-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_8162076-8309440

-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_24-snap.1708-T1
Valid prediction for snap_scaffold_24-snap.1694-T1
Valid prediction for GeneMark_model.94544_t
Valid prediction for GeneMark_model.94562_t
Valid prediction for snap_scaffold_24-snap.1715-T1
Valid prediction for GlimmerHMM_glimmerT_54244-T1
Valid prediction for GeneMark_model.94551_t
Valid prediction for GlimmerHMM_glimmerT_54248-T1
Valid prediction for Augustus_model.g36323.t1
Valid prediction for Augustus_model.g36314.t1
Valid prediction for snap_scaffold_24-snap.1713-T1
Valid prediction for GeneMark_model.94563_t
Valid prediction for GeneMark_model.94564_t
Valid prediction for snap_scaffold_24-snap.1714-T1
Valid prediction for Augustus_model.g36317.t1
Valid prediction for snap_scaffold_24-snap.1697-T1
Valid prediction for GlimmerHMM_glimmerT_54262-T1
Valid prediction for Augustus_model.g36322.t1
Valid prediction for snap_scaffold_24-snap.1704-T1
Valid prediction for GeneMark_model.94559_t
Valid prediction for Augustus_model.g36316.t1
Valid prediction for GeneMark_model.94578_t
Valid prediction for Augustus_model.g36315.t1
Valid prediction for GeneMark_model.94565_t
Valid prediction for snap_scaffold_24-snap.1701-T1
Valid prediction for GeneMark_model.94572_t
Valid prediction for snap_scaffold_24-snap.1720-T1
Valid prediction for GlimmerHMM_glimmerT_54255-T1
Valid prediction for Augustus_model.g36324.t1
Valid prediction for snap_scaffold_24-snap.1696-T1
Valid prediction for snap_scaffold_24-snap.1693-T1
Valid prediction for GeneMark_model.94574_t
Valid prediction for Augustus_model.g36328.t1
Valid prediction for Augustus_model.g36318.t1
Valid prediction for GeneMark_model.94550_t
Valid prediction for GeneMark_model.94569_t
Valid prediction for GlimmerHMM_glimmerT_54258-T1
Valid prediction for GeneMark_model.94567_t
Valid prediction for snap_scaffold_24-snap.1699-T1
Valid prediction for snap_scaffold_24-snap.1710-T1
Valid prediction for GeneMark_model.94548_t
Valid prediction for GlimmerHMM_glimmerT_54251-T1
Valid prediction for GeneMark_model.94561_t
Valid prediction for GeneMark_model.94575_t
Valid prediction for Augustus_model.g36326.t1
Valid prediction for GlimmerHMM_glimmerT_54247-T1
Valid prediction for GeneMark_model.94555_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 Augustus_model.g36313.t1
Valid prediction for snap_scaffold_24-snap.1692-T1
Valid prediction for GlimmerHMM_glimmerT_54253-T1
Valid prediction for snap_scaffold_24-snap.1695-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.1703-T1
Valid prediction for GeneMark_model.94556_t
Valid prediction for GeneMark_model.94571_t
Valid prediction for GeneMark_model.94558_t
Valid prediction for snap_scaffold_24-snap.1702-T1
Valid prediction for GlimmerHMM_glimmerT_54261-T1
Valid prediction for snap_scaffold_24-snap.1706-T1
Valid prediction for GeneMark_model.94570_t
Valid prediction for GlimmerHMM_glimmerT_54259-T1
Valid prediction for GeneMark_model.94577_t
Valid prediction for GeneMark_model.94543_t
Valid prediction for GlimmerHMM_glimmerT_54250-T1
Valid prediction for GlimmerHMM_glimmerT_54246-T1
Valid prediction for GeneMark_model.94568_t
Valid prediction for GlimmerHMM_glimmerT_54256-T1
Valid prediction for CodingQuarry_transcript_37302-T1
Valid prediction for GlimmerHMM_glimmerT_54245-T1
Valid prediction for Augustus_model.g36325.t1
Valid prediction for GlimmerHMM_glimmerT_54266-T1
Valid prediction for snap_scaffold_24-snap.1707-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_54263-T1
Valid prediction for GeneMark_model.94560_t
Valid prediction for GeneMark_model.94554_t
Valid prediction for snap_scaffold_24-snap.1705-T1
Valid prediction for GeneMark_model.94573_t
Valid prediction for snap_scaffold_24-snap.1700-T1
Valid prediction for Augustus_model.g36319.t1
Valid prediction for GeneMark_model.94552_t
Valid prediction for GlimmerHMM_glimmerT_54249-T1
Valid prediction for GeneMark_model.94566_t
Valid prediction for GeneMark_model.94546_t
Valid prediction for GlimmerHMM_glimmerT_54257-T1
Valid prediction for snap_scaffold_24-snap.1719-T1
Valid prediction for Augustus_model.g36320.t1
Valid prediction for snap_scaffold_24-snap.1712-T1
Valid prediction for snap_scaffold_24-snap.1717-T1
Valid prediction for snap_scaffold_24-snap.1698-T1
Valid prediction for GlimmerHMM_glimmerT_54260-T1
Valid prediction for snap_scaffold_24-snap.1711-T1
Couldn't classify 89642, 89656
Sorry, prediction pasa_asmbl_33071.p1 fails validation.
(GGA)	 CA	89642-89656	GT	AGG
(GCA)	 AG	89856-89974	GT	CTG
(GTT)	 AG	90132-90217	GT	CGG
(GTC)	 AG	90302-90510	GG	GAG
-recovered pasa_asmbl_33071.p1, terminal, 90302, 90510
-recovered pasa_asmbl_33071.p1, internal, 89856, 89974
-recovered pasa_asmbl_33071.p1, internal, 90132, 90217
Valid prediction for Augustus_model.g36327.t1
Valid prediction for snap_scaffold_24-snap.1716-T1
Valid prediction for GeneMark_model.94545_t
Valid prediction for GeneMark_model.94553_t
Valid prediction for Augustus_model.g36321.t1
Valid prediction for GeneMark_model.94549_t
Valid prediction for GeneMark_model.94576_t
Valid prediction for GlimmerHMM_glimmerT_54252-T1
Valid prediction for GlimmerHMM_glimmerT_54264-T1
Valid prediction for snap_scaffold_24-snap.1709-T1
Valid prediction for GlimmerHMM_glimmerT_54254-T1
Valid prediction for GeneMark_model.94547_t
Valid prediction for snap_scaffold_24-snap.1718-T1
Couldn't classify 87558, 87686
Couldn't classify 88812, 88867
Sorry, prediction pasa_asmbl_33072.p1 fails validation.
(CTG)	 GA	87558-87686	GT	AGG
(GTG)	 AG	88249-88321	GT	AGG
(GAG)	 AG	88436-88585	GT	AGG
(GGA)	 AG	88812-88867	CC	ACC
-recovered pasa_asmbl_33072.p1, internal, 88249, 88321
-recovered pasa_asmbl_33072.p1, internal, 88436, 88585
Valid prediction for GlimmerHMM_glimmerT_54265-T1
Valid prediction for GeneMark_model.94557_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 43818, rend_intergenic: 38217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54484, rend_intergenic: 51934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65707, rend_intergenic: 62697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73040, rend_intergenic: 69376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73778, rend_intergenic: 73408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132667, rend_intergenic: 129786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 147365
-exon list size: 462


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 43818, rend_intergenic: 38217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54484, rend_intergenic: 51934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65707, rend_intergenic: 62697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73040, rend_intergenic: 69376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73778, rend_intergenic: 73408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132667, rend_intergenic: 129786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 134490 - 147365
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 134675 - 147365
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support