-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_3442707-3615146

-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.66690_t
Valid prediction for snap_scaffold_16-snap.677-T1
Valid prediction for GlimmerHMM_glimmerT_38939-T1
Valid prediction for GeneMark_model.66678_t
Valid prediction for snap_scaffold_16-snap.668-T1
Valid prediction for GeneMark_model.66687_t
Valid prediction for snap_scaffold_16-snap.673-T1
Valid prediction for snap_scaffold_16-snap.659-T1
Valid prediction for GeneMark_model.66679_t
Valid prediction for GeneMark_model.66673_t
Valid prediction for GlimmerHMM_glimmerT_38930-T1
Valid prediction for snap_scaffold_16-snap.656-T1
Valid prediction for GeneMark_model.66667_t
Valid prediction for GeneMark_model.66671_t
Valid prediction for Augustus_model.g26145.t1
Valid prediction for Augustus_model.g26134.t1
Valid prediction for GeneMark_model.66666_t
Valid prediction for snap_scaffold_16-snap.672-T1
Valid prediction for GeneMark_model.66688_t
Valid prediction for snap_scaffold_16-snap.680-T1
Valid prediction for snap_scaffold_16-snap.688-T1
Valid prediction for GeneMark_model.66684_t
Valid prediction for GeneMark_model.66691_t
Valid prediction for GlimmerHMM_glimmerT_38924-T1
Valid prediction for snap_scaffold_16-snap.674-T1
Valid prediction for snap_scaffold_16-snap.693-T1
Valid prediction for GeneMark_model.66662_t
Valid prediction for GeneMark_model.66683_t
Valid prediction for snap_scaffold_16-snap.658-T1
Valid prediction for GlimmerHMM_glimmerT_38947-T1
Valid prediction for GeneMark_model.66682_t
Valid prediction for GlimmerHMM_glimmerT_38929-T1
Valid prediction for Augustus_model.g26136.t1
Valid prediction for snap_scaffold_16-snap.661-T1
Valid prediction for GeneMark_model.66668_t
Valid prediction for snap_scaffold_16-snap.692-T1
Valid prediction for snap_scaffold_16-snap.665-T1
Valid prediction for Augustus_model.g26146.t1
Valid prediction for GeneMark_model.66676_t
Valid prediction for snap_scaffold_16-snap.681-T1
Valid prediction for GlimmerHMM_glimmerT_38932-T1
Valid prediction for snap_scaffold_16-snap.690-T1
Valid prediction for GeneMark_model.66665_t
Valid prediction for snap_scaffold_16-snap.657-T1
Valid prediction for GeneMark_model.66686_t
Valid prediction for GlimmerHMM_glimmerT_38940-T1
Valid prediction for GeneMark_model.66660_t
Valid prediction for GeneMark_model.66677_t
Valid prediction for GlimmerHMM_glimmerT_38935-T1
Valid prediction for snap_scaffold_16-snap.691-T1
Valid prediction for GlimmerHMM_glimmerT_38936-T1
Valid prediction for snap_scaffold_16-snap.675-T1
Valid prediction for snap_scaffold_16-snap.689-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.66672_t
Valid prediction for GlimmerHMM_glimmerT_38925-T1
Valid prediction for snap_scaffold_16-snap.679-T1
Valid prediction for snap_scaffold_16-snap.671-T1
Valid prediction for snap_scaffold_16-snap.682-T1
Valid prediction for GeneMark_model.66661_t
Valid prediction for snap_scaffold_16-snap.667-T1
Valid prediction for Augustus_model.g26141.t1
Valid prediction for GlimmerHMM_glimmerT_38933-T1
Valid prediction for snap_scaffold_16-snap.666-T1
Valid prediction for snap_scaffold_16-snap.663-T1
Valid prediction for snap_scaffold_16-snap.662-T1
Couldn't classify 145249, 146109
Sorry, prediction pasa_asmbl_16153.p1 fails validation.
(AGT)	 TA	145249-146109	CT	AAC
Valid prediction for Augustus_model.g26139.t1
Valid prediction for Augustus_model.g26135.t1
Valid prediction for snap_scaffold_16-snap.664-T1
Valid prediction for HiQ_model.g26144.t1
Valid prediction for Augustus_model.g26138.t1
Valid prediction for GeneMark_model.66670_t
Valid prediction for CodingQuarry_transcript_19883-T1
Valid prediction for GlimmerHMM_glimmerT_38938-T1
Valid prediction for GeneMark_model.66663_t
Valid prediction for snap_scaffold_16-snap.670-T1
Valid prediction for snap_scaffold_16-snap.678-T1
Valid prediction for GlimmerHMM_glimmerT_38941-T1
Valid prediction for GeneMark_model.66669_t
Valid prediction for snap_scaffold_16-snap.660-T1
Valid prediction for pasa_asmbl_16155.p1
Valid prediction for Augustus_model.g26140.t1
Valid prediction for GlimmerHMM_glimmerT_38944-T1
Valid prediction for snap_scaffold_16-snap.684-T1
Valid prediction for CodingQuarry_transcript_19884-T1
Valid prediction for GlimmerHMM_glimmerT_38928-T1
Valid prediction for snap_scaffold_16-snap.669-T1
Valid prediction for GeneMark_model.66664_t
Valid prediction for GeneMark_model.66685_t
Valid prediction for GeneMark_model.66689_t
Couldn't classify 41151, 41195
Sorry, prediction pasa_asmbl_16162.p1 fails validation.
(ATG)	 TG	38348-38506	GT	TGG
(AAA)	 AG	38613-38660	GT	AGG
(GCT)	 AG	38746-38855	GT	AGG
(CGG)	 AG	39041-39127	GT	GGG
(GTT)	 AG	40400-40511	GT	AGG
(GTT)	 AG	41151-41195	CC	GCC
-recovered pasa_asmbl_16162.p1, initial, 38348, 38506
-recovered pasa_asmbl_16162.p1, internal, 38613, 38660
-recovered pasa_asmbl_16162.p1, internal, 38746, 38855
-recovered pasa_asmbl_16162.p1, internal, 39041, 39127
-recovered pasa_asmbl_16162.p1, internal, 40400, 40511
Valid prediction for snap_scaffold_16-snap.685-T1
Valid prediction for GeneMark_model.66675_t
Valid prediction for GeneMark_model.66674_t
Valid prediction for GlimmerHMM_glimmerT_38931-T1
Valid prediction for GeneMark_model.66680_t
Valid prediction for pasa_asmbl_16157.p1
Valid prediction for GlimmerHMM_glimmerT_38945-T1
Valid prediction for snap_scaffold_16-snap.683-T1
Valid prediction for GlimmerHMM_glimmerT_38943-T1
Valid prediction for GlimmerHMM_glimmerT_38926-T1
Valid prediction for snap_scaffold_16-snap.686-T1
Valid prediction for GeneMark_model.66681_t
Valid prediction for GlimmerHMM_glimmerT_38937-T1
Valid prediction for GlimmerHMM_glimmerT_38946-T1
Valid prediction for Augustus_model.g26142.t1
Valid prediction for snap_scaffold_16-snap.676-T1
Valid prediction for GlimmerHMM_glimmerT_38934-T1
Valid prediction for Augustus_model.g26137.t1
Valid prediction for GlimmerHMM_glimmerT_38942-T1
Valid prediction for Augustus_model.g26133.t1
Valid prediction for snap_scaffold_16-snap.687-T1
Valid prediction for HiQ_model.g26143.t1
Valid prediction for GlimmerHMM_glimmerT_38927-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16054, rend_intergenic: 15303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31898, rend_intergenic: 30540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70462, rend_intergenic: 65982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77090, rend_intergenic: 72601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113856, rend_intergenic: 109846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172440
-exon list size: 463


building trellis

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99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 16054, rend_intergenic: 15303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31898, rend_intergenic: 30540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70462, rend_intergenic: 65982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77090, rend_intergenic: 72601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113856, rend_intergenic: 109846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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