-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_3028716-3133785

-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: +)Couldn't classify 99815, 100270
Sorry, prediction pasa_asmbl_36150.p1 fails validation.
(CCC)	 AT	99815-100270	GT	TGG
(GTT)	 AG	101258-101334	GT	CGG
(CCC)	 AG	101436-101596	GT	CTG
(ATG)	 AG	102468-102503	GT	AGG
(ATC)	 AG	102809-102877	GT	CGG
(GTG)	 AG	102981-103237	GT	GGG
(GTG)	 AG	103324-103445	GT	TGG
(TGT)	 AG	103915-104116	GT	AGG
(GTC)	 AG	104222-104279	GT	GAG
(GTG)	 AG	104407-104502	GT	AAG
(GCG)	 AG	104589-104647	CA	AAC
-recovered pasa_asmbl_36150.p1, initial, 102468, 102503
-recovered pasa_asmbl_36150.p1, terminal, 104589, 104647
-recovered pasa_asmbl_36150.p1, internal, 101258, 101334
-recovered pasa_asmbl_36150.p1, internal, 101436, 101596
-recovered pasa_asmbl_36150.p1, internal, 102468, 102503
-recovered pasa_asmbl_36150.p1, internal, 102809, 102877
-recovered pasa_asmbl_36150.p1, internal, 102981, 103237
-recovered pasa_asmbl_36150.p1, internal, 103324, 103445
-recovered pasa_asmbl_36150.p1, internal, 103915, 104116
-recovered pasa_asmbl_36150.p1, internal, 104222, 104279
-recovered pasa_asmbl_36150.p1, internal, 104407, 104502
Valid prediction for CodingQuarry_transcript_41757-T1
Valid prediction for snap_scaffold_27-snap.734-T1
Valid prediction for GlimmerHMM_glimmerT_58326-T1
Valid prediction for Augustus_model.g38855.t1
Valid prediction for GlimmerHMM_glimmerT_58321-T1
Valid prediction for GeneMark_model.101458_t
Valid prediction for HiQ_model.g38859.t1
Valid prediction for GlimmerHMM_glimmerT_58327-T1
Valid prediction for Augustus_model.g38861.t1
Valid prediction for snap_scaffold_27-snap.740-T1
Valid prediction for GlimmerHMM_glimmerT_58330-T1
Valid prediction for GlimmerHMM_glimmerT_58325-T1
Valid prediction for CodingQuarry_transcript_41756-T1
Valid prediction for GlimmerHMM_glimmerT_58336-T1
Valid prediction for GeneMark_model.101444_t
Valid prediction for Augustus_model.g38864.t1
Valid prediction for Augustus_model.g38867.t1
Valid prediction for CodingQuarry_transcript_41754-T1
Valid prediction for GeneMark_model.101440_t
Valid prediction for Augustus_model.g38863.t1
Valid prediction for GlimmerHMM_glimmerT_58338-T1
Valid prediction for HiQ_model.g38868.t1
Valid prediction for snap_scaffold_27-snap.727-T1
Valid prediction for GlimmerHMM_glimmerT_58322-T1
Valid prediction for snap_scaffold_27-snap.732-T1
Valid prediction for snap_scaffold_27-snap.723-T1
Valid prediction for GlimmerHMM_glimmerT_58331-T1
Valid prediction for GlimmerHMM_glimmerT_58340-T1
Valid prediction for snap_scaffold_27-snap.729-T1
Valid prediction for pasa_asmbl_36145.p2
Valid prediction for pasa_asmbl_36138.p1
Valid prediction for snap_scaffold_27-snap.742-T1
Valid prediction for GlimmerHMM_glimmerT_58329-T1
Valid prediction for snap_scaffold_27-snap.722-T1
Valid prediction for pasa_asmbl_36147.p1
Valid prediction for snap_scaffold_27-snap.720-T1
Valid prediction for pasa_asmbl_36149.p1
Valid prediction for snap_scaffold_27-snap.724-T1
Valid prediction for snap_scaffold_27-snap.741-T1
Valid prediction for GeneMark_model.101441_t
Valid prediction for Augustus_model.g38869.t1
Valid prediction for snap_scaffold_27-snap.735-T1
Valid prediction for GeneMark_model.101457_t
Valid prediction for pasa_asmbl_36140.p1
Valid prediction for GlimmerHMM_glimmerT_58324-T1
Valid prediction for GlimmerHMM_glimmerT_58335-T1
Valid prediction for GeneMark_model.101462_t
Valid prediction for GlimmerHMM_glimmerT_58333-T1
Valid prediction for GeneMark_model.101447_t
Valid prediction for CodingQuarry_transcript_41753-T1
Valid prediction for snap_scaffold_27-snap.728-T1
Valid prediction for Augustus_model.g38857.t1
Valid prediction for GeneMark_model.101460_t
Valid prediction for snap_scaffold_27-snap.737-T1
Couldn't classify 104395, 104502
Sorry, prediction CodingQuarry_transcript_41758-T1 fails validation.
(ATG)	 TG	101545-101596	GT	CTG
(ATG)	 AG	102468-102503	GT	AGG
(ATC)	 AG	102809-102877	GT	CGG
(GTG)	 AG	102981-103237	GT	GGG
(GTG)	 AG	103324-103445	GT	TGG
(TGT)	 AG	103915-104116	GT	AGG
(GTC)	 AG	104222-104279	GT	GAG
(GTG)	 GG	104395-104502	GT	AAG
(GCG)	 AG	104589-104647	CA	AAC
-recovered CodingQuarry_transcript_41758-T1, initial, 101545, 101596
-recovered CodingQuarry_transcript_41758-T1, initial, 102468, 102503
-recovered CodingQuarry_transcript_41758-T1, terminal, 104589, 104647
-recovered CodingQuarry_transcript_41758-T1, internal, 102468, 102503
-recovered CodingQuarry_transcript_41758-T1, internal, 102809, 102877
-recovered CodingQuarry_transcript_41758-T1, internal, 102981, 103237
-recovered CodingQuarry_transcript_41758-T1, internal, 103324, 103445
-recovered CodingQuarry_transcript_41758-T1, internal, 103915, 104116
-recovered CodingQuarry_transcript_41758-T1, internal, 104222, 104279
Valid prediction for snap_scaffold_27-snap.725-T1
Valid prediction for GeneMark_model.101449_t
Valid prediction for GlimmerHMM_glimmerT_58339-T1
Valid prediction for Augustus_model.g38860.t1
Valid prediction for HiQ_model.g38866.t1
Valid prediction for GeneMark_model.101455_t
Valid prediction for GeneMark_model.101438_t
Valid prediction for snap_scaffold_27-snap.731-T1
Valid prediction for HiQ_model.g38858.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 Augustus_model.g38862.t1
Valid prediction for GeneMark_model.101454_t
Valid prediction for GeneMark_model.101452_t
Valid prediction for GeneMark_model.101450_t
Valid prediction for GlimmerHMM_glimmerT_58332-T1
Valid prediction for snap_scaffold_27-snap.736-T1
Valid prediction for snap_scaffold_27-snap.721-T1
Valid prediction for snap_scaffold_27-snap.739-T1
Valid prediction for GeneMark_model.101453_t
Valid prediction for Augustus_model.g38865.t1
Valid prediction for snap_scaffold_27-snap.733-T1
Valid prediction for snap_scaffold_27-snap.730-T1
Valid prediction for CodingQuarry_transcript_41755-T1
Valid prediction for GeneMark_model.101439_t
Valid prediction for GeneMark_model.101451_t
Valid prediction for GlimmerHMM_glimmerT_58328-T1
Valid prediction for GlimmerHMM_glimmerT_58334-T1
Valid prediction for GeneMark_model.101461_t
Valid prediction for GeneMark_model.101442_t
Valid prediction for GeneMark_model.101445_t
Valid prediction for GlimmerHMM_glimmerT_58337-T1
Valid prediction for GlimmerHMM_glimmerT_58323-T1
Valid prediction for GeneMark_model.101448_t
Couldn't classify 43628, 43651
Sorry, prediction pasa_asmbl_36840.p2 fails validation.
(ATG)	 TC	41894-42086	GT	CGG
(GTC)	 AG	42348-42502	GT	AGG
(GGT)	 AG	42628-42760	GT	GGG
(CTC)	 AG	42961-43132	GT	TGG
(GCA)	 AG	43263-43386	GT	AGG
(ATT)	 AG	43628-43651	TA	AGT
-recovered pasa_asmbl_36840.p2, initial, 41894, 42086
-recovered pasa_asmbl_36840.p2, internal, 42348, 42502
-recovered pasa_asmbl_36840.p2, internal, 42628, 42760
-recovered pasa_asmbl_36840.p2, internal, 42961, 43132
-recovered pasa_asmbl_36840.p2, internal, 43263, 43386
Valid prediction for Augustus_model.g38856.t1
Valid prediction for GeneMark_model.101456_t
Valid prediction for snap_scaffold_27-snap.726-T1
Valid prediction for GeneMark_model.101446_t
Valid prediction for snap_scaffold_27-snap.738-T1
Valid prediction for GeneMark_model.101459_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 33507, rend_intergenic: 29143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82493, rend_intergenic: 79327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90740, rend_intergenic: 87266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 105070
-exon list size: 360


building trellis

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-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 33507, rend_intergenic: 29143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82493, rend_intergenic: 79327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90740, rend_intergenic: 87266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support