-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_1639550-1872590

-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_15-snap.370-T1
Valid prediction for CodingQuarry_transcript_17871-T1
Valid prediction for snap_scaffold_15-snap.350-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.62606_t
Valid prediction for GeneMark_model.62605_t
Valid prediction for GeneMark_model.62586_t
Valid prediction for GeneMark_model.62623_t
Valid prediction for GlimmerHMM_glimmerT_36401-T1
Valid prediction for GeneMark_model.62594_t
Valid prediction for snap_scaffold_15-snap.346-T1
Valid prediction for GeneMark_model.62597_t
Valid prediction for snap_scaffold_15-snap.382-T1
Valid prediction for GeneMark_model.62600_t
Valid prediction for snap_scaffold_15-snap.368-T1
Valid prediction for GlimmerHMM_glimmerT_36395-T1
Valid prediction for GlimmerHMM_glimmerT_36391-T1
Valid prediction for Augustus_model.g24475.t1
Valid prediction for pasa_asmbl_13974.p1
Valid prediction for GeneMark_model.62621_t
Valid prediction for CodingQuarry_transcript_17872-T1
Valid prediction for snap_scaffold_15-snap.381-T1
Valid prediction for snap_scaffold_15-snap.373-T1
Valid prediction for Augustus_model.g24467.t1
Valid prediction for snap_scaffold_15-snap.384-T1
Valid prediction for snap_scaffold_15-snap.360-T1
Valid prediction for GeneMark_model.62612_t
Valid prediction for snap_scaffold_15-snap.351-T1
Valid prediction for GlimmerHMM_glimmerT_36405-T1
Valid prediction for snap_scaffold_15-snap.372-T1
Valid prediction for GeneMark_model.62611_t
Valid prediction for Augustus_model.g24470.t1
Valid prediction for GeneMark_model.62619_t
Valid prediction for Augustus_model.g24476.t1
Valid prediction for HiQ_model.g24462.t1
Valid prediction for GeneMark_model.62607_t
Valid prediction for GeneMark_model.62615_t
Valid prediction for GlimmerHMM_glimmerT_36404-T1
Valid prediction for GeneMark_model.62588_t
Valid prediction for snap_scaffold_15-snap.377-T1
Valid prediction for GlimmerHMM_glimmerT_36394-T1
Valid prediction for snap_scaffold_15-snap.358-T1
Valid prediction for GeneMark_model.62601_t
Valid prediction for Augustus_model.g24465.t1
Valid prediction for GeneMark_model.62609_t
Valid prediction for snap_scaffold_15-snap.379-T1
Valid prediction for snap_scaffold_15-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_36393-T1
Valid prediction for snap_scaffold_15-snap.362-T1
Valid prediction for GlimmerHMM_glimmerT_36412-T1
Valid prediction for snap_scaffold_15-snap.385-T1
Couldn't classify 48438, 48515
Sorry, prediction pasa_asmbl_14848.p1 fails validation.
(GAA)	 AG	48438-48515	GT	GGG
(GCG)	 AG	48627-48890	TT	AAT
-recovered pasa_asmbl_14848.p1, terminal, 48627, 48890
-recovered pasa_asmbl_14848.p1, internal, 48438, 48515
Valid prediction for HiQ_model.g24461.t1
Valid prediction for GeneMark_model.62602_t
Valid prediction for GeneMark_model.62592_t
Valid prediction for snap_scaffold_15-snap.366-T1
Valid prediction for snap_scaffold_15-snap.371-T1
Valid prediction for GeneMark_model.62596_t
Valid prediction for GeneMark_model.62603_t
Valid prediction for GlimmerHMM_glimmerT_36408-T1
Valid prediction for GlimmerHMM_glimmerT_36413-T1
Valid prediction for GeneMark_model.62585_t
Valid prediction for pasa_asmbl_13969.p1
Valid prediction for GeneMark_model.62616_t
Valid prediction for CodingQuarry_transcript_17873-T1
Valid prediction for GlimmerHMM_glimmerT_36402-T1
Valid prediction for snap_scaffold_15-snap.353-T1
Valid prediction for GlimmerHMM_glimmerT_36396-T1
Valid prediction for snap_scaffold_15-snap.348-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 GlimmerHMM_glimmerT_36410-T1
Valid prediction for snap_scaffold_15-snap.383-T1
Valid prediction for CodingQuarry_transcript_17874-T1
Valid prediction for GeneMark_model.62617_t
Valid prediction for GlimmerHMM_glimmerT_36399-T1
Couldn't classify 156310, 156346
Sorry, prediction pasa_asmbl_14981.p1 fails validation.
(GGG)	 CA	156310-156346	GT	AGG
(ATC)	 AG	156638-156792	GT	TGG
(GTA)	 AG	156893-157001	GT	TGG
(GTT)	 AG	157395-157544	GT	AGG
(GTT)	 AG	157780-157980	GT	CGG
(GTG)	 AG	158222-158382	CG	AAC
-recovered pasa_asmbl_14981.p1, terminal, 158222, 158382
-recovered pasa_asmbl_14981.p1, internal, 156638, 156792
-recovered pasa_asmbl_14981.p1, internal, 156893, 157001
-recovered pasa_asmbl_14981.p1, internal, 157395, 157544
-recovered pasa_asmbl_14981.p1, internal, 157780, 157980
Valid prediction for GlimmerHMM_glimmerT_36397-T1
Valid prediction for snap_scaffold_15-snap.352-T1
Valid prediction for snap_scaffold_15-snap.380-T1
Valid prediction for GlimmerHMM_glimmerT_36403-T1
Valid prediction for GeneMark_model.62622_t
Valid prediction for Augustus_model.g24468.t1
Valid prediction for snap_scaffold_15-snap.369-T1
Valid prediction for Augustus_model.g24464.t1
Valid prediction for snap_scaffold_15-snap.374-T1
Valid prediction for Augustus_model.g24472.t1
Valid prediction for snap_scaffold_15-snap.375-T1
Valid prediction for snap_scaffold_15-snap.345-T1
Valid prediction for GeneMark_model.62598_t
Valid prediction for snap_scaffold_15-snap.347-T1
Valid prediction for snap_scaffold_15-snap.354-T1
Valid prediction for snap_scaffold_15-snap.376-T1
Valid prediction for GlimmerHMM_glimmerT_36406-T1
Valid prediction for GeneMark_model.62589_t
Valid prediction for GeneMark_model.62599_t
Valid prediction for GeneMark_model.62595_t
Valid prediction for GeneMark_model.62590_t
Valid prediction for GlimmerHMM_glimmerT_36414-T1
Valid prediction for GeneMark_model.62587_t
Valid prediction for GeneMark_model.62620_t
Valid prediction for GlimmerHMM_glimmerT_36411-T1
Valid prediction for GeneMark_model.62613_t
Valid prediction for GlimmerHMM_glimmerT_36390-T1
Valid prediction for Augustus_model.g24471.t1
Valid prediction for GeneMark_model.62618_t
Valid prediction for snap_scaffold_15-snap.361-T1
Valid prediction for snap_scaffold_15-snap.367-T1
Valid prediction for GlimmerHMM_glimmerT_36398-T1
Valid prediction for snap_scaffold_15-snap.357-T1
Valid prediction for snap_scaffold_15-snap.356-T1
Valid prediction for GlimmerHMM_glimmerT_36409-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g24463.t1
Valid prediction for GeneMark_model.62593_t
Valid prediction for GlimmerHMM_glimmerT_36407-T1
Valid prediction for snap_scaffold_15-snap.378-T1
Valid prediction for Augustus_model.g24469.t1
Valid prediction for GeneMark_model.62610_t
Valid prediction for snap_scaffold_15-snap.349-T1
Valid prediction for snap_scaffold_15-snap.359-T1
Valid prediction for snap_scaffold_15-snap.355-T1
Valid prediction for Augustus_model.g24460.t1
Valid prediction for Augustus_model.g24473.t1
Valid prediction for GeneMark_model.62608_t
Valid prediction for snap_scaffold_15-snap.363-T1
Valid prediction for GlimmerHMM_glimmerT_36392-T1
Valid prediction for GeneMark_model.62591_t
Valid prediction for Augustus_model.g24474.t1
Valid prediction for GlimmerHMM_glimmerT_36400-T1
Valid prediction for snap_scaffold_15-snap.364-T1
Valid prediction for GeneMark_model.62614_t
Valid prediction for Augustus_model.g24466.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32137, rend_intergenic: 30034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68859, rend_intergenic: 62768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101295, rend_intergenic: 98842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108035, rend_intergenic: 107359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151022, rend_intergenic: 146152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179037, rend_intergenic: 167236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186503, rend_intergenic: 185128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201915, rend_intergenic: 193949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218896, rend_intergenic: 218263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226735, rend_intergenic: 219300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233041
-exon list size: 651


building trellis

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98.6    
98.8    
98.9    
99.1    
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99.4    
99.5    
99.7    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 32137, rend_intergenic: 30034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68859, rend_intergenic: 62768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101295, rend_intergenic: 98842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108035, rend_intergenic: 107359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151022, rend_intergenic: 146152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179037, rend_intergenic: 167236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186503, rend_intergenic: 185128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201915, rend_intergenic: 193949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218896, rend_intergenic: 218263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226735, rend_intergenic: 219300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support