-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_18832111-19055775

-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_2-snap.3708-T1
Valid prediction for GlimmerHMM_glimmerT_5591-T1
Valid prediction for snap_scaffold_2-snap.3714-T1
Valid prediction for snap_scaffold_2-snap.3716-T1
Valid prediction for snap_scaffold_2-snap.3718-T1
Valid prediction for snap_scaffold_2-snap.3712-T1
Valid prediction for Augustus_model.g3759.t1
Valid prediction for GlimmerHMM_glimmerT_5607-T1
Valid prediction for GlimmerHMM_glimmerT_5588-T1
Valid prediction for GlimmerHMM_glimmerT_5601-T1
Valid prediction for snap_scaffold_2-snap.3694-T1
Valid prediction for snap_scaffold_2-snap.3686-T1
Valid prediction for GlimmerHMM_glimmerT_5605-T1
Valid prediction for GlimmerHMM_glimmerT_5618-T1
Valid prediction for GlimmerHMM_glimmerT_5597-T1
Valid prediction for snap_scaffold_2-snap.3679-T1
Valid prediction for snap_scaffold_2-snap.3703-T1
Valid prediction for GlimmerHMM_glimmerT_5608-T1
Valid prediction for GlimmerHMM_glimmerT_5613-T1
Valid prediction for pasa_asmbl_25253.p1
Valid prediction for Augustus_model.g3750.t1
Valid prediction for snap_scaffold_2-snap.3717-T1
Valid prediction for snap_scaffold_2-snap.3719-T1
Valid prediction for Augustus_model.g3749.t1
Valid prediction for GlimmerHMM_glimmerT_5599-T1
Valid prediction for snap_scaffold_2-snap.3690-T1
Valid prediction for snap_scaffold_2-snap.3696-T1
Valid prediction for snap_scaffold_2-snap.3684-T1
Valid prediction for snap_scaffold_2-snap.3677-T1
Couldn't classify 131863, 132414
Sorry, prediction pasa_asmbl_25258.p1 fails validation.
(GAT)	 TG	131863-132414	AT	GAA
Valid prediction for GlimmerHMM_glimmerT_5615-T1
Valid prediction for GlimmerHMM_glimmerT_5596-T1
Valid prediction for snap_scaffold_2-snap.3692-T1
Valid prediction for GlimmerHMM_glimmerT_5594-T1
Valid prediction for snap_scaffold_2-snap.3702-T1
Valid prediction for snap_scaffold_2-snap.3697-T1
Valid prediction for snap_scaffold_2-snap.3706-T1
Valid prediction for GlimmerHMM_glimmerT_5606-T1
Valid prediction for CodingQuarry_transcript_28854-T1
Valid prediction for Augustus_model.g3753.t1
Valid prediction for GlimmerHMM_glimmerT_5598-T1
Valid prediction for CodingQuarry_transcript_28853-T1
Valid prediction for snap_scaffold_2-snap.3682-T1
Valid prediction for HiQ_model.g3756.t1
Valid prediction for Augustus_model.g3752.t1
Valid prediction for GlimmerHMM_glimmerT_5589-T1
Valid prediction for Augustus_model.g3757.t1
Valid prediction for snap_scaffold_2-snap.3689-T1
Valid prediction for snap_scaffold_2-snap.3715-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_2-snap.3699-T1
Valid prediction for snap_scaffold_2-snap.3713-T1
Valid prediction for GlimmerHMM_glimmerT_5593-T1
Valid prediction for snap_scaffold_2-snap.3680-T1
Valid prediction for snap_scaffold_2-snap.3707-T1
Valid prediction for snap_scaffold_2-snap.3688-T1
Valid prediction for snap_scaffold_2-snap.3720-T1
Valid prediction for GlimmerHMM_glimmerT_5610-T1
Valid prediction for snap_scaffold_2-snap.3701-T1
Valid prediction for CodingQuarry_transcript_28858-T1
Valid prediction for snap_scaffold_2-snap.3685-T1
Valid prediction for snap_scaffold_2-snap.3705-T1
Valid prediction for HiQ_model.g3754.t1
Valid prediction for snap_scaffold_2-snap.3693-T1
Valid prediction for snap_scaffold_2-snap.3700-T1
Valid prediction for snap_scaffold_2-snap.3698-T1
Valid prediction for CodingQuarry_transcript_28856-T1
Valid prediction for CodingQuarry_transcript_28851-T1
Valid prediction for pasa_asmbl_23847.p2
Valid prediction for GlimmerHMM_glimmerT_5604-T1
Valid prediction for GlimmerHMM_glimmerT_5616-T1
Valid prediction for Augustus_model.g3760.t1
Valid prediction for snap_scaffold_2-snap.3681-T1
Valid prediction for Augustus_model.g3755.t1
Valid prediction for snap_scaffold_2-snap.3710-T1
Valid prediction for GlimmerHMM_glimmerT_5617-T1
Valid prediction for GlimmerHMM_glimmerT_5614-T1
Valid prediction for snap_scaffold_2-snap.3683-T1
Valid prediction for HiQ_model.g3758.t1
Valid prediction for CodingQuarry_transcript_28852-T1
Valid prediction for GlimmerHMM_glimmerT_5609-T1
Couldn't classify 25962, 26049
Couldn't classify 27185, 27465
Sorry, prediction pasa_asmbl_23848.p1 fails validation.
(TTA)	 GG	25962-26049	GT	GTG
(TTC)	 AG	26137-26406	GT	ACG
(GTC)	 AG	26629-26898	GT	AAG
(AAG)	 AG	27185-27465	AT	GCA
-recovered pasa_asmbl_23848.p1, internal, 26137, 26406
-recovered pasa_asmbl_23848.p1, internal, 26629, 26898
Valid prediction for GlimmerHMM_glimmerT_5602-T1
Valid prediction for pasa_asmbl_23835.p1
Valid prediction for GlimmerHMM_glimmerT_5600-T1
Valid prediction for pasa_asmbl_23843.p1
Valid prediction for GlimmerHMM_glimmerT_5595-T1
Valid prediction for snap_scaffold_2-snap.3695-T1
Valid prediction for CodingQuarry_transcript_28857-T1
Valid prediction for snap_scaffold_2-snap.3687-T1
Valid prediction for Augustus_model.g3751.t1
Valid prediction for snap_scaffold_2-snap.3691-T1
Valid prediction for snap_scaffold_2-snap.3678-T1
Valid prediction for snap_scaffold_2-snap.3722-T1
Valid prediction for GlimmerHMM_glimmerT_5611-T1
Valid prediction for snap_scaffold_2-snap.3721-T1
Valid prediction for GlimmerHMM_glimmerT_5592-T1
Valid prediction for GlimmerHMM_glimmerT_5590-T1
Valid prediction for snap_scaffold_2-snap.3704-T1
Couldn't classify 25268, 25374
Sorry, prediction pasa_asmbl_23849.p1 fails validation.
(ATG)	 TG	24547-24721	GT	CAG
(AGC)	 AG	24823-25086	GT	ACG
(AAC)	 AG	25268-25374	GC	TCG
-recovered pasa_asmbl_23849.p1, initial, 24547, 24721
-recovered pasa_asmbl_23849.p1, internal, 24823, 25086
-recovered pasa_asmbl_23849.p1, internal, 25268, 25374
Valid prediction for snap_scaffold_2-snap.3711-T1
Valid prediction for GlimmerHMM_glimmerT_5612-T1
Valid prediction for GlimmerHMM_glimmerT_5603-T1
Couldn't classify 145444, 145890
Sorry, prediction pasa_asmbl_23832.p1 fails validation.
(CAT)	 CC	145444-145890	AC	AGA
Valid prediction for snap_scaffold_2-snap.3709-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6845, rend_intergenic: 5842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11644, rend_intergenic: 6884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13953, rend_intergenic: 12062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20815, rend_intergenic: 18686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21959, rend_intergenic: 21110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26926, rend_intergenic: 22126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30626, rend_intergenic: 28248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32532, rend_intergenic: 30932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35477, rend_intergenic: 32881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43186, rend_intergenic: 35950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43952, rend_intergenic: 43779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49170, rend_intergenic: 46662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56209, rend_intergenic: 49174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60536, rend_intergenic: 58431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72728, rend_intergenic: 61148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78510, rend_intergenic: 75333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96436, rend_intergenic: 88826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106251, rend_intergenic: 101390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109920, rend_intergenic: 106297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120274, rend_intergenic: 115414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179583, rend_intergenic: 134555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 223665
-exon list size: 371


building trellis

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33.5    
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34.6    
34.9    
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37.3    
37.5    
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42.4    
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90.6    
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97.6    
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98.1    
98.4    
98.7    
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99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 6845, rend_intergenic: 5842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11644, rend_intergenic: 6884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13953, rend_intergenic: 12062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20815, rend_intergenic: 18686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21959, rend_intergenic: 21110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26926, rend_intergenic: 22126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30626, rend_intergenic: 28248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32532, rend_intergenic: 30932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35477, rend_intergenic: 32881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43186, rend_intergenic: 35950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43952, rend_intergenic: 43779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49170, rend_intergenic: 46662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56209, rend_intergenic: 49174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60536, rend_intergenic: 58431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72728, rend_intergenic: 61148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78510, rend_intergenic: 75333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96436, rend_intergenic: 88826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106251, rend_intergenic: 101390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109920, rend_intergenic: 106297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120274, rend_intergenic: 115414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179583, rend_intergenic: 134555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support