-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_1077899-1248793

-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 snap_scaffold_12-snap.285-T1
Valid prediction for GeneMark_model.50814_t
Valid prediction for Augustus_model.g19597.t1
Valid prediction for GlimmerHMM_glimmerT_29435-T1
Valid prediction for Augustus_model.g19592.t1
Valid prediction for snap_scaffold_12-snap.287-T1
Valid prediction for GeneMark_model.50786_t
Valid prediction for snap_scaffold_12-snap.260-T1
Valid prediction for GeneMark_model.50816_t
Valid prediction for CodingQuarry_transcript_10100-T1
Valid prediction for GlimmerHMM_glimmerT_29426-T1
Valid prediction for GeneMark_model.50828_t
Valid prediction for GlimmerHMM_glimmerT_29433-T1
Valid prediction for GeneMark_model.50812_t
Valid prediction for snap_scaffold_12-snap.259-T1
Valid prediction for Augustus_model.g19598.t1
Valid prediction for GeneMark_model.50784_t
Valid prediction for snap_scaffold_12-snap.248-T1
Valid prediction for GlimmerHMM_glimmerT_29430-T1
Couldn't classify 158486, 158896
Sorry, prediction pasa_asmbl_8429.p2 fails validation.
(GAC)	 CA	158486-158896	GG	GAG
Valid prediction for GlimmerHMM_glimmerT_29423-T1
Valid prediction for HiQ_model.g19599.t1
Valid prediction for Augustus_model.g19600.t1
Couldn't classify 98895, 98968
Sorry, prediction pasa_asmbl_8424.p1 fails validation.
(GTG)	 AG	98895-98968	GT	AGG
(CTG)	 AG	99263-99321	GT	TGG
(GTA)	 AG	100037-100178	GT	CAG
(GTA)	 AG	100447-100528	GT	TGG
(GAT)	 AG	100822-101014	GT	GGG
(TGG)	 AG	102474-102663	GT	TGG
(GGA)	 AG	103065-103178	GT	TGG
(GGA)	 AG	103874-104030	GT	AGG
(GGT)	 AG	105023-105238	GT	AGG
(CCT)	 AG	107662-107781	GT	AGG
(AAG)	 AG	108384-108522	GT	AGG
(CAG)	 AG	108634-108749	GT	AGG
(AAA)	 AG	109291-109347	AG	GAA
-recovered pasa_asmbl_8424.p1, terminal, 109291, 109347
-recovered pasa_asmbl_8424.p1, internal, 98895, 98968
-recovered pasa_asmbl_8424.p1, internal, 99263, 99321
-recovered pasa_asmbl_8424.p1, internal, 100037, 100178
-recovered pasa_asmbl_8424.p1, internal, 100447, 100528
-recovered pasa_asmbl_8424.p1, internal, 100822, 101014
-recovered pasa_asmbl_8424.p1, internal, 102474, 102663
-recovered pasa_asmbl_8424.p1, internal, 103065, 103178
-recovered pasa_asmbl_8424.p1, internal, 103874, 104030
-recovered pasa_asmbl_8424.p1, internal, 105023, 105238
-recovered pasa_asmbl_8424.p1, internal, 107662, 107781
-recovered pasa_asmbl_8424.p1, internal, 108384, 108522
-recovered pasa_asmbl_8424.p1, internal, 108634, 108749
Valid prediction for GeneMark_model.50830_t
Valid prediction for GlimmerHMM_glimmerT_29438-T1
Valid prediction for snap_scaffold_12-snap.274-T1
Valid prediction for snap_scaffold_12-snap.263-T1
Valid prediction for snap_scaffold_12-snap.266-T1
Valid prediction for GeneMark_model.50805_t
Valid prediction for snap_scaffold_12-snap.250-T1
Valid prediction for GeneMark_model.50781_t
Valid prediction for GeneMark_model.50820_t
Valid prediction for snap_scaffold_12-snap.276-T1
Valid prediction for GlimmerHMM_glimmerT_29429-T1
Valid prediction for snap_scaffold_12-snap.265-T1
Valid prediction for GlimmerHMM_glimmerT_29440-T1
Valid prediction for GlimmerHMM_glimmerT_29420-T1
Valid prediction for GlimmerHMM_glimmerT_29441-T1
Valid prediction for Augustus_model.g19602.t1
Valid prediction for GlimmerHMM_glimmerT_29436-T1
Valid prediction for GeneMark_model.50807_t
Valid prediction for snap_scaffold_12-snap.283-T1
Valid prediction for GeneMark_model.50796_t
Valid prediction for GeneMark_model.50790_t
Valid prediction for GeneMark_model.50798_t
Valid prediction for GeneMark_model.50787_t
Valid prediction for HiQ_model.g19603.t1
Valid prediction for GeneMark_model.50811_t
Valid prediction for GeneMark_model.50799_t
Valid prediction for snap_scaffold_12-snap.277-T1
Valid prediction for Augustus_model.g19593.t1
Valid prediction for GeneMark_model.50800_t
Valid prediction for Augustus_model.g19601.t1
Valid prediction for GlimmerHMM_glimmerT_29419-T1
Valid prediction for Augustus_model.g19596.t1
Valid prediction for GeneMark_model.50824_t
Valid prediction for GlimmerHMM_glimmerT_29431-T1
Valid prediction for HiQ_model.g19595.t1
Valid prediction for snap_scaffold_12-snap.272-T1
Valid prediction for GeneMark_model.50802_t
Valid prediction for snap_scaffold_12-snap.249-T1
Valid prediction for GlimmerHMM_glimmerT_29443-T1
Valid prediction for snap_scaffold_12-snap.271-T1
Couldn't classify 145024, 147855
Couldn't classify 152208, 152352
Sorry, prediction pasa_asmbl_8428.p1 fails validation.
(CTG)	 TG	145024-147855	GT	AGG
(CAG)	 AG	150619-150710	GC	TGG
(GTC)	 AG	152208-152352	GG	CCG
-recovered pasa_asmbl_8428.p1, internal, 150619, 150710
Valid prediction for Augustus_model.g19604.t1
Valid prediction for GlimmerHMM_glimmerT_29434-T1
Valid prediction for snap_scaffold_12-snap.257-T1
Valid prediction for snap_scaffold_12-snap.279-T1
Valid prediction for GeneMark_model.50788_t
Valid prediction for GeneMark_model.50794_t
Valid prediction for GeneMark_model.50809_t
Valid prediction for Augustus_model.g19591.t1
Valid prediction for GeneMark_model.50821_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_12-snap.255-T1
Valid prediction for GeneMark_model.50791_t
Valid prediction for GeneMark_model.50827_t
Valid prediction for snap_scaffold_12-snap.264-T1
Valid prediction for snap_scaffold_12-snap.282-T1
Valid prediction for GlimmerHMM_glimmerT_29427-T1
Valid prediction for snap_scaffold_12-snap.284-T1
Valid prediction for snap_scaffold_12-snap.270-T1
Valid prediction for GeneMark_model.50813_t
Valid prediction for GeneMark_model.50793_t
Valid prediction for GeneMark_model.50803_t
Valid prediction for snap_scaffold_12-snap.273-T1
Valid prediction for GeneMark_model.50829_t
Valid prediction for snap_scaffold_12-snap.252-T1
Valid prediction for GlimmerHMM_glimmerT_29428-T1
Valid prediction for snap_scaffold_12-snap.275-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g19605.t1
Valid prediction for GeneMark_model.50801_t
Valid prediction for snap_scaffold_12-snap.281-T1
Valid prediction for snap_scaffold_12-snap.258-T1
Valid prediction for GeneMark_model.50823_t
Valid prediction for GlimmerHMM_glimmerT_29421-T1
Valid prediction for GeneMark_model.50806_t
Valid prediction for Augustus_model.g19594.t1
Valid prediction for snap_scaffold_12-snap.269-T1
Valid prediction for snap_scaffold_12-snap.278-T1
Valid prediction for GeneMark_model.50822_t
Valid prediction for GeneMark_model.50782_t
Valid prediction for snap_scaffold_12-snap.247-T1
Valid prediction for snap_scaffold_12-snap.261-T1
Valid prediction for GlimmerHMM_glimmerT_29432-T1
Valid prediction for GlimmerHMM_glimmerT_29439-T1
Valid prediction for GlimmerHMM_glimmerT_29425-T1
Valid prediction for GeneMark_model.50819_t
Valid prediction for GeneMark_model.50817_t
Valid prediction for snap_scaffold_12-snap.251-T1
Valid prediction for snap_scaffold_12-snap.254-T1
Valid prediction for snap_scaffold_12-snap.256-T1
Valid prediction for snap_scaffold_12-snap.253-T1
Valid prediction for GeneMark_model.50783_t
Valid prediction for snap_scaffold_12-snap.268-T1
Valid prediction for snap_scaffold_12-snap.280-T1
Valid prediction for GeneMark_model.50789_t
Valid prediction for GeneMark_model.50808_t
Valid prediction for snap_scaffold_12-snap.262-T1
Valid prediction for GlimmerHMM_glimmerT_29424-T1
Valid prediction for GeneMark_model.50825_t
Valid prediction for GlimmerHMM_glimmerT_29442-T1
Valid prediction for GeneMark_model.50810_t
Valid prediction for GeneMark_model.50815_t
Valid prediction for snap_scaffold_12-snap.267-T1
Valid prediction for GeneMark_model.50797_t
Valid prediction for GeneMark_model.50795_t
Valid prediction for snap_scaffold_12-snap.286-T1
Valid prediction for GlimmerHMM_glimmerT_29422-T1
Valid prediction for GlimmerHMM_glimmerT_29437-T1
Valid prediction for GeneMark_model.50785_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14196, rend_intergenic: 2637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62599, rend_intergenic: 25155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68111, rend_intergenic: 67592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70624, rend_intergenic: 68186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75319, rend_intergenic: 71696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83822, rend_intergenic: 76694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84656, rend_intergenic: 84139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87867, rend_intergenic: 85626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104084, rend_intergenic: 96996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109347, rend_intergenic: 107410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122277, rend_intergenic: 116273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130647, rend_intergenic: 126445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138665, rend_intergenic: 132418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158896, rend_intergenic: 152669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161343, rend_intergenic: 160076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170895
-exon list size: 662


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 14196, rend_intergenic: 2637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62599, rend_intergenic: 25155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68111, rend_intergenic: 67592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70624, rend_intergenic: 68186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75319, rend_intergenic: 71696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83822, rend_intergenic: 76694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84656, rend_intergenic: 84139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87867, rend_intergenic: 85626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104084, rend_intergenic: 96996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109347, rend_intergenic: 107410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122277, rend_intergenic: 116273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130647, rend_intergenic: 126445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138665, rend_intergenic: 132418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158896, rend_intergenic: 152669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161343, rend_intergenic: 160076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support