-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_306

-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 70, 214
Sorry, prediction Augustus_model.g40999.t1 fails validation.
(GTG)	 AG	70-214	GT	TGG
(GCT)	 AG	408-505	GT	CGG
(ATG)	 AG	766-909	GT	TGG
(CTG)	 AG	1233-1397	GT	AGG
(GTG)	 AG	1672-1799	GT	GGG
(ATG)	 AG	1965-2148	GT	AGG
(TCC)	 AG	2276-2363	GT	TCG
(CTC)	 AG	2741-2949	GT	ACG
(GTA)	 AG	3441-3585	GT	GAG
(AGT)	 AG	4077-4324	GT	TGG
(GTG)	 AG	4656-4780	GT	AGG
(ACC)	 AG	5165-5263	GT	AGG
(GCG)	 AG	6060-6221	GT	GAG
(GGA)	 AG	6487-6649	GT	CAG
(CTC)	 AG	7214-7420	GT	CTG
(CTG)	 AG	7677-7812	GT	ACG
(GGA)	 AG	8091-8290	CC	GAC
-recovered Augustus_model.g40999.t1, initial, 766, 909
add_exon() Sorry, Augustus_model.g40999.t1 1965-2148-initial-1 is invalid.
-recovered Augustus_model.g40999.t1, initial, 1965, 2148
-recovered Augustus_model.g40999.t1, terminal, 8091, 8290
-recovered Augustus_model.g40999.t1, internal, 70, 214
-recovered Augustus_model.g40999.t1, internal, 408, 505
-recovered Augustus_model.g40999.t1, internal, 766, 909
-recovered Augustus_model.g40999.t1, internal, 1233, 1397
-recovered Augustus_model.g40999.t1, internal, 1672, 1799
-recovered Augustus_model.g40999.t1, internal, 1965, 2148
-recovered Augustus_model.g40999.t1, internal, 2276, 2363
-recovered Augustus_model.g40999.t1, internal, 2741, 2949
-recovered Augustus_model.g40999.t1, internal, 3441, 3585
-recovered Augustus_model.g40999.t1, internal, 4077, 4324
-recovered Augustus_model.g40999.t1, internal, 4656, 4780
-recovered Augustus_model.g40999.t1, internal, 5165, 5263
-recovered Augustus_model.g40999.t1, internal, 6060, 6221
-recovered Augustus_model.g40999.t1, internal, 6487, 6649
-recovered Augustus_model.g40999.t1, internal, 7214, 7420
-recovered Augustus_model.g40999.t1, internal, 7677, 7812
Valid prediction for GeneMark_model.107252_t
Couldn't classify 8091, 8234
Sorry, prediction GlimmerHMM_glimmerT_61669-T1 fails validation.
(ATG)	 CC	2818-2949	GT	ACG
(GTA)	 AG	3441-3585	GT	GAG
(AGT)	 AG	4077-4324	GT	TGG
(GTG)	 AG	4656-4780	GT	AGG
(GCG)	 AG	6060-6221	GT	GAG
(GGA)	 AG	6487-6649	GT	CAG
(CTC)	 AG	7214-7420	GT	CTG
(CTG)	 AG	7677-7812	GT	ACG
(GGA)	 AG	8091-8234	GT	GGG
-recovered GlimmerHMM_glimmerT_61669-T1, initial, 2818, 2949
-recovered GlimmerHMM_glimmerT_61669-T1, internal, 3441, 3585
-recovered GlimmerHMM_glimmerT_61669-T1, internal, 4077, 4324
-recovered GlimmerHMM_glimmerT_61669-T1, internal, 4656, 4780
-recovered GlimmerHMM_glimmerT_61669-T1, internal, 6060, 6221
-recovered GlimmerHMM_glimmerT_61669-T1, internal, 6487, 6649
-recovered GlimmerHMM_glimmerT_61669-T1, internal, 7214, 7420
-recovered GlimmerHMM_glimmerT_61669-T1, internal, 7677, 7812
-recovered GlimmerHMM_glimmerT_61669-T1, internal, 8091, 8234
Couldn't classify 8091, 8234
Sorry, prediction snap_scaffold_306-snap.3-T1 fails validation.
(ATG)	 GG	5873-5883	GT	TTG
(GCG)	 AG	6060-6221	GT	GAG
(GGA)	 AG	6487-6649	GT	CAG
(CTC)	 AG	7214-7420	GT	CTG
(CTG)	 AG	7677-7812	GT	ACG
(GGA)	 AG	8091-8234	GT	GGG
-recovered snap_scaffold_306-snap.3-T1, initial, 5873, 5883
-recovered snap_scaffold_306-snap.3-T1, internal, 6060, 6221
-recovered snap_scaffold_306-snap.3-T1, internal, 6487, 6649
-recovered snap_scaffold_306-snap.3-T1, internal, 7214, 7420
-recovered snap_scaffold_306-snap.3-T1, internal, 7677, 7812
-recovered snap_scaffold_306-snap.3-T1, internal, 8091, 8234
Couldn't classify 70, 214
Sorry, prediction snap_scaffold_306-snap.1-T1 fails validation.
(GTG)	 AG	70-214	GT	TGG
(GCT)	 AG	408-505	GT	CGG
(ATG)	 AG	766-909	GT	TGG
(CTG)	 AG	1233-1397	GT	AGG
(GTG)	 AG	1672-1799	GT	GGG
(ATG)	 AG	1965-2148	GT	AGG
(TCC)	 AG	2276-2363	GT	TCG
(CTC)	 AG	2741-2949	GT	ACG
(GTA)	 AG	3441-3585	GT	GAG
(AGT)	 AG	4077-4162	GT	ACG
(GTC)	 AG	4211-4324	GT	TGG
(GTG)	 AG	4656-4780	GT	AGG
(GTA)	 AG	5264-5531	TA	AAT
-recovered snap_scaffold_306-snap.1-T1, initial, 766, 909
add_exon() Sorry, snap_scaffold_306-snap.1-T1 1965-2148-initial-1 is invalid.
-recovered snap_scaffold_306-snap.1-T1, initial, 1965, 2148
-recovered snap_scaffold_306-snap.1-T1, terminal, 5264, 5531
-recovered snap_scaffold_306-snap.1-T1, internal, 70, 214
-recovered snap_scaffold_306-snap.1-T1, internal, 408, 505
-recovered snap_scaffold_306-snap.1-T1, internal, 766, 909
-recovered snap_scaffold_306-snap.1-T1, internal, 1233, 1397
-recovered snap_scaffold_306-snap.1-T1, internal, 1672, 1799
-recovered snap_scaffold_306-snap.1-T1, internal, 1965, 2148
-recovered snap_scaffold_306-snap.1-T1, internal, 2276, 2363
-recovered snap_scaffold_306-snap.1-T1, internal, 2741, 2949
-recovered snap_scaffold_306-snap.1-T1, internal, 3441, 3585
-recovered snap_scaffold_306-snap.1-T1, internal, 4077, 4162
-recovered snap_scaffold_306-snap.1-T1, internal, 4211, 4324
-recovered snap_scaffold_306-snap.1-T1, internal, 4656, 4780
Valid prediction for GlimmerHMM_glimmerT_61668-T1
Valid prediction for GeneMark_model.107250_t
Couldn't classify 8091, 8234
Sorry, prediction GeneMark_model.107254_t fails validation.
(ATG)	 AC	7286-7420	GT	CTG
(CTG)	 AG	7677-7906	GT	GAG
(TTT)	 AG	7933-7979	GT	GTG
(GGA)	 AG	8091-8234	GT	GGG
-recovered GeneMark_model.107254_t, initial, 7286, 7420
-recovered GeneMark_model.107254_t, internal, 7677, 7906
-recovered GeneMark_model.107254_t, internal, 7933, 7979
-recovered GeneMark_model.107254_t, internal, 8091, 8234
Couldn't classify 70, 135
Sorry, prediction GeneMark_model.107248_t fails validation.
(GTG)	 AG	70-135	GT	ACG
(AGG)	 AG	188-262	CA	AAC
-recovered GeneMark_model.107248_t, terminal, 188, 262
-recovered GeneMark_model.107248_t, internal, 70, 135

-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.107251_t
Valid prediction for GeneMark_model.107253_t
Valid prediction for GeneMark_model.107249_t
Couldn't classify 901, 1462
Sorry, prediction snap_scaffold_306-snap.2-T1 fails validation.
(GAT)	 AG	901-1462	GT	GGG
(CGT)	 AG	2121-2389	GT	ACG
(CCA)	 AG	3567-3741	GT	AGG
(CAC)	 AG	3998-4060	GT	AGG
(CGG)	 AG	4115-4307	GT	AGG
(ATC)	 AG	6152-6816	CT	GAC
-recovered snap_scaffold_306-snap.2-T1, terminal, 6152, 6816
-recovered snap_scaffold_306-snap.2-T1, internal, 901, 1462
-recovered snap_scaffold_306-snap.2-T1, internal, 2121, 2389
-recovered snap_scaffold_306-snap.2-T1, internal, 3567, 3741
-recovered snap_scaffold_306-snap.2-T1, internal, 3998, 4060
-recovered snap_scaffold_306-snap.2-T1, internal, 4115, 4307

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5531, rend_intergenic: 1503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7418, rend_intergenic: 5873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 8318
-exon list size: 89


building trellis

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97.8    
98.9    
-found 2 predictions from path traversal
Error with prediction: snap lend_intergenic: 5531, rend_intergenic: 1503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7418, rend_intergenic: 5873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support