T1
Valid prediction for GlimmerHMM_glimmerT_13376-T1
Valid prediction for snap_scaffold_5-snap.3027-T1
Valid prediction for GlimmerHMM_glimmerT_13363-T1
Valid prediction for Augustus_model.g8887.t1
Couldn't classify 24444, 24498
Sorry, prediction pasa_asmbl_46092.p1 fails validation.
(GAC)	 CA	24444-24498	GT	CGG
(TCC)	 AG	25262-25464	GT	GAG
(GGA)	 AG	25579-25683	GT	AGG
(GTA)	 AG	25825-26460	GA	GAG
-recovered pasa_asmbl_46092.p1, terminal, 25825, 26460
-recovered pasa_asmbl_46092.p1, internal, 25262, 25464
-recovered pasa_asmbl_46092.p1, internal, 25579, 25683
Valid prediction for GlimmerHMM_glimmerT_13377-T1
Valid prediction for GlimmerHMM_glimmerT_13375-T1
Valid prediction for snap_scaffold_5-snap.3028-T1
Valid prediction for Augustus_model.g8886.t1
Valid prediction for snap_scaffold_5-snap.3011-T1
Valid prediction for Augustus_model.g8893.t1
Valid prediction for HiQ_model.g8874.t1
Valid prediction for snap_scaffold_5-snap.3013-T1
Valid prediction for Augustus_model.g8878.t1
Valid prediction for snap_scaffold_5-snap.3034-T1
Couldn't classify 74981, 75127
Couldn't classify 76262, 76280
Sorry, prediction pasa_asmbl_46097.p1 fails validation.
(ATC)	 CA	74981-75127	GT	AGG
(GCG)	 AG	75647-75817	GT	AGG
(GGT)	 AG	76095-76156	GT	AGG
(GGT)	 AG	76262-76280	GG	GGG
-recovered pasa_asmbl_46097.p1, internal, 75647, 75817
-recovered pasa_asmbl_46097.p1, internal, 76095, 76156
Valid prediction for pasa_asmbl_46093.p1
Valid prediction for snap_scaffold_5-snap.3009-T1
Valid prediction for snap_scaffold_5-snap.3048-T1
Valid prediction for Augustus_model.g8890.t1
Couldn't classify 69585, 69669
Couldn't classify 71244, 71444
Sorry, prediction pasa_asmbl_46096.p1 fails validation.
(CTG)	 GC	69585-69669	GT	AGG
(CTC)	 AG	69892-70028	GT	AGG
(GTC)	 AG	70144-70224	GT	CAG
(GGC)	 AG	70644-70771	GT	AGG
(GAT)	 AG	70891-71005	GT	AGG
(GCC)	 AG	71244-71444	GG	CCG
-recovered pasa_asmbl_46096.p1, internal, 69892, 70028
-recovered pasa_asmbl_46096.p1, internal, 70144, 70224
-recovered pasa_asmbl_46096.p1, internal, 70644, 70771
-recovered pasa_asmbl_46096.p1, internal, 70891, 71005
Couldn't classify 192582, 192647
Sorry, prediction pasa_asmbl_46104.p2 fails validation.
(ATG)	 CC	191892-192025	GT	TGG
(GGA)	 AG	192182-192326	GT	TGG
(AAT)	 AG	192582-192647	TT	GGT
-recovered pasa_asmbl_46104.p2, initial, 191892, 192025
-recovered pasa_asmbl_46104.p2, internal, 192182, 192326
Valid prediction for snap_scaffold_5-snap.3010-T1
Valid prediction for GlimmerHMM_glimmerT_13359-T1
Valid prediction for Augustus_model.g8883.t1
Valid prediction for snap_scaffold_5-snap.3044-T1
Couldn't classify 76311, 76319
Sorry, prediction pasa_asmbl_46098.p1 fails validation.
(TCA)	 AG	76311-76319	GT	CTG
(ATT)	 AG	76451-76525	GT	AGG
(ATC)	 AG	76659-76833	GT	AGG
(ACC)	 AG	76935-77058	GT	AGG
(CGC)	 AG	77448-77700	AG	GAA
-recovered pasa_asmbl_46098.p1, terminal, 77448, 77700
-recovered pasa_asmbl_46098.p1, internal, 76311, 76319
-recovered pasa_asmbl_46098.p1, internal, 76451, 76525
-recovered pasa_asmbl_46098.p1, internal, 76659, 76833
-recovered pasa_asmbl_46098.p1, internal, 76935, 77058
Valid prediction for snap_scaffold_5-snap.3029-T1
Valid prediction for Augustus_model.g8876.t1
Valid prediction for snap_scaffold_5-snap.3038-T1
Valid prediction for HiQ_model.g8877.t1
Valid prediction for Augustus_model.g8880.t1
Couldn't classify 21369, 21377
Couldn't classify 21492, 21872
Sorry, prediction pasa_asmbl_46090.p1 fails validation.
(CCT)	 TC	21369-21377	GT	TGG
(GAG)	 AG	21492-21872	CC	CCC
Valid prediction for snap_scaffold_5-snap.3051-T1
Valid prediction for pasa_asmbl_46082.p1
Valid prediction for snap_scaffold_5-snap.3017-T1
Valid prediction for GlimmerHMM_glimmerT_13372-T1
Valid prediction for GlimmerHMM_glimmerT_13352-T1
Valid prediction for snap_scaffold_5-snap.3041-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 snap_scaffold_5-snap.3026-T1
Valid prediction for Augustus_model.g8892.t1
Valid prediction for snap_scaffold_5-snap.3036-T1
Valid prediction for snap_scaffold_5-snap.3045-T1
Valid prediction for snap_scaffold_5-snap.3040-T1
Valid prediction for GlimmerHMM_glimmerT_13357-T1
Valid prediction for GlimmerHMM_glimmerT_13360-T1
Valid prediction for GlimmerHMM_glimmerT_13370-T1
Valid prediction for snap_scaffold_5-snap.3023-T1
Valid prediction for snap_scaffold_5-snap.3025-T1
Valid prediction for GlimmerHMM_glimmerT_13353-T1
Valid prediction for snap_scaffold_5-snap.3018-T1
Valid prediction for GlimmerHMM_glimmerT_13368-T1
Valid prediction for snap_scaffold_5-snap.3020-T1
Valid prediction for Augustus_model.g8891.t1
Valid prediction for GlimmerHMM_glimmerT_13371-T1
Valid prediction for GlimmerHMM_glimmerT_13373-T1
Valid prediction for GlimmerHMM_glimmerT_13369-T1
Valid prediction for snap_scaffold_5-snap.3016-T1
Valid prediction for GlimmerHMM_glimmerT_13378-T1
Valid prediction for GlimmerHMM_glimmerT_13366-T1
Valid prediction for snap_scaffold_5-snap.3039-T1
Valid prediction for GlimmerHMM_glimmerT_13362-T1
Valid prediction for Augustus_model.g8889.t1
Valid prediction for snap_scaffold_5-snap.3014-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3019-T1
Valid prediction for snap_scaffold_5-snap.3050-T1
Valid prediction for Augustus_model.g8882.t1
Valid prediction for GlimmerHMM_glimmerT_13354-T1
Valid prediction for snap_scaffold_5-snap.3030-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.3049-T1
Valid prediction for snap_scaffold_5-snap.3043-T1
Valid prediction for snap_scaffold_5-snap.3047-T1
Valid prediction for Augustus_model.g8881.t1
Valid prediction for GlimmerHMM_glimmerT_13365-T1
Valid prediction for GlimmerHMM_glimmerT_13367-T1
Valid prediction for GlimmerHMM_glimmerT_13374-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 41438, rend_intergenic: 37633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59323, rend_intergenic: 57733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71504, rend_intergenic: 59783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78226, rend_intergenic: 71842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94202, rend_intergenic: 92681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113797, rend_intergenic: 109313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148042, rend_intergenic: 141519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153073, rend_intergenic: 149516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159975, rend_intergenic: 157680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163093, rend_intergenic: 162116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170883, rend_intergenic: 169078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175220, rend_intergenic: 171742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183330, rend_intergenic: 180178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203226
-exon list size: 467


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 41438, rend_intergenic: 37633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59323, rend_intergenic: 57733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71504, rend_intergenic: 59783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78226, rend_intergenic: 71842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94202, rend_intergenic: 92681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113797, rend_intergenic: 109313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148042, rend_intergenic: 141519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153073, rend_intergenic: 149516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159975, rend_intergenic: 157680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163093, rend_intergenic: 162116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170883, rend_intergenic: 169078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175220, rend_intergenic: 171742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183330, rend_intergenic: 180178  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