-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_12074454-12277023

-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 GlimmerHMM_glimmerT_13058-T1
Valid prediction for snap_scaffold_5-snap.2260-T1
Valid prediction for pasa_asmbl_44456.p1
Valid prediction for snap_scaffold_5-snap.2244-T1
Valid prediction for GeneMark_model.22003_t
Valid prediction for GeneMark_model.22027_t
Valid prediction for snap_scaffold_5-snap.2241-T1
Valid prediction for GlimmerHMM_glimmerT_13035-T1
Valid prediction for Augustus_model.g8686.t1
Valid prediction for snap_scaffold_5-snap.2243-T1
Valid prediction for GlimmerHMM_glimmerT_13044-T1
Valid prediction for GeneMark_model.22008_t
Valid prediction for Augustus_model.g8690.t1
Valid prediction for snap_scaffold_5-snap.2258-T1
Valid prediction for CodingQuarry_transcript_52153-T1
Valid prediction for GeneMark_model.22015_t
Couldn't classify 87284, 87343
Couldn't classify 89659, 89747
Sorry, prediction pasa_asmbl_44454.p1 fails validation.
(AAC)	 GG	87284-87343	GT	AGG
(GAT)	 AG	87781-87921	GT	GGG
(GTT)	 AG	88073-88211	GT	TGG
(ACG)	 AG	89659-89747	TC	CCT
-recovered pasa_asmbl_44454.p1, internal, 87781, 87921
-recovered pasa_asmbl_44454.p1, internal, 88073, 88211
Valid prediction for GlimmerHMM_glimmerT_13050-T1
Valid prediction for HiQ_model.g8705.t1
Valid prediction for GeneMark_model.22019_t
Valid prediction for snap_scaffold_5-snap.2261-T1
Valid prediction for GeneMark_model.21998_t
Valid prediction for GeneMark_model.22007_t
Valid prediction for snap_scaffold_5-snap.2254-T1
Valid prediction for GeneMark_model.22012_t
Valid prediction for snap_scaffold_5-snap.2242-T1
Valid prediction for Augustus_model.g8696.t1
Valid prediction for snap_scaffold_5-snap.2272-T1
Valid prediction for snap_scaffold_5-snap.2264-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g8698.t1
Valid prediction for GeneMark_model.22014_t
Valid prediction for snap_scaffold_5-snap.2253-T1
Valid prediction for GlimmerHMM_glimmerT_13057-T1
Valid prediction for GeneMark_model.22030_t
Valid prediction for snap_scaffold_5-snap.2274-T1
Valid prediction for GlimmerHMM_glimmerT_13045-T1
Valid prediction for GeneMark_model.22000_t
Valid prediction for GeneMark_model.22011_t
Valid prediction for CodingQuarry_transcript_52149-T1
Valid prediction for snap_scaffold_5-snap.2245-T1
Valid prediction for snap_scaffold_5-snap.2252-T1
Valid prediction for pasa_asmbl_44461.p1
Valid prediction for snap_scaffold_5-snap.2238-T1
Valid prediction for GeneMark_model.22001_t
Valid prediction for GlimmerHMM_glimmerT_13060-T1
Valid prediction for GlimmerHMM_glimmerT_13040-T1
Valid prediction for GeneMark_model.22022_t
Valid prediction for snap_scaffold_5-snap.2278-T1
Valid prediction for GlimmerHMM_glimmerT_13056-T1
Valid prediction for Augustus_model.g8693.t1
Valid prediction for GlimmerHMM_glimmerT_13039-T1
Valid prediction for GeneMark_model.22006_t
Valid prediction for GlimmerHMM_glimmerT_13048-T1
Valid prediction for snap_scaffold_5-snap.2271-T1
Valid prediction for snap_scaffold_5-snap.2249-T1
Valid prediction for Augustus_model.g8701.t1
Valid prediction for GlimmerHMM_glimmerT_13061-T1
Valid prediction for GeneMark_model.22028_t
Valid prediction for Augustus_model.g8691.t1
Valid prediction for GlimmerHMM_glimmerT_13055-T1
Valid prediction for snap_scaffold_5-snap.2255-T1
Valid prediction for Augustus_model.g8702.t1
Valid prediction for GlimmerHMM_glimmerT_13052-T1
Valid prediction for snap_scaffold_5-snap.2268-T1
Valid prediction for GeneMark_model.22025_t
Valid prediction for GlimmerHMM_glimmerT_13041-T1
Valid prediction for GlimmerHMM_glimmerT_13043-T1
Valid prediction for Augustus_model.g8692.t1
Valid prediction for GeneMark_model.22010_t
Valid prediction for snap_scaffold_5-snap.2262-T1
Valid prediction for GlimmerHMM_glimmerT_13038-T1
Valid prediction for Augustus_model.g8689.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 CodingQuarry_transcript_52150-T1
Valid prediction for GlimmerHMM_glimmerT_13037-T1
Valid prediction for snap_scaffold_5-snap.2270-T1
Valid prediction for snap_scaffold_5-snap.2266-T1
Valid prediction for snap_scaffold_5-snap.2277-T1
Valid prediction for Augustus_model.g8704.t1
Valid prediction for GlimmerHMM_glimmerT_13062-T1
Valid prediction for GlimmerHMM_glimmerT_13042-T1
Valid prediction for snap_scaffold_5-snap.2240-T1
Valid prediction for snap_scaffold_5-snap.2276-T1
Valid prediction for GeneMark_model.22021_t
Valid prediction for GeneMark_model.22026_t
Valid prediction for snap_scaffold_5-snap.2239-T1
Valid prediction for GeneMark_model.22017_t
Valid prediction for GeneMark_model.22002_t
Valid prediction for snap_scaffold_5-snap.2279-T1
Valid prediction for GlimmerHMM_glimmerT_13047-T1
Valid prediction for CodingQuarry_transcript_52147-T1
Valid prediction for snap_scaffold_5-snap.2257-T1
Valid prediction for snap_scaffold_5-snap.2250-T1
Valid prediction for HiQ_model.g8700.t1
Valid prediction for GeneMark_model.22020_t
Couldn't classify 3608, 4117
Sorry, prediction pasa_asmbl_45826.p1 fails validation.
(TTC)	 AC	3608-4117	TG	AAT
Valid prediction for GeneMark_model.21999_t
Valid prediction for snap_scaffold_5-snap.2247-T1
Couldn't classify 39560, 39703
Sorry, prediction pasa_asmbl_45821.p1 fails validation.
(TGT)	 GG	39560-39703	GT	AGG
(GCC)	 AG	40168-40318	GT	AGG
(CTG)	 AG	40443-40552	GT	CGG
(GTG)	 AG	40677-40752	GT	GGG
(GGG)	 AG	40833-40897	GT	AGG
(GTT)	 AG	41045-41098	GT	AGG
(GTC)	 AG	41201-41264	GT	CGG
(GAG)	 AG	41366-41437	GT	AGG
(GAG)	 AG	41542-41627	GT	AGG
(ATC)	 AG	41748-41834	GT	AGG
(GCC)	 AG	41915-42014	GT	TGG
(GTT)	 AG	42211-42289	GT	AGG
(GGG)	 AG	42365-42604	GT	TGG
(GTG)	 AG	42865-42957	GT	AGG
(ACG)	 AG	43055-43192	GT	AGG
(GGA)	 AG	43324-43411	GT	GGG
(GTG)	 AG	43573-43719	GT	AGG
(ATG)	 AG	43812-43913	GT	AGG
(GTG)	 AG	44014-44106	GT	AGG
(GAC)	 AG	44257-44387	GT	CTG
(ATT)	 AG	44494-44560	GT	AGG
(AAT)	 AG	44640-44765	GT	AGG
(CTT)	 AG	44899-44949	GG	GAG
-recovered pasa_asmbl_45821.p1, initial, 43812, 43913
-recovered pasa_asmbl_45821.p1, terminal, 44899, 44949
-recovered pasa_asmbl_45821.p1, internal, 40168, 40318
-recovered pasa_asmbl_45821.p1, internal, 40443, 40552
-recovered pasa_asmbl_45821.p1, internal, 40677, 40752
-recovered pasa_asmbl_45821.p1, internal, 40833, 40897
-recovered pasa_asmbl_45821.p1, internal, 41045, 41098
-recovered pasa_asmbl_45821.p1, internal, 41201, 41264
-recovered pasa_asmbl_45821.p1, internal, 41366, 41437
-recovered pasa_asmbl_45821.p1, internal, 41542, 41627
-recovered pasa_asmbl_45821.p1, internal, 41748, 41834
-recovered pasa_asmbl_45821.p1, internal, 41915, 42014
-recovered pasa_asmbl_45821.p1, internal, 42211, 42289
-recovered pasa_asmbl_45821.p1, internal, 42365, 42604
-recovered pasa_asmbl_45821.p1, internal, 42865, 42957
-recovered pasa_asmbl_45821.p1, internal, 43055, 43192
-recovered pasa_asmbl_45821.p1, internal, 43324, 43411
-recovered pasa_asmbl_45821.p1, internal, 43573, 43719
-recovered pasa_asmbl_45821.p1, internal, 43812, 43913
-recovered pasa_asmbl_45821.p1, internal, 44014, 44106
-recovered pasa_asmbl_45821.p1, internal, 44257, 44387
-recovered pasa_asmbl_45821.p1, internal, 44494, 44560
-recovered pasa_asmbl_45821.p1, internal, 44640, 44765
Valid prediction for snap_scaffold_5-snap.2265-T1
Valid prediction for Augustus_model.g8699.t1
Valid prediction for Augustus_model.g8695.t1
Valid prediction for GlimmerHMM_glimmerT_13036-T1
Valid prediction for snap_scaffold_5-snap.2248-T1
Valid prediction for pasa_asmbl_45824.p1
Valid prediction for snap_scaffold_5-snap.2251-T1
Valid prediction for GeneMark_model.22024_t
Valid prediction for CodingQuarry_transcript_52152-T1
Valid prediction for GeneMark_model.22023_t
Valid prediction for GeneMark_model.22018_t
Valid prediction for GeneMark_model.22029_t
Valid prediction for snap_scaffold_5-snap.2259-T1
Valid prediction for GlimmerHMM_glimmerT_13051-T1
Couldn't classify 49301, 49400
Sorry, prediction pasa_asmbl_45820.p1 fails validation.
(CTG)	 CC	49301-49400	GT	ACG
(GTC)	 AG	49489-49643	GT	AAG
(TAT)	 AG	49741-49855	GT	GGG
(GTT)	 AG	49959-50067	GT	AAG
(GTA)	 AG	50149-50297	GT	AGG
(TGA)	 AG	50405-50495	GT	TGG
(TCC)	 AG	50608-50797	CT	AGC
-recovered pasa_asmbl_45820.p1, terminal, 50608, 50797
-recovered pasa_asmbl_45820.p1, internal, 49489, 49643
-recovered pasa_asmbl_45820.p1, internal, 49741, 49855
-recovered pasa_asmbl_45820.p1, internal, 49959, 50067
-recovered pasa_asmbl_45820.p1, internal, 50149, 50297
-recovered pasa_asmbl_45820.p1, internal, 50405, 50495
Valid prediction for snap_scaffold_5-snap.2267-T1
Valid prediction for snap_scaffold_5-snap.2275-T1
Valid prediction for CodingQuarry_transcript_52151-T1
Valid prediction for HiQ_model.g8697.t1
Valid prediction for HiQ_model.g8703.t1
Valid prediction for snap_scaffold_5-snap.2246-T1
Valid prediction for GlimmerHMM_glimmerT_13059-T1
Valid prediction for GlimmerHMM_glimmerT_13053-T1
Valid prediction for Augustus_model.g8694.t1
Valid prediction for Augustus_model.g8687.t1
Valid prediction for GeneMark_model.22004_t
Valid prediction for CodingQuarry_transcript_52148-T1
Valid prediction for snap_scaffold_5-snap.2273-T1
Valid prediction for GeneMark_model.22009_t
Valid prediction for snap_scaffold_5-snap.2269-T1
Valid prediction for GlimmerHMM_glimmerT_13049-T1
Valid prediction for Augustus_model.g8688.t1
Valid prediction for GeneMark_model.22016_t
Valid prediction for Augustus_model.g8706.t1
Valid prediction for pasa_asmbl_45823.p1
Valid prediction for snap_scaffold_5-snap.2256-T1
Valid prediction for GeneMark_model.22005_t
Valid prediction for GlimmerHMM_glimmerT_13054-T1
Valid prediction for snap_scaffold_5-snap.2263-T1
Valid prediction for GlimmerHMM_glimmerT_13046-T1
Valid prediction for pasa_asmbl_45818.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 109990, rend_intergenic: 109987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53706, rend_intergenic: 40554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71740, rend_intergenic: 60454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90812, rend_intergenic: 88633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122015, rend_intergenic: 114645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132926, rend_intergenic: 132117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135964, rend_intergenic: 134124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138599, rend_intergenic: 136640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181985, rend_intergenic: 177046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202570
-exon list size: 529


building trellis

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-found 29 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 109990, rend_intergenic: 109987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53706, rend_intergenic: 40554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71740, rend_intergenic: 60454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90812, rend_intergenic: 88633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122015, rend_intergenic: 114645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132926, rend_intergenic: 132117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135964, rend_intergenic: 134124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138599, rend_intergenic: 136640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181985, rend_intergenic: 177046  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