-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_13760663-13965418

-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_11-snap.2939-T1
Valid prediction for GlimmerHMM_glimmerT_28814-T1
Valid prediction for GeneMark_model.49730_t
Valid prediction for GeneMark_model.49727_t
Valid prediction for GlimmerHMM_glimmerT_28806-T1
Valid prediction for Augustus_model.g19240.t1
Valid prediction for GeneMark_model.49737_t
Valid prediction for snap_scaffold_11-snap.2954-T1
Valid prediction for GlimmerHMM_glimmerT_28807-T1
Valid prediction for GeneMark_model.49740_t
Valid prediction for GeneMark_model.49754_t
Valid prediction for GeneMark_model.49724_t
Valid prediction for GeneMark_model.49759_t
Valid prediction for GeneMark_model.49753_t
Valid prediction for GeneMark_model.49729_t
Valid prediction for snap_scaffold_11-snap.2942-T1
Valid prediction for GeneMark_model.49748_t
Valid prediction for Augustus_model.g19239.t1
Valid prediction for snap_scaffold_11-snap.2949-T1
Valid prediction for GlimmerHMM_glimmerT_28805-T1
Valid prediction for GeneMark_model.49751_t
Valid prediction for snap_scaffold_11-snap.2929-T1
Valid prediction for GeneMark_model.49760_t
Valid prediction for snap_scaffold_11-snap.2945-T1
Valid prediction for GlimmerHMM_glimmerT_28803-T1
Valid prediction for GlimmerHMM_glimmerT_28813-T1
Valid prediction for Augustus_model.g19242.t1
Valid prediction for GlimmerHMM_glimmerT_28809-T1
Valid prediction for GeneMark_model.49742_t
Valid prediction for snap_scaffold_11-snap.2953-T1
Valid prediction for snap_scaffold_11-snap.2943-T1
Valid prediction for GeneMark_model.49756_t
Couldn't classify 11442, 11580
Couldn't classify 12842, 12847
Sorry, prediction pasa_asmbl_6056.p1 fails validation.
(AGC)	 CC	11442-11580	GT	GAG
(AGT)	 AG	12026-12118	GT	AGG
(GAC)	 AG	12239-12387	GT	AGG
(GCA)	 AG	12842-12847	GA	AGG
-recovered pasa_asmbl_6056.p1, internal, 12026, 12118
-recovered pasa_asmbl_6056.p1, internal, 12239, 12387
Valid prediction for snap_scaffold_11-snap.2934-T1
Valid prediction for GeneMark_model.49763_t
Valid prediction for GeneMark_model.49761_t
Valid prediction for GlimmerHMM_glimmerT_28812-T1
Valid prediction for GlimmerHMM_glimmerT_28818-T1
Valid prediction for snap_scaffold_11-snap.2933-T1
Valid prediction for Augustus_model.g19241.t1
Valid prediction for Augustus_model.g19243.t1
Valid prediction for GeneMark_model.49749_t
Valid prediction for GeneMark_model.49747_t
Valid prediction for GlimmerHMM_glimmerT_28817-T1
Valid prediction for snap_scaffold_11-snap.2951-T1
Valid prediction for snap_scaffold_11-snap.2936-T1
Valid prediction for GeneMark_model.49735_t
Valid prediction for GlimmerHMM_glimmerT_28816-T1
Valid prediction for GeneMark_model.49745_t
Valid prediction for snap_scaffold_11-snap.2958-T1
Valid prediction for GlimmerHMM_glimmerT_28815-T1
Valid prediction for GeneMark_model.49733_t
Valid prediction for GeneMark_model.49726_t
Valid prediction for snap_scaffold_11-snap.2935-T1
Valid prediction for snap_scaffold_11-snap.2948-T1
Valid prediction for snap_scaffold_11-snap.2956-T1
Valid prediction for snap_scaffold_11-snap.2930-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.49739_t
Valid prediction for snap_scaffold_11-snap.2941-T1
Valid prediction for GeneMark_model.49732_t
Valid prediction for GlimmerHMM_glimmerT_28801-T1
Valid prediction for GeneMark_model.49741_t
Valid prediction for snap_scaffold_11-snap.2952-T1
Valid prediction for GeneMark_model.49746_t
Valid prediction for GeneMark_model.49752_t
Valid prediction for GeneMark_model.49743_t
Valid prediction for snap_scaffold_11-snap.2947-T1
Valid prediction for snap_scaffold_11-snap.2944-T1
Valid prediction for GlimmerHMM_glimmerT_28808-T1
Valid prediction for GlimmerHMM_glimmerT_28802-T1
Valid prediction for snap_scaffold_11-snap.2938-T1
Valid prediction for snap_scaffold_11-snap.2946-T1
Valid prediction for GeneMark_model.49728_t
Valid prediction for GeneMark_model.49738_t
Valid prediction for GeneMark_model.49750_t
Valid prediction for GeneMark_model.49755_t
Valid prediction for snap_scaffold_11-snap.2955-T1
Valid prediction for GlimmerHMM_glimmerT_28810-T1
Valid prediction for snap_scaffold_11-snap.2931-T1
Valid prediction for GlimmerHMM_glimmerT_28819-T1
Valid prediction for snap_scaffold_11-snap.2932-T1
Valid prediction for Augustus_model.g19238.t1
Valid prediction for GeneMark_model.49758_t
Valid prediction for snap_scaffold_11-snap.2950-T1
Valid prediction for GeneMark_model.49723_t
Valid prediction for snap_scaffold_11-snap.2937-T1
Valid prediction for GeneMark_model.49762_t
Valid prediction for snap_scaffold_11-snap.2940-T1
Valid prediction for GlimmerHMM_glimmerT_28804-T1
Valid prediction for snap_scaffold_11-snap.2957-T1
Valid prediction for GeneMark_model.49736_t
Valid prediction for GeneMark_model.49725_t
Valid prediction for GeneMark_model.49734_t
Valid prediction for GeneMark_model.49744_t
Valid prediction for GeneMark_model.49757_t
Valid prediction for GeneMark_model.49731_t
Valid prediction for snap_scaffold_11-snap.2928-T1
Valid prediction for GlimmerHMM_glimmerT_28811-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21048, rend_intergenic: 15916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61726, rend_intergenic: 57653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84117, rend_intergenic: 72802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105007, rend_intergenic: 102392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129891, rend_intergenic: 126093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136461, rend_intergenic: 129950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153636, rend_intergenic: 151559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 204756
-exon list size: 486


building trellis

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-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 21048, rend_intergenic: 15916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61726, rend_intergenic: 57653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84117, rend_intergenic: 72802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105007, rend_intergenic: 102392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129891, rend_intergenic: 126093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136461, rend_intergenic: 129950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153636, rend_intergenic: 151559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support