-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_15536421-15691076

-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_8-snap.2837-T1
Valid prediction for Augustus_model.g14347.t1
Valid prediction for snap_scaffold_8-snap.2852-T1
Valid prediction for Augustus_model.g14354.t1
Valid prediction for GeneMark_model.36589_t
Valid prediction for GeneMark_model.36606_t
Valid prediction for Augustus_model.g14352.t1
Valid prediction for GeneMark_model.36607_t
Valid prediction for GlimmerHMM_glimmerT_21445-T1
Valid prediction for snap_scaffold_8-snap.2862-T1
Valid prediction for snap_scaffold_8-snap.2835-T1
Valid prediction for GeneMark_model.36609_t
Valid prediction for GeneMark_model.36602_t
Valid prediction for GeneMark_model.36593_t
Valid prediction for snap_scaffold_8-snap.2863-T1
Valid prediction for Augustus_model.g14349.t1
Valid prediction for snap_scaffold_8-snap.2834-T1
Valid prediction for GeneMark_model.36577_t
Couldn't classify 37127, 37253
Sorry, prediction pasa_asmbl_52402.p2 fails validation.
(AGG)	 GC	37127-37253	GT	GGG
(GCT)	 AG	38771-38926	GC	CGG
(GCA)	 AG	40163-40221	CC	AAC
-recovered pasa_asmbl_52402.p2, terminal, 40163, 40221
-recovered pasa_asmbl_52402.p2, internal, 38771, 38926
Valid prediction for snap_scaffold_8-snap.2849-T1
Valid prediction for GeneMark_model.36584_t
Valid prediction for GeneMark_model.36582_t
Valid prediction for GeneMark_model.36600_t
Valid prediction for GlimmerHMM_glimmerT_21426-T1
Valid prediction for GlimmerHMM_glimmerT_21434-T1
Valid prediction for GeneMark_model.36594_t
Valid prediction for snap_scaffold_8-snap.2838-T1
Valid prediction for snap_scaffold_8-snap.2846-T1
Valid prediction for GeneMark_model.36604_t
Valid prediction for snap_scaffold_8-snap.2858-T1
Valid prediction for GeneMark_model.36586_t
Valid prediction for snap_scaffold_8-snap.2847-T1
Valid prediction for GeneMark_model.36580_t
Valid prediction for GeneMark_model.36610_t
Valid prediction for GlimmerHMM_glimmerT_21443-T1
Valid prediction for Augustus_model.g14350.t1
Valid prediction for GeneMark_model.36575_t
Valid prediction for snap_scaffold_8-snap.2841-T1
Valid prediction for GlimmerHMM_glimmerT_21447-T1
Valid prediction for GeneMark_model.36590_t
Valid prediction for GeneMark_model.36613_t
Valid prediction for GeneMark_model.36611_t
Valid prediction for snap_scaffold_8-snap.2842-T1
Valid prediction for GeneMark_model.36595_t
Valid prediction for GlimmerHMM_glimmerT_21444-T1
Valid prediction for snap_scaffold_8-snap.2856-T1
Valid prediction for GeneMark_model.36588_t
Valid prediction for GlimmerHMM_glimmerT_21430-T1
Valid prediction for snap_scaffold_8-snap.2854-T1
Valid prediction for snap_scaffold_8-snap.2831-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_21448-T1
Valid prediction for GlimmerHMM_glimmerT_21428-T1
Valid prediction for Augustus_model.g14355.t1
Valid prediction for snap_scaffold_8-snap.2859-T1
Valid prediction for GlimmerHMM_glimmerT_21432-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 GeneMark_model.36585_t
Valid prediction for snap_scaffold_8-snap.2832-T1
Valid prediction for snap_scaffold_8-snap.2851-T1
Valid prediction for GlimmerHMM_glimmerT_21431-T1
Valid prediction for GlimmerHMM_glimmerT_21438-T1
Valid prediction for GeneMark_model.36605_t
Valid prediction for GeneMark_model.36598_t
Valid prediction for snap_scaffold_8-snap.2833-T1
Couldn't classify 3125, 3190
Sorry, prediction pasa_asmbl_53343.p1 fails validation.
(CAA)	 CA	3125-3190	GT	TGG
(GGC)	 AG	3922-4013	GT	AGG
(AAC)	 AG	4826-4991	CT	AAC
-recovered pasa_asmbl_53343.p1, terminal, 4826, 4991
-recovered pasa_asmbl_53343.p1, internal, 3922, 4013
Valid prediction for GlimmerHMM_glimmerT_21435-T1
Valid prediction for GeneMark_model.36612_t
Valid prediction for GlimmerHMM_glimmerT_21441-T1
Valid prediction for GlimmerHMM_glimmerT_21451-T1
Valid prediction for GeneMark_model.36601_t
Valid prediction for Augustus_model.g14348.t1
Valid prediction for GlimmerHMM_glimmerT_21449-T1
Valid prediction for Augustus_model.g14353.t1
Valid prediction for Augustus_model.g14356.t1
Valid prediction for snap_scaffold_8-snap.2839-T1
Valid prediction for GlimmerHMM_glimmerT_21437-T1
Valid prediction for snap_scaffold_8-snap.2861-T1
Valid prediction for GlimmerHMM_glimmerT_21446-T1
Valid prediction for GeneMark_model.36579_t
Valid prediction for GeneMark_model.36608_t
Valid prediction for GeneMark_model.36583_t
Valid prediction for snap_scaffold_8-snap.2850-T1
Valid prediction for GeneMark_model.36591_t
Valid prediction for GeneMark_model.36578_t
Valid prediction for snap_scaffold_8-snap.2855-T1
Valid prediction for GeneMark_model.36576_t
Valid prediction for GeneMark_model.36581_t
Valid prediction for GeneMark_model.36592_t
Valid prediction for GlimmerHMM_glimmerT_21440-T1
Valid prediction for GeneMark_model.36597_t
Valid prediction for GeneMark_model.36587_t
Valid prediction for snap_scaffold_8-snap.2840-T1
Valid prediction for snap_scaffold_8-snap.2843-T1
Valid prediction for GlimmerHMM_glimmerT_21436-T1
Valid prediction for GeneMark_model.36603_t
Valid prediction for GlimmerHMM_glimmerT_21427-T1
Valid prediction for GeneMark_model.36599_t
Valid prediction for GlimmerHMM_glimmerT_21450-T1
Valid prediction for snap_scaffold_8-snap.2836-T1
Valid prediction for Augustus_model.g14351.t1
Valid prediction for snap_scaffold_8-snap.2860-T1
Valid prediction for GlimmerHMM_glimmerT_21439-T1
Valid prediction for snap_scaffold_8-snap.2844-T1
Valid prediction for GeneMark_model.36596_t
Valid prediction for snap_scaffold_8-snap.2864-T1
Valid prediction for snap_scaffold_8-snap.2857-T1
Valid prediction for snap_scaffold_8-snap.2848-T1
Valid prediction for CodingQuarry_transcript_59760-T1
Valid prediction for GlimmerHMM_glimmerT_21433-T1
Valid prediction for snap_scaffold_8-snap.2845-T1
Valid prediction for snap_scaffold_8-snap.2853-T1
Valid prediction for GlimmerHMM_glimmerT_21442-T1
Valid prediction for GlimmerHMM_glimmerT_21429-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11551, rend_intergenic: 1837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17090, rend_intergenic: 11562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20439, rend_intergenic: 17752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67893, rend_intergenic: 65345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108417, rend_intergenic: 103020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154656
-exon list size: 502


building trellis

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-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 11551, rend_intergenic: 1837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17090, rend_intergenic: 11562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20439, rend_intergenic: 17752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67893, rend_intergenic: 65345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108417, rend_intergenic: 103020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support