-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_1890048-2040726

-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_2-snap.457-T1
Valid prediction for GeneMark_model.5405_t
Valid prediction for snap_scaffold_2-snap.446-T1
Valid prediction for snap_scaffold_2-snap.477-T1
Valid prediction for GeneMark_model.5394_t
Valid prediction for GeneMark_model.5403_t
Valid prediction for snap_scaffold_2-snap.470-T1
Valid prediction for GeneMark_model.5417_t
Valid prediction for GeneMark_model.5401_t
Valid prediction for GeneMark_model.5409_t
Valid prediction for GeneMark_model.5431_t
Valid prediction for snap_scaffold_2-snap.443-T1
Valid prediction for Augustus_model.g2260.t1
Valid prediction for GlimmerHMM_glimmerT_3360-T1
Valid prediction for GlimmerHMM_glimmerT_3363-T1
Valid prediction for snap_scaffold_2-snap.453-T1
Valid prediction for CodingQuarry_transcript_28407-T1
Valid prediction for GeneMark_model.5433_t
Valid prediction for GeneMark_model.5436_t
Valid prediction for GeneMark_model.5390_t
Valid prediction for Augustus_model.g2251.t1
Valid prediction for Augustus_model.g2255.t1
Valid prediction for Augustus_model.g2252.t1
Valid prediction for snap_scaffold_2-snap.474-T1
Valid prediction for snap_scaffold_2-snap.460-T1
Valid prediction for GlimmerHMM_glimmerT_3358-T1
Valid prediction for GeneMark_model.5419_t
Valid prediction for snap_scaffold_2-snap.450-T1
Valid prediction for GeneMark_model.5415_t
Valid prediction for snap_scaffold_2-snap.472-T1
Valid prediction for GlimmerHMM_glimmerT_3371-T1
Valid prediction for GeneMark_model.5420_t
Valid prediction for GeneMark_model.5413_t
Valid prediction for snap_scaffold_2-snap.451-T1
Valid prediction for GeneMark_model.5396_t
Valid prediction for GlimmerHMM_glimmerT_3364-T1
Valid prediction for snap_scaffold_2-snap.464-T1
Valid prediction for GeneMark_model.5426_t
Valid prediction for GlimmerHMM_glimmerT_3361-T1
Valid prediction for Augustus_model.g2258.t1
Valid prediction for Augustus_model.g2247.t1
Valid prediction for snap_scaffold_2-snap.467-T1
Valid prediction for Augustus_model.g2249.t1
Valid prediction for GlimmerHMM_glimmerT_3357-T1
Valid prediction for GeneMark_model.5422_t
Valid prediction for snap_scaffold_2-snap.459-T1
Valid prediction for snap_scaffold_2-snap.479-T1
Valid prediction for snap_scaffold_2-snap.473-T1
Valid prediction for snap_scaffold_2-snap.475-T1
Valid prediction for GlimmerHMM_glimmerT_3352-T1
Valid prediction for GlimmerHMM_glimmerT_3351-T1
Valid prediction for GeneMark_model.5423_t
Valid prediction for Augustus_model.g2248.t1
Valid prediction for snap_scaffold_2-snap.468-T1
Valid prediction for GeneMark_model.5406_t
Valid prediction for GeneMark_model.5411_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.g2259.t1
Valid prediction for Augustus_model.g2253.t1
Valid prediction for snap_scaffold_2-snap.444-T1
Valid prediction for GeneMark_model.5421_t
Valid prediction for GeneMark_model.5393_t
Valid prediction for GlimmerHMM_glimmerT_3350-T1
Valid prediction for GlimmerHMM_glimmerT_3354-T1
Valid prediction for GlimmerHMM_glimmerT_3359-T1
Valid prediction for GeneMark_model.5429_t
Valid prediction for GlimmerHMM_glimmerT_3365-T1
Valid prediction for GlimmerHMM_glimmerT_3372-T1
Valid prediction for GeneMark_model.5404_t
Valid prediction for snap_scaffold_2-snap.452-T1
Valid prediction for GlimmerHMM_glimmerT_3366-T1
Valid prediction for GeneMark_model.5398_t
Valid prediction for Augustus_model.g2254.t1
Valid prediction for GeneMark_model.5434_t
Valid prediction for GeneMark_model.5395_t
Valid prediction for snap_scaffold_2-snap.456-T1
Valid prediction for GeneMark_model.5428_t
Valid prediction for GeneMark_model.5424_t
Valid prediction for GeneMark_model.5412_t
Valid prediction for snap_scaffold_2-snap.447-T1
Valid prediction for GeneMark_model.5391_t
Valid prediction for snap_scaffold_2-snap.454-T1
Valid prediction for snap_scaffold_2-snap.465-T1
Valid prediction for GlimmerHMM_glimmerT_3348-T1
Valid prediction for GlimmerHMM_glimmerT_3353-T1
Valid prediction for GlimmerHMM_glimmerT_3368-T1
Valid prediction for snap_scaffold_2-snap.442-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3373-T1
Valid prediction for GlimmerHMM_glimmerT_3369-T1
Valid prediction for GeneMark_model.5430_t
Valid prediction for snap_scaffold_2-snap.448-T1
Valid prediction for Augustus_model.g2256.t1
Valid prediction for GeneMark_model.5397_t
Valid prediction for snap_scaffold_2-snap.455-T1
Valid prediction for GeneMark_model.5408_t
Valid prediction for Augustus_model.g2250.t1
Valid prediction for snap_scaffold_2-snap.445-T1
Valid prediction for GlimmerHMM_glimmerT_3347-T1
Valid prediction for GlimmerHMM_glimmerT_3349-T1
Valid prediction for GlimmerHMM_glimmerT_3362-T1
Valid prediction for snap_scaffold_2-snap.462-T1
Valid prediction for GeneMark_model.5418_t
Valid prediction for snap_scaffold_2-snap.458-T1
Valid prediction for snap_scaffold_2-snap.449-T1
Valid prediction for GlimmerHMM_glimmerT_3367-T1
Valid prediction for Augustus_model.g2257.t1
Valid prediction for GeneMark_model.5425_t
Valid prediction for GeneMark_model.5432_t
Valid prediction for GeneMark_model.5400_t
Valid prediction for GeneMark_model.5435_t
Valid prediction for snap_scaffold_2-snap.466-T1
Valid prediction for GeneMark_model.5414_t
Valid prediction for GeneMark_model.5392_t
Valid prediction for snap_scaffold_2-snap.476-T1
Valid prediction for GlimmerHMM_glimmerT_3370-T1
Valid prediction for Augustus_model.g2246.t1
Valid prediction for GeneMark_model.5399_t
Valid prediction for snap_scaffold_2-snap.461-T1
Valid prediction for GeneMark_model.5416_t
Valid prediction for GlimmerHMM_glimmerT_3356-T1
Valid prediction for snap_scaffold_2-snap.471-T1
Valid prediction for GlimmerHMM_glimmerT_3355-T1
Valid prediction for snap_scaffold_2-snap.469-T1
Valid prediction for snap_scaffold_2-snap.463-T1
Valid prediction for GeneMark_model.5437_t
Valid prediction for snap_scaffold_2-snap.478-T1
Valid prediction for GeneMark_model.5410_t
Valid prediction for GeneMark_model.5407_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11691, rend_intergenic: 8217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17503, rend_intergenic: 12133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32051, rend_intergenic: 17793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34292, rend_intergenic: 32169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39766, rend_intergenic: 36997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43939, rend_intergenic: 40422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47903, rend_intergenic: 44297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58849, rend_intergenic: 56592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66661, rend_intergenic: 61467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69809, rend_intergenic: 67518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78144, rend_intergenic: 76015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93807, rend_intergenic: 88182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97251, rend_intergenic: 95345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131101, rend_intergenic: 129259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148356, rend_intergenic: 138217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150679
-exon list size: 632


building trellis

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-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 11691, rend_intergenic: 8217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17503, rend_intergenic: 12133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32051, rend_intergenic: 17793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34292, rend_intergenic: 32169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39766, rend_intergenic: 36997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43939, rend_intergenic: 40422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47903, rend_intergenic: 44297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58849, rend_intergenic: 56592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66661, rend_intergenic: 61467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69809, rend_intergenic: 67518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78144, rend_intergenic: 76015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93807, rend_intergenic: 88182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97251, rend_intergenic: 95345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131101, rend_intergenic: 129259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148356, rend_intergenic: 138217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support