-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_3894616-4064304

-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 GeneMark_model.74425_t
Valid prediction for GlimmerHMM_glimmerT_43092-T1
Valid prediction for snap_scaffold_18-snap.825-T1
Valid prediction for snap_scaffold_18-snap.804-T1
Valid prediction for GeneMark_model.74410_t
Valid prediction for GeneMark_model.74418_t
Valid prediction for snap_scaffold_18-snap.809-T1
Valid prediction for GeneMark_model.74415_t
Valid prediction for snap_scaffold_18-snap.822-T1
Valid prediction for GlimmerHMM_glimmerT_43099-T1
Valid prediction for Augustus_model.g28824.t1
Valid prediction for GlimmerHMM_glimmerT_43096-T1
Valid prediction for GeneMark_model.74433_t
Valid prediction for GeneMark_model.74416_t
Valid prediction for snap_scaffold_18-snap.823-T1
Valid prediction for GeneMark_model.74428_t
Valid prediction for GlimmerHMM_glimmerT_43089-T1
Valid prediction for snap_scaffold_18-snap.820-T1
Valid prediction for GlimmerHMM_glimmerT_43104-T1
Valid prediction for Augustus_model.g28829.t1
Valid prediction for snap_scaffold_18-snap.800-T1
Valid prediction for GeneMark_model.74423_t
Valid prediction for GeneMark_model.74408_t
Valid prediction for Augustus_model.g28836.t1
Valid prediction for GeneMark_model.74426_t
Valid prediction for Augustus_model.g28835.t1
Valid prediction for GeneMark_model.74414_t
Valid prediction for GeneMark_model.74417_t
Valid prediction for snap_scaffold_18-snap.811-T1
Couldn't classify 41130, 41160
Sorry, prediction pasa_asmbl_20517.p1 fails validation.
(GAG)	 AG	41130-41160	GT	AGG
(ACT)	 AG	41467-41609	GT	AGG
(AAT)	 AG	42078-42178	GT	AGG
(GTT)	 AG	42327-42429	GG	GAG
-recovered pasa_asmbl_20517.p1, terminal, 42327, 42429
-recovered pasa_asmbl_20517.p1, internal, 41130, 41160
-recovered pasa_asmbl_20517.p1, internal, 41467, 41609
-recovered pasa_asmbl_20517.p1, internal, 42078, 42178
Valid prediction for GeneMark_model.74412_t
Valid prediction for snap_scaffold_18-snap.806-T1
Valid prediction for snap_scaffold_18-snap.796-T1
Valid prediction for GlimmerHMM_glimmerT_43093-T1
Valid prediction for snap_scaffold_18-snap.799-T1
Valid prediction for GlimmerHMM_glimmerT_43090-T1
Valid prediction for GeneMark_model.74431_t
Valid prediction for Augustus_model.g28833.t1
Valid prediction for snap_scaffold_18-snap.805-T1
Valid prediction for GlimmerHMM_glimmerT_43107-T1
Valid prediction for snap_scaffold_18-snap.792-T1
Valid prediction for GlimmerHMM_glimmerT_43098-T1
Valid prediction for snap_scaffold_18-snap.818-T1
Valid prediction for GlimmerHMM_glimmerT_43102-T1
Valid prediction for snap_scaffold_18-snap.815-T1
Valid prediction for snap_scaffold_18-snap.813-T1
Valid prediction for snap_scaffold_18-snap.824-T1
Valid prediction for Augustus_model.g28820.t1
Valid prediction for GeneMark_model.74421_t
Valid prediction for GlimmerHMM_glimmerT_43103-T1
Valid prediction for Augustus_model.g28826.t1
Valid prediction for Augustus_model.g28825.t1
Valid prediction for Augustus_model.g28828.t1
Valid prediction for GeneMark_model.74419_t
Valid prediction for snap_scaffold_18-snap.808-T1
Valid prediction for GeneMark_model.74406_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.g28832.t1
Valid prediction for GlimmerHMM_glimmerT_43088-T1
Valid prediction for GeneMark_model.74411_t
Valid prediction for snap_scaffold_18-snap.801-T1
Valid prediction for snap_scaffold_18-snap.803-T1
Valid prediction for snap_scaffold_18-snap.812-T1
Valid prediction for snap_scaffold_18-snap.826-T1
Couldn't classify 153429, 153836
Sorry, prediction pasa_asmbl_20253.p1 fails validation.
(CTA)	 CT	153429-153836	AA	AAA
Valid prediction for GeneMark_model.74429_t
Valid prediction for GlimmerHMM_glimmerT_43105-T1
Valid prediction for GeneMark_model.74407_t
Valid prediction for GeneMark_model.74422_t
Valid prediction for GeneMark_model.74409_t
Valid prediction for snap_scaffold_18-snap.814-T1
Couldn't classify 151013, 151123
Couldn't classify 152047, 152168
Sorry, prediction pasa_asmbl_19818.p1 fails validation.
(TTC)	 AC	151013-151123	GT	CTG
(GTG)	 AG	151360-151681	GT	GGG
(ACA)	 AG	151845-151895	GT	GGG
(ACA)	 AG	152047-152168	CA	CAC
-recovered pasa_asmbl_19818.p1, internal, 151360, 151681
-recovered pasa_asmbl_19818.p1, internal, 151845, 151895
Valid prediction for GlimmerHMM_glimmerT_43091-T1
Valid prediction for GeneMark_model.74405_t
Valid prediction for GlimmerHMM_glimmerT_43097-T1
Valid prediction for GlimmerHMM_glimmerT_43108-T1
Valid prediction for GeneMark_model.74434_t
Valid prediction for GeneMark_model.74424_t
Valid prediction for snap_scaffold_18-snap.817-T1
Valid prediction for snap_scaffold_18-snap.798-T1
Valid prediction for CodingQuarry_transcript_23672-T1
Valid prediction for GeneMark_model.74430_t
Valid prediction for Augustus_model.g28831.t1
Valid prediction for snap_scaffold_18-snap.802-T1
Valid prediction for Augustus_model.g28834.t1
Valid prediction for GlimmerHMM_glimmerT_43087-T1
Valid prediction for snap_scaffold_18-snap.797-T1
Valid prediction for GlimmerHMM_glimmerT_43101-T1
Valid prediction for snap_scaffold_18-snap.810-T1
Valid prediction for snap_scaffold_18-snap.821-T1
Valid prediction for snap_scaffold_18-snap.794-T1
Valid prediction for Augustus_model.g28830.t1
Valid prediction for GlimmerHMM_glimmerT_43109-T1
Valid prediction for snap_scaffold_18-snap.795-T1
Valid prediction for GlimmerHMM_glimmerT_43095-T1
Valid prediction for Augustus_model.g28821.t1
Valid prediction for GlimmerHMM_glimmerT_43106-T1
Valid prediction for Augustus_model.g28823.t1
Valid prediction for GeneMark_model.74413_t
Valid prediction for GeneMark_model.74432_t
Valid prediction for snap_scaffold_18-snap.816-T1
Valid prediction for Augustus_model.g28822.t1
Valid prediction for GlimmerHMM_glimmerT_43094-T1
Valid prediction for snap_scaffold_18-snap.819-T1
Valid prediction for Augustus_model.g28827.t1
Valid prediction for pasa_asmbl_19820.p1
Valid prediction for Augustus_model.g28819.t1
Valid prediction for snap_scaffold_18-snap.791-T1
Valid prediction for GlimmerHMM_glimmerT_43100-T1
Valid prediction for snap_scaffold_18-snap.793-T1
Valid prediction for snap_scaffold_18-snap.807-T1
Couldn't classify 152670, 153119
Sorry, prediction pasa_asmbl_19817.p1 fails validation.
(TTT)	 AC	152670-153119	GC	CAG
Valid prediction for GeneMark_model.74420_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13491, rend_intergenic: 9290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39152, rend_intergenic: 28886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52347, rend_intergenic: 47952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81607, rend_intergenic: 78885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149409, rend_intergenic: 143941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168747, rend_intergenic: 162174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 169689
-exon list size: 516


building trellis

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-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 13491, rend_intergenic: 9290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39152, rend_intergenic: 28886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52347, rend_intergenic: 47952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81607, rend_intergenic: 78885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149409, rend_intergenic: 143941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168747, rend_intergenic: 162174  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