-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_9256125-9677187

-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 GlimmerHMM_glimmerT_15270-T1
Valid prediction for Augustus_model.g10156.t1
Valid prediction for Augustus_model.g10127.t1
Valid prediction for HiQ_model.g10149.t1
Valid prediction for GlimmerHMM_glimmerT_15286-T1
Valid prediction for Augustus_model.g10141.t1
Valid prediction for Augustus_model.g10129.t1
Valid prediction for pasa_asmbl_47231.p1
Valid prediction for Augustus_model.g10154.t1
Valid prediction for snap_scaffold_6-snap.2080-T1
Valid prediction for pasa_asmbl_47233.p1
Valid prediction for Augustus_model.g10139.t1
Valid prediction for Augustus_model.g10153.t1
Valid prediction for Augustus_model.g10158.t1
Valid prediction for GlimmerHMM_glimmerT_15274-T1
Valid prediction for snap_scaffold_6-snap.2070-T1
Valid prediction for snap_scaffold_6-snap.2064-T1
Valid prediction for snap_scaffold_6-snap.2061-T1
Valid prediction for snap_scaffold_6-snap.2041-T1
Valid prediction for Augustus_model.g10133.t1
Valid prediction for GlimmerHMM_glimmerT_15264-T1
Valid prediction for GlimmerHMM_glimmerT_15278-T1
Valid prediction for snap_scaffold_6-snap.2043-T1
Valid prediction for GlimmerHMM_glimmerT_15281-T1
Valid prediction for GlimmerHMM_glimmerT_15284-T1
Valid prediction for HiQ_model.g10151.t1
Valid prediction for Augustus_model.g10155.t1
Valid prediction for Augustus_model.g10157.t1
Valid prediction for snap_scaffold_6-snap.2075-T1
Valid prediction for GlimmerHMM_glimmerT_15272-T1
Valid prediction for GlimmerHMM_glimmerT_15255-T1
Valid prediction for GlimmerHMM_glimmerT_15282-T1
Valid prediction for snap_scaffold_6-snap.2049-T1
Valid prediction for Augustus_model.g10144.t1
Couldn't classify 412396, 412501
Sorry, prediction pasa_asmbl_47235.p2 fails validation.
(CGC)	 TG	412396-412501	GT	AGG
(GTG)	 AG	413152-413259	GT	GTG
(CAG)	 AG	414983-415125	TG	AGT
-recovered pasa_asmbl_47235.p2, terminal, 414983, 415125
-recovered pasa_asmbl_47235.p2, internal, 413152, 413259
Valid prediction for snap_scaffold_6-snap.2060-T1
Valid prediction for GlimmerHMM_glimmerT_15277-T1
Valid prediction for GlimmerHMM_glimmerT_15265-T1
Valid prediction for GlimmerHMM_glimmerT_15287-T1
Valid prediction for snap_scaffold_6-snap.2042-T1
Valid prediction for snap_scaffold_6-snap.2044-T1
Valid prediction for snap_scaffold_6-snap.2074-T1
Valid prediction for Augustus_model.g10145.t1
Valid prediction for Augustus_model.g10128.t1
Valid prediction for CodingQuarry_transcript_55168-T1
Valid prediction for GlimmerHMM_glimmerT_15291-T1
Couldn't classify 138589, 139032
Sorry, prediction pasa_asmbl_47229.p1 fails validation.
(ACA)	 CC	138589-139032	AG	AGA
Valid prediction for snap_scaffold_6-snap.2058-T1
Valid prediction for snap_scaffold_6-snap.2065-T1
Valid prediction for snap_scaffold_6-snap.2078-T1
Valid prediction for GlimmerHMM_glimmerT_15290-T1
Valid prediction for Augustus_model.g10142.t1
Valid prediction for snap_scaffold_6-snap.2051-T1
Valid prediction for GlimmerHMM_glimmerT_15289-T1
Valid prediction for snap_scaffold_6-snap.2062-T1
Valid prediction for GlimmerHMM_glimmerT_15275-T1
Valid prediction for snap_scaffold_6-snap.2068-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 GlimmerHMM_glimmerT_15261-T1
Valid prediction for Augustus_model.g10134.t1
Valid prediction for GlimmerHMM_glimmerT_15271-T1
Valid prediction for GlimmerHMM_glimmerT_15280-T1
Valid prediction for snap_scaffold_6-snap.2063-T1
Couldn't classify 303611, 303685
Sorry, prediction pasa_asmbl_48624.p1 fails validation.
(ATG)	 GG	301967-302188	GT	AGG
(GAT)	 AG	303611-303685	AA	GGA
-recovered pasa_asmbl_48624.p1, initial, 301967, 302188
Couldn't classify 387802, 387899
Couldn't classify 390142, 390276
Sorry, prediction pasa_asmbl_48617.p1 fails validation.
(TGT)	 AG	387802-387899	GT	AGG
(GTC)	 AG	388360-388477	GT	AGG
(ATA)	 AG	388615-388699	GT	AAG
(GAA)	 AG	388906-389072	GT	ATG
(ATA)	 AG	389948-390001	GT	AGG
(ACC)	 AG	390142-390276	AC	CCA
-recovered pasa_asmbl_48617.p1, internal, 387802, 387899
-recovered pasa_asmbl_48617.p1, internal, 388360, 388477
-recovered pasa_asmbl_48617.p1, internal, 388615, 388699
-recovered pasa_asmbl_48617.p1, internal, 388906, 389072
-recovered pasa_asmbl_48617.p1, internal, 389948, 390001
Valid prediction for Augustus_model.g10140.t1
Valid prediction for Augustus_model.g10135.t1
Valid prediction for HiQ_model.g10137.t1
Valid prediction for snap_scaffold_6-snap.2056-T1
Valid prediction for GlimmerHMM_glimmerT_15292-T1
Valid prediction for GlimmerHMM_glimmerT_15269-T1
Valid prediction for GlimmerHMM_glimmerT_15276-T1
Valid prediction for GlimmerHMM_glimmerT_15259-T1
Valid prediction for Augustus_model.g10143.t1
Valid prediction for snap_scaffold_6-snap.2081-T1
Valid prediction for snap_scaffold_6-snap.2050-T1
Valid prediction for GlimmerHMM_glimmerT_15283-T1
Valid prediction for snap_scaffold_6-snap.2071-T1
Valid prediction for GlimmerHMM_glimmerT_15279-T1
Valid prediction for snap_scaffold_6-snap.2047-T1
Valid prediction for snap_scaffold_6-snap.2079-T1
Valid prediction for HiQ_model.g10148.t1
Valid prediction for snap_scaffold_6-snap.2052-T1
Valid prediction for HiQ_model.g10147.t1
Valid prediction for snap_scaffold_6-snap.2045-T1
Valid prediction for GlimmerHMM_glimmerT_15273-T1
Valid prediction for CodingQuarry_transcript_55169-T1
Valid prediction for snap_scaffold_6-snap.2054-T1
Valid prediction for snap_scaffold_6-snap.2067-T1
Valid prediction for GlimmerHMM_glimmerT_15258-T1
Valid prediction for snap_scaffold_6-snap.2046-T1
Valid prediction for pasa_asmbl_48625.p1
Valid prediction for pasa_asmbl_48621.p1
Valid prediction for Augustus_model.g10132.t1
Valid prediction for Augustus_model.g10130.t1
Valid prediction for CodingQuarry_transcript_55167-T1
Valid prediction for Augustus_model.g10131.t1
Valid prediction for snap_scaffold_6-snap.2073-T1
Valid prediction for snap_scaffold_6-snap.2057-T1
Valid prediction for Augustus_model.g10138.t1
Valid prediction for GlimmerHMM_glimmerT_15263-T1
Valid prediction for GlimmerHMM_glimmerT_15262-T1
Valid prediction for GlimmerHMM_glimmerT_15256-T1
Valid prediction for snap_scaffold_6-snap.2072-T1
Couldn't classify 390494, 390572
Sorry, prediction pasa_asmbl_48616.p1 fails validation.
(CTC)	 AT	390494-390572	GT	AAG
(ATC)	 AG	390646-390882	GT	GGG
(GTT)	 AG	390992-391188	GT	AGG
(GCC)	 AG	391294-391551	GT	GGG
(GTA)	 AG	391744-391899	TG	GAT
-recovered pasa_asmbl_48616.p1, terminal, 391744, 391899
-recovered pasa_asmbl_48616.p1, internal, 390646, 390882
-recovered pasa_asmbl_48616.p1, internal, 390992, 391188
-recovered pasa_asmbl_48616.p1, internal, 391294, 391551
Valid prediction for Augustus_model.g10136.t1
Valid prediction for snap_scaffold_6-snap.2066-T1
Valid prediction for GlimmerHMM_glimmerT_15257-T1
Valid prediction for snap_scaffold_6-snap.2069-T1
Valid prediction for GlimmerHMM_glimmerT_15288-T1
Valid prediction for Augustus_model.g10146.t1
Valid prediction for snap_scaffold_6-snap.2059-T1
Valid prediction for pasa_asmbl_48626.p1
Valid prediction for GlimmerHMM_glimmerT_15268-T1
Valid prediction for snap_scaffold_6-snap.2077-T1
Valid prediction for snap_scaffold_6-snap.2053-T1
Valid prediction for GlimmerHMM_glimmerT_15260-T1
Valid prediction for snap_scaffold_6-snap.2083-T1
Valid prediction for GlimmerHMM_glimmerT_15285-T1
Valid prediction for GlimmerHMM_glimmerT_15267-T1
Valid prediction for HiQ_model.g10152.t1
Valid prediction for snap_scaffold_6-snap.2076-T1
Valid prediction for snap_scaffold_6-snap.2055-T1
Valid prediction for Augustus_model.g10150.t1
Valid prediction for GlimmerHMM_glimmerT_15266-T1
Valid prediction for pasa_asmbl_48629.p1
Valid prediction for snap_scaffold_6-snap.2048-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 346430, rend_intergenic: 343608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 372468, rend_intergenic: 359025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 383305, rend_intergenic: 376262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 395759, rend_intergenic: 395373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 398221, rend_intergenic: 396042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 421063
-exon list size: 498


building trellis

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-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 346430, rend_intergenic: 343608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 372468, rend_intergenic: 359025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 383305, rend_intergenic: 376262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 395759, rend_intergenic: 395373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 398221, rend_intergenic: 396042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support