-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_11192391-11354812

-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 GeneMark_model.12430_t
Valid prediction for pasa_asmbl_40295.p1
Valid prediction for GlimmerHMM_glimmerT_7503-T1
Valid prediction for snap_scaffold_3-snap.2258-T1
Valid prediction for GeneMark_model.12404_t
Valid prediction for snap_scaffold_3-snap.2256-T1
Couldn't classify 78370, 78454
Sorry, prediction pasa_asmbl_40291.p1 fails validation.
(TTC)	 GC	78370-78454	GT	CTG
(CTC)	 AG	79167-79496	GT	TGG
(TGC)	 AG	81962-82246	GT	GAG
(TTG)	 AG	82725-82826	GT	GGG
(ACT)	 AG	84026-84030	GT	GAG
-recovered pasa_asmbl_40291.p1, terminal, 84026, 84030
-recovered pasa_asmbl_40291.p1, internal, 79167, 79496
-recovered pasa_asmbl_40291.p1, internal, 81962, 82246
-recovered pasa_asmbl_40291.p1, internal, 82725, 82826
-recovered pasa_asmbl_40291.p1, internal, 84026, 84030
Valid prediction for snap_scaffold_3-snap.2242-T1
Valid prediction for GlimmerHMM_glimmerT_7495-T1
Valid prediction for GeneMark_model.12402_t
Valid prediction for GeneMark_model.12421_t
Valid prediction for GeneMark_model.12416_t
Valid prediction for snap_scaffold_3-snap.2251-T1
Valid prediction for snap_scaffold_3-snap.2265-T1
Valid prediction for GlimmerHMM_glimmerT_7485-T1
Valid prediction for snap_scaffold_3-snap.2253-T1
Valid prediction for GlimmerHMM_glimmerT_7488-T1
Valid prediction for snap_scaffold_3-snap.2261-T1
Valid prediction for GeneMark_model.12432_t
Valid prediction for GlimmerHMM_glimmerT_7492-T1
Valid prediction for GeneMark_model.12418_t
Valid prediction for GeneMark_model.12420_t
Valid prediction for snap_scaffold_3-snap.2267-T1
Valid prediction for Augustus_model.g4914.t1
Valid prediction for GeneMark_model.12422_t
Valid prediction for GeneMark_model.12403_t
Valid prediction for GeneMark_model.12411_t
Valid prediction for snap_scaffold_3-snap.2247-T1
Valid prediction for GeneMark_model.12424_t
Valid prediction for snap_scaffold_3-snap.2263-T1
Valid prediction for Augustus_model.g4909.t1
Valid prediction for GlimmerHMM_glimmerT_7501-T1
Valid prediction for snap_scaffold_3-snap.2260-T1
Valid prediction for GeneMark_model.12414_t
Valid prediction for Augustus_model.g4905.t1
Valid prediction for Augustus_model.g4913.t1
Valid prediction for snap_scaffold_3-snap.2245-T1
Valid prediction for Augustus_model.g4911.t1
Valid prediction for GlimmerHMM_glimmerT_7490-T1
Valid prediction for GlimmerHMM_glimmerT_7481-T1
Couldn't classify 105105, 105165
Couldn't classify 105533, 105601
Sorry, prediction pasa_asmbl_40292.p2 fails validation.
(CGC)	 AC	105105-105165	GT	ACG
(TGA)	 AG	105278-105447	GT	GAG
(CCT)	 AG	105533-105601	AC	CAA
-recovered pasa_asmbl_40292.p2, internal, 105278, 105447
Valid prediction for Augustus_model.g4907.t1
Valid prediction for GeneMark_model.12399_t
Valid prediction for snap_scaffold_3-snap.2255-T1
Valid prediction for GeneMark_model.12400_t
Valid prediction for snap_scaffold_3-snap.2246-T1
Valid prediction for snap_scaffold_3-snap.2241-T1
Valid prediction for snap_scaffold_3-snap.2264-T1
Valid prediction for Augustus_model.g4917.t1
Valid prediction for GlimmerHMM_glimmerT_7496-T1
Valid prediction for GeneMark_model.12417_t
Valid prediction for GeneMark_model.12408_t
Valid prediction for GlimmerHMM_glimmerT_7491-T1
Valid prediction for Augustus_model.g4919.t1
Valid prediction for GeneMark_model.12426_t

-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_3-snap.2254-T1
Valid prediction for GeneMark_model.12415_t
Valid prediction for GlimmerHMM_glimmerT_7497-T1
Valid prediction for GlimmerHMM_glimmerT_7479-T1
Valid prediction for GlimmerHMM_glimmerT_7483-T1
Valid prediction for GeneMark_model.12419_t
Valid prediction for GeneMark_model.12423_t
Valid prediction for snap_scaffold_3-snap.2243-T1
Valid prediction for CodingQuarry_transcript_46171-T1
Valid prediction for snap_scaffold_3-snap.2244-T1
Valid prediction for GeneMark_model.12406_t
Valid prediction for GlimmerHMM_glimmerT_7499-T1
Valid prediction for snap_scaffold_3-snap.2269-T1
Valid prediction for Augustus_model.g4906.t1
Valid prediction for snap_scaffold_3-snap.2248-T1
Valid prediction for GlimmerHMM_glimmerT_7498-T1
Valid prediction for Augustus_model.g4908.t1
Valid prediction for Augustus_model.g4918.t1
Valid prediction for snap_scaffold_3-snap.2250-T1
Valid prediction for GlimmerHMM_glimmerT_7484-T1
Valid prediction for snap_scaffold_3-snap.2266-T1
Valid prediction for GeneMark_model.12425_t
Valid prediction for GlimmerHMM_glimmerT_7487-T1
Valid prediction for snap_scaffold_3-snap.2249-T1
Valid prediction for CodingQuarry_transcript_46174-T1
Valid prediction for snap_scaffold_3-snap.2262-T1
Valid prediction for GlimmerHMM_glimmerT_7500-T1
Valid prediction for snap_scaffold_3-snap.2240-T1
Valid prediction for GeneMark_model.12431_t
Valid prediction for HiQ_model.g4910.t1
Valid prediction for GeneMark_model.12405_t
Valid prediction for GlimmerHMM_glimmerT_7489-T1
Couldn't classify 30074, 30439
Sorry, prediction pasa_asmbl_39102.p1 fails validation.
(CCC)	 TG	30074-30439	TA	CCT
Valid prediction for pasa_asmbl_39094.p1
Valid prediction for GeneMark_model.12427_t
Valid prediction for CodingQuarry_transcript_46176-T1
Valid prediction for CodingQuarry_transcript_46175-T1
Valid prediction for GeneMark_model.12410_t
Valid prediction for Augustus_model.g4920.t1
Valid prediction for snap_scaffold_3-snap.2259-T1
Valid prediction for GlimmerHMM_glimmerT_7494-T1
Valid prediction for GlimmerHMM_glimmerT_7480-T1
Valid prediction for GeneMark_model.12412_t
Couldn't classify 26550, 26615
Couldn't classify 29633, 29848
Sorry, prediction pasa_asmbl_39103.p1 fails validation.
(CCT)	 GG	26550-26615	GT	TGG
(ATC)	 AG	26696-26821	GT	AGG
(GTA)	 AG	27002-27097	GT	AGG
(GGT)	 AG	27202-27438	GT	AGG
(CTG)	 AG	28219-28274	GT	AGG
(GTA)	 AG	28531-28633	GT	AGG
(AAA)	 AG	29633-29848	CT	CAC
-recovered pasa_asmbl_39103.p1, internal, 26696, 26821
-recovered pasa_asmbl_39103.p1, internal, 27002, 27097
-recovered pasa_asmbl_39103.p1, internal, 27202, 27438
-recovered pasa_asmbl_39103.p1, internal, 28219, 28274
-recovered pasa_asmbl_39103.p1, internal, 28531, 28633
Valid prediction for pasa_asmbl_39107.p2
Valid prediction for GlimmerHMM_glimmerT_7482-T1
Valid prediction for GlimmerHMM_glimmerT_7493-T1
Valid prediction for Augustus_model.g4916.t1
Valid prediction for GeneMark_model.12413_t
Valid prediction for GeneMark_model.12401_t
Valid prediction for Augustus_model.g4915.t1
Valid prediction for GlimmerHMM_glimmerT_7486-T1
Valid prediction for GlimmerHMM_glimmerT_7502-T1
Valid prediction for GeneMark_model.12429_t
Valid prediction for snap_scaffold_3-snap.2252-T1
Valid prediction for GlimmerHMM_glimmerT_7504-T1
Valid prediction for Augustus_model.g4904.t1
Valid prediction for GeneMark_model.12407_t
Valid prediction for snap_scaffold_3-snap.2257-T1
Valid prediction for GeneMark_model.12409_t
Valid prediction for Augustus_model.g4912.t1
Valid prediction for snap_scaffold_3-snap.2268-T1
Valid prediction for GeneMark_model.12398_t
Valid prediction for CodingQuarry_transcript_46172-T1
Couldn't classify 42829, 42912
Sorry, prediction pasa_asmbl_39097.p1 fails validation.
(GGG)	 CC	42829-42912	GT	AGG
(AAA)	 AG	45552-45662	GT	AGG
(CTC)	 AG	45884-46014	GT	AGG
(TGC)	 AG	46197-46303	GT	AGG
(ATG)	 AG	46694-46791	GT	AGG
(GTT)	 AG	47001-47096	GT	AGG
(GTG)	 AG	48285-48471	GT	GGG
(AGC)	 AG	48797-48895	GT	AGG
(ATG)	 AG	49101-49168	AC	GAA
add_exon() Sorry, pasa_asmbl_39097.p1 46694-46791-initial-1 is invalid.
-recovered pasa_asmbl_39097.p1, initial, 46694, 46791
-recovered pasa_asmbl_39097.p1, terminal, 46197, 46303
-recovered pasa_asmbl_39097.p1, terminal, 49101, 49168
-recovered pasa_asmbl_39097.p1, internal, 45552, 45662
-recovered pasa_asmbl_39097.p1, internal, 45884, 46014
-recovered pasa_asmbl_39097.p1, internal, 46197, 46303
-recovered pasa_asmbl_39097.p1, internal, 46694, 46791
-recovered pasa_asmbl_39097.p1, internal, 47001, 47096
-recovered pasa_asmbl_39097.p1, internal, 48285, 48471
-recovered pasa_asmbl_39097.p1, internal, 48797, 48895

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 148326, rend_intergenic: 148323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8414, rend_intergenic: 5233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18426, rend_intergenic: 10287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30977, rend_intergenic: 25537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57873, rend_intergenic: 54071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73168, rend_intergenic: 72473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85655, rend_intergenic: 81696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126836, rend_intergenic: 115678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139169, rend_intergenic: 133781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 162422
-exon list size: 442


building trellis

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-found 20 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 148326, rend_intergenic: 148323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8414, rend_intergenic: 5233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18426, rend_intergenic: 10287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30977, rend_intergenic: 25537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57873, rend_intergenic: 54071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73168, rend_intergenic: 72473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85655, rend_intergenic: 81696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126836, rend_intergenic: 115678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139169, rend_intergenic: 133781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support