-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_2485759-2647423

-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_18-snap.502-T1
Valid prediction for Augustus_model.g28706.t1
Valid prediction for GlimmerHMM_glimmerT_42893-T1
Valid prediction for GlimmerHMM_glimmerT_42902-T1
Valid prediction for GeneMark_model.74115_t
Valid prediction for GlimmerHMM_glimmerT_42905-T1
Valid prediction for snap_scaffold_18-snap.527-T1
Valid prediction for snap_scaffold_18-snap.522-T1
Valid prediction for snap_scaffold_18-snap.509-T1
Valid prediction for snap_scaffold_18-snap.524-T1
Valid prediction for GlimmerHMM_glimmerT_42898-T1
Valid prediction for GlimmerHMM_glimmerT_42888-T1
Valid prediction for snap_scaffold_18-snap.507-T1
Valid prediction for HiQ_model.g28697.t1
Valid prediction for GeneMark_model.74111_t
Valid prediction for GeneMark_model.74120_t
Valid prediction for snap_scaffold_18-snap.510-T1
Valid prediction for Augustus_model.g28701.t1
Valid prediction for snap_scaffold_18-snap.504-T1
Valid prediction for GeneMark_model.74110_t
Valid prediction for pasa_asmbl_20436.p1
Valid prediction for snap_scaffold_18-snap.526-T1
Valid prediction for Augustus_model.g28693.t1
Valid prediction for GeneMark_model.74116_t
Valid prediction for snap_scaffold_18-snap.535-T1
Valid prediction for HiQ_model.g28696.t1
Valid prediction for snap_scaffold_18-snap.511-T1
Valid prediction for CodingQuarry_transcript_23648-T1
Valid prediction for snap_scaffold_18-snap.530-T1
Valid prediction for snap_scaffold_18-snap.508-T1
Valid prediction for Augustus_model.g28698.t1
Valid prediction for snap_scaffold_18-snap.520-T1
Valid prediction for Augustus_model.g28691.t1
Valid prediction for CodingQuarry_transcript_23647-T1
Valid prediction for GeneMark_model.74096_t
Valid prediction for GlimmerHMM_glimmerT_42896-T1
Valid prediction for pasa_asmbl_20438.p1
Valid prediction for snap_scaffold_18-snap.529-T1
Valid prediction for GeneMark_model.74113_t
Valid prediction for GlimmerHMM_glimmerT_42904-T1
Valid prediction for GlimmerHMM_glimmerT_42906-T1
Valid prediction for GlimmerHMM_glimmerT_42892-T1
Valid prediction for GlimmerHMM_glimmerT_42899-T1
Valid prediction for GlimmerHMM_glimmerT_42907-T1
Valid prediction for snap_scaffold_18-snap.521-T1
Valid prediction for Augustus_model.g28704.t1
Valid prediction for snap_scaffold_18-snap.500-T1
Valid prediction for snap_scaffold_18-snap.513-T1
Valid prediction for GeneMark_model.74108_t
Valid prediction for GlimmerHMM_glimmerT_42887-T1
Valid prediction for GlimmerHMM_glimmerT_42891-T1
Couldn't classify 49056, 49376
Sorry, prediction pasa_asmbl_20435.p1 fails validation.
(ATG)	 AA	49056-49376	AA	AGA
Valid prediction for GeneMark_model.74107_t
Valid prediction for GeneMark_model.74104_t
Valid prediction for Augustus_model.g28705.t1
Valid prediction for snap_scaffold_18-snap.534-T1
Valid prediction for GeneMark_model.74100_t
Valid prediction for GeneMark_model.74121_t
Valid prediction for GlimmerHMM_glimmerT_42894-T1
Valid prediction for snap_scaffold_18-snap.518-T1
Valid prediction for GeneMark_model.74106_t
Valid prediction for Augustus_model.g28695.t1
Valid prediction for snap_scaffold_18-snap.525-T1
Valid prediction for GlimmerHMM_glimmerT_42885-T1
Valid prediction for Augustus_model.g28694.t1
Valid prediction for snap_scaffold_18-snap.515-T1
Valid prediction for GeneMark_model.74102_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.g28700.t1
Valid prediction for GlimmerHMM_glimmerT_42897-T1
Valid prediction for snap_scaffold_18-snap.506-T1
Valid prediction for snap_scaffold_18-snap.523-T1
Valid prediction for GlimmerHMM_glimmerT_42910-T1
Valid prediction for Augustus_model.g28703.t1
Valid prediction for GlimmerHMM_glimmerT_42901-T1
Valid prediction for snap_scaffold_18-snap.512-T1
Valid prediction for GlimmerHMM_glimmerT_42890-T1
Valid prediction for GeneMark_model.74118_t
Valid prediction for GeneMark_model.74119_t
Valid prediction for GlimmerHMM_glimmerT_42886-T1
Valid prediction for snap_scaffold_18-snap.503-T1
Valid prediction for GeneMark_model.74101_t
Valid prediction for snap_scaffold_18-snap.501-T1
Valid prediction for GeneMark_model.74103_t
Valid prediction for GlimmerHMM_glimmerT_42900-T1
Couldn't classify 100335, 100397
Sorry, prediction pasa_asmbl_20251.p1 fails validation.
(GGC)	 AG	100335-100397	GT	GGG
(CTG)	 AG	100546-100658	GC	AGG
(GTC)	 AG	100852-100969	GT	ATG
(GAA)	 AG	101059-101157	GT	GCG
(GAT)	 AG	101307-101478	GT	TCG
(CGG)	 AG	101595-101728	CC	GAC
-recovered pasa_asmbl_20251.p1, terminal, 101595, 101728
-recovered pasa_asmbl_20251.p1, internal, 100335, 100397
-recovered pasa_asmbl_20251.p1, internal, 100546, 100658
-recovered pasa_asmbl_20251.p1, internal, 100852, 100969
-recovered pasa_asmbl_20251.p1, internal, 101059, 101157
-recovered pasa_asmbl_20251.p1, internal, 101307, 101478
Valid prediction for GeneMark_model.74098_t
Valid prediction for snap_scaffold_18-snap.531-T1
Valid prediction for pasa_asmbl_19765.p1
Valid prediction for snap_scaffold_18-snap.532-T1
Valid prediction for GlimmerHMM_glimmerT_42889-T1
Valid prediction for GeneMark_model.74117_t
Valid prediction for GeneMark_model.74109_t
Valid prediction for Augustus_model.g28692.t1
Valid prediction for GeneMark_model.74122_t
Valid prediction for snap_scaffold_18-snap.528-T1
Valid prediction for snap_scaffold_18-snap.517-T1
Valid prediction for GlimmerHMM_glimmerT_42903-T1
Valid prediction for GeneMark_model.74105_t
Valid prediction for snap_scaffold_18-snap.505-T1
Valid prediction for GeneMark_model.74097_t
Valid prediction for GeneMark_model.74112_t
Valid prediction for GlimmerHMM_glimmerT_42911-T1
Valid prediction for snap_scaffold_18-snap.514-T1
Valid prediction for GeneMark_model.74095_t
Valid prediction for GeneMark_model.74092_t
Valid prediction for GlimmerHMM_glimmerT_42895-T1
Valid prediction for GeneMark_model.74114_t
Valid prediction for snap_scaffold_18-snap.536-T1
Valid prediction for snap_scaffold_18-snap.516-T1
Valid prediction for Augustus_model.g28699.t1
Valid prediction for snap_scaffold_18-snap.533-T1
Valid prediction for GeneMark_model.74099_t
Couldn't classify 143143, 143303
Sorry, prediction pasa_asmbl_20265.p1 fails validation.
(ATG)	 GG	141092-141188	GT	AGG
(GTA)	 AG	141530-141703	GT	AGG
(GAG)	 AG	143143-143303	GG	AAG
-recovered pasa_asmbl_20265.p1, initial, 141092, 141188
-recovered pasa_asmbl_20265.p1, internal, 141530, 141703
Valid prediction for Augustus_model.g28702.t1
Valid prediction for Augustus_model.g28707.t1
Valid prediction for GeneMark_model.74094_t
Valid prediction for GlimmerHMM_glimmerT_42909-T1
Valid prediction for snap_scaffold_18-snap.519-T1
Valid prediction for GlimmerHMM_glimmerT_42908-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22114, rend_intergenic: 18152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35322, rend_intergenic: 29614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68028, rend_intergenic: 63876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72472, rend_intergenic: 68696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75537, rend_intergenic: 73734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89636, rend_intergenic: 89037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106425, rend_intergenic: 105562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134571, rend_intergenic: 130917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146009, rend_intergenic: 134832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158508, rend_intergenic: 153590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161665
-exon list size: 473


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 22114, rend_intergenic: 18152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35322, rend_intergenic: 29614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68028, rend_intergenic: 63876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72472, rend_intergenic: 68696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75537, rend_intergenic: 73734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89636, rend_intergenic: 89037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106425, rend_intergenic: 105562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134571, rend_intergenic: 130917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146009, rend_intergenic: 134832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158508, rend_intergenic: 153590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support