-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_2065329-2209287

-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 GlimmerHMM_glimmerT_31877-T1
Valid prediction for snap_scaffold_13-snap.417-T1
Valid prediction for snap_scaffold_13-snap.394-T1
Valid prediction for GlimmerHMM_glimmerT_31859-T1
Valid prediction for GeneMark_model.54744_t
Valid prediction for GeneMark_model.54734_t
Valid prediction for GeneMark_model.54748_t
Valid prediction for snap_scaffold_13-snap.402-T1
Valid prediction for GlimmerHMM_glimmerT_31881-T1
Valid prediction for Augustus_model.g21315.t1
Valid prediction for GlimmerHMM_glimmerT_31856-T1
Valid prediction for snap_scaffold_13-snap.392-T1
Valid prediction for Augustus_model.g21310.t1
Valid prediction for Augustus_model.g21309.t1
Valid prediction for GeneMark_model.54738_t
Valid prediction for GlimmerHMM_glimmerT_31864-T1
Valid prediction for snap_scaffold_13-snap.420-T1
Valid prediction for GeneMark_model.54752_t
Valid prediction for GlimmerHMM_glimmerT_31866-T1
Valid prediction for HiQ_model.g21308.t1
Valid prediction for GlimmerHMM_glimmerT_31855-T1
Valid prediction for GlimmerHMM_glimmerT_31876-T1
Valid prediction for GlimmerHMM_glimmerT_31867-T1
Valid prediction for snap_scaffold_13-snap.423-T1
Valid prediction for GeneMark_model.54758_t
Valid prediction for GeneMark_model.54743_t
Valid prediction for snap_scaffold_13-snap.412-T1
Valid prediction for snap_scaffold_13-snap.405-T1
Valid prediction for snap_scaffold_13-snap.415-T1
Valid prediction for snap_scaffold_13-snap.407-T1
Valid prediction for Augustus_model.g21314.t1
Valid prediction for GlimmerHMM_glimmerT_31879-T1
Valid prediction for snap_scaffold_13-snap.399-T1
Valid prediction for GeneMark_model.54761_t
Valid prediction for GeneMark_model.54755_t
Valid prediction for snap_scaffold_13-snap.398-T1
Valid prediction for GlimmerHMM_glimmerT_31872-T1
Valid prediction for GeneMark_model.54749_t
Valid prediction for GlimmerHMM_glimmerT_31873-T1
Valid prediction for GeneMark_model.54763_t
Valid prediction for GlimmerHMM_glimmerT_31880-T1
Valid prediction for snap_scaffold_13-snap.409-T1
Valid prediction for GeneMark_model.54736_t
Valid prediction for snap_scaffold_13-snap.408-T1
Valid prediction for snap_scaffold_13-snap.421-T1
Valid prediction for snap_scaffold_13-snap.410-T1
Valid prediction for Augustus_model.g21313.t1
Valid prediction for snap_scaffold_13-snap.401-T1
Valid prediction for GeneMark_model.54742_t
Valid prediction for snap_scaffold_13-snap.403-T1
Valid prediction for snap_scaffold_13-snap.393-T1
Valid prediction for GeneMark_model.54751_t
Valid prediction for GlimmerHMM_glimmerT_31857-T1
Valid prediction for GlimmerHMM_glimmerT_31869-T1
Valid prediction for GlimmerHMM_glimmerT_31865-T1
Valid prediction for GlimmerHMM_glimmerT_31863-T1
Couldn't classify 2944, 3057
Sorry, prediction pasa_asmbl_10547.p1 fails validation.
(CAG)	 CT	2944-3057	GT	AGG
(GTC)	 AG	3735-3768	GT	AGG
(ACG)	 AG	3972-4054	GT	AGG
(GAA)	 AG	5481-5530	GT	CTG
(GGC)	 AG	6563-6637	GT	TGG
(TCT)	 AG	7005-7176	GT	AGG
(TTT)	 AG	7894-8040	GA	GAG
-recovered pasa_asmbl_10547.p1, terminal, 7894, 8040
-recovered pasa_asmbl_10547.p1, internal, 3735, 3768
-recovered pasa_asmbl_10547.p1, internal, 3972, 4054
-recovered pasa_asmbl_10547.p1, internal, 5481, 5530
-recovered pasa_asmbl_10547.p1, internal, 6563, 6637
-recovered pasa_asmbl_10547.p1, internal, 7005, 7176
Valid prediction for snap_scaffold_13-snap.419-T1
Valid prediction for GlimmerHMM_glimmerT_31875-T1
Valid prediction for GlimmerHMM_glimmerT_31858-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 Augustus_model.g21316.t1
Valid prediction for GeneMark_model.54740_t
Valid prediction for snap_scaffold_13-snap.413-T1
Valid prediction for GlimmerHMM_glimmerT_31871-T1
Valid prediction for GeneMark_model.54764_t
Valid prediction for GeneMark_model.54735_t
Valid prediction for GeneMark_model.54739_t
Valid prediction for GeneMark_model.54756_t
Valid prediction for GeneMark_model.54754_t
Valid prediction for snap_scaffold_13-snap.395-T1
Valid prediction for GlimmerHMM_glimmerT_31878-T1
Valid prediction for GeneMark_model.54750_t
Valid prediction for GeneMark_model.54746_t
Valid prediction for snap_scaffold_13-snap.406-T1
Valid prediction for snap_scaffold_13-snap.411-T1
Valid prediction for GeneMark_model.54757_t
Valid prediction for Augustus_model.g21311.t1
Valid prediction for GeneMark_model.54745_t
Valid prediction for GeneMark_model.54760_t
Valid prediction for GeneMark_model.54741_t
Valid prediction for GeneMark_model.54753_t
Valid prediction for GlimmerHMM_glimmerT_31861-T1
Valid prediction for snap_scaffold_13-snap.396-T1
Valid prediction for GlimmerHMM_glimmerT_31868-T1
Valid prediction for GlimmerHMM_glimmerT_31874-T1
Valid prediction for GlimmerHMM_glimmerT_31860-T1
Valid prediction for snap_scaffold_13-snap.422-T1
Valid prediction for Augustus_model.g21312.t1
Valid prediction for GlimmerHMM_glimmerT_31862-T1
Valid prediction for Augustus_model.g21317.t1
Valid prediction for GlimmerHMM_glimmerT_31870-T1
Valid prediction for snap_scaffold_13-snap.414-T1
Valid prediction for snap_scaffold_13-snap.404-T1
Valid prediction for GeneMark_model.54747_t
Valid prediction for snap_scaffold_13-snap.400-T1
Valid prediction for snap_scaffold_13-snap.416-T1
Valid prediction for GeneMark_model.54737_t
Valid prediction for snap_scaffold_13-snap.397-T1
Valid prediction for Augustus_model.g21318.t1
Valid prediction for snap_scaffold_13-snap.418-T1
Valid prediction for Augustus_model.g21319.t1
Valid prediction for GeneMark_model.54759_t
Valid prediction for GeneMark_model.54762_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 72289, rend_intergenic: 68057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77936, rend_intergenic: 72308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99773, rend_intergenic: 99429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109049, rend_intergenic: 101837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122568, rend_intergenic: 119368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140067, rend_intergenic: 136532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 143959
-exon list size: 429


building trellis

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99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 72289, rend_intergenic: 68057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77936, rend_intergenic: 72308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99773, rend_intergenic: 99429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109049, rend_intergenic: 101837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122568, rend_intergenic: 119368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140067, rend_intergenic: 136532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support