-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_1530989-1743446

-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_35613-T1
Valid prediction for pasa_asmbl_15033.p1
Valid prediction for GlimmerHMM_glimmerT_35627-T1
Valid prediction for snap_scaffold_15-snap.315-T1
Valid prediction for snap_scaffold_15-snap.346-T1
Valid prediction for snap_scaffold_15-snap.313-T1
Couldn't classify 67684, 67767
Sorry, prediction pasa_asmbl_15023.p1 fails validation.
(TTG)	 AG	67684-67767	GT	AGG
(AAA)	 AG	67878-67975	GT	AGG
(TTC)	 AG	68047-68102	GT	TGG
(GTA)	 AG	68213-68296	GT	TGG
(GAA)	 AG	68399-68475	GT	ATG
(GTC)	 AG	68589-68747	GT	AGG
(CGT)	 AG	68923-69029	GT	GAG
(GAG)	 AG	69213-69308	GT	AGG
(AGA)	 AG	69433-69493	GT	TGG
(ACA)	 AG	69594-69670	GT	AGG
(GTG)	 AG	69761-69885	GT	GAG
(CCA)	 AG	70161-70228	GT	AGG
(GAC)	 AG	70332-70441	GT	AGG
(TTT)	 AG	70528-70623	GT	CGG
(CTG)	 AG	70728-70802	GT	TGG
(TCA)	 AG	70889-70952	GT	AGG
(GCA)	 AG	71090-71176	CC	AGC
add_exon() Sorry, pasa_asmbl_15023.p1 67878-67975-terminal-2 is invalid.
-recovered pasa_asmbl_15023.p1, terminal, 67878, 67975
-recovered pasa_asmbl_15023.p1, terminal, 71090, 71176
-recovered pasa_asmbl_15023.p1, internal, 67684, 67767
-recovered pasa_asmbl_15023.p1, internal, 67878, 67975
-recovered pasa_asmbl_15023.p1, internal, 68047, 68102
-recovered pasa_asmbl_15023.p1, internal, 68213, 68296
-recovered pasa_asmbl_15023.p1, internal, 68399, 68475
-recovered pasa_asmbl_15023.p1, internal, 68589, 68747
-recovered pasa_asmbl_15023.p1, internal, 68923, 69029
-recovered pasa_asmbl_15023.p1, internal, 69213, 69308
-recovered pasa_asmbl_15023.p1, internal, 69433, 69493
-recovered pasa_asmbl_15023.p1, internal, 69594, 69670
-recovered pasa_asmbl_15023.p1, internal, 69761, 69885
-recovered pasa_asmbl_15023.p1, internal, 70161, 70228
-recovered pasa_asmbl_15023.p1, internal, 70332, 70441
-recovered pasa_asmbl_15023.p1, internal, 70528, 70623
-recovered pasa_asmbl_15023.p1, internal, 70728, 70802
-recovered pasa_asmbl_15023.p1, internal, 70889, 70952
Valid prediction for GlimmerHMM_glimmerT_35626-T1
Valid prediction for snap_scaffold_15-snap.343-T1
Valid prediction for snap_scaffold_15-snap.324-T1
Valid prediction for HiQ_model.g23772.t1
Valid prediction for HiQ_model.g23781.t1
Valid prediction for HiQ_model.g23782.t1
Valid prediction for CodingQuarry_transcript_17916-T1
Valid prediction for pasa_asmbl_15891.p1
Valid prediction for snap_scaffold_15-snap.321-T1
Valid prediction for snap_scaffold_15-snap.339-T1
Valid prediction for snap_scaffold_15-snap.351-T1
Valid prediction for snap_scaffold_15-snap.341-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35620-T1
Valid prediction for snap_scaffold_15-snap.322-T1
Valid prediction for snap_scaffold_15-snap.331-T1
Valid prediction for snap_scaffold_15-snap.309-T1
Valid prediction for Augustus_model.g23766.t1
Valid prediction for GlimmerHMM_glimmerT_35610-T1
Valid prediction for pasa_asmbl_15021.p1
Valid prediction for snap_scaffold_15-snap.334-T1
Valid prediction for snap_scaffold_15-snap.323-T1
Valid prediction for HiQ_model.g23771.t1
Valid prediction for GlimmerHMM_glimmerT_35619-T1
Valid prediction for GlimmerHMM_glimmerT_35618-T1
Valid prediction for snap_scaffold_15-snap.320-T1
Valid prediction for pasa_asmbl_15028.p1
Valid prediction for GlimmerHMM_glimmerT_35628-T1
Valid prediction for Augustus_model.g23768.t1
Valid prediction for GlimmerHMM_glimmerT_35629-T1
Valid prediction for snap_scaffold_15-snap.317-T1
Valid prediction for snap_scaffold_15-snap.311-T1
Valid prediction for snap_scaffold_15-snap.345-T1
Valid prediction for CodingQuarry_transcript_17915-T1
Valid prediction for CodingQuarry_transcript_17909-T1
Valid prediction for CodingQuarry_transcript_17910-T1
Valid prediction for snap_scaffold_15-snap.337-T1
Valid prediction for Augustus_model.g23770.t1
Valid prediction for CodingQuarry_transcript_17914-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_35621-T1
Valid prediction for snap_scaffold_15-snap.349-T1
Valid prediction for GlimmerHMM_glimmerT_35612-T1
Valid prediction for Augustus_model.g23773.t1
Couldn't classify 112522, 113226
Sorry, prediction pasa_asmbl_13970.p1 fails validation.
(AAC)	 CC	112522-113226	GC	GGG
Valid prediction for snap_scaffold_15-snap.312-T1
Valid prediction for GlimmerHMM_glimmerT_35623-T1
Valid prediction for Augustus_model.g23774.t1
Valid prediction for GlimmerHMM_glimmerT_35625-T1
Valid prediction for snap_scaffold_15-snap.348-T1
Valid prediction for snap_scaffold_15-snap.336-T1
Valid prediction for snap_scaffold_15-snap.347-T1
Valid prediction for snap_scaffold_15-snap.332-T1
Valid prediction for snap_scaffold_15-snap.329-T1
Valid prediction for snap_scaffold_15-snap.342-T1
Valid prediction for snap_scaffold_15-snap.338-T1
Valid prediction for GlimmerHMM_glimmerT_35630-T1
Couldn't classify 27166, 27202
Sorry, prediction pasa_asmbl_13971.p1 fails validation.
(GGG)	 CA	27166-27202	GT	AGG
(ATC)	 AG	27494-27648	GT	TGG
(GTA)	 AG	27749-27857	GT	TGG
(GTT)	 AG	28251-28400	GT	AGG
(GTT)	 AG	28636-28836	GT	CGG
(GTG)	 AG	29078-29238	CG	AAC
-recovered pasa_asmbl_13971.p1, terminal, 29078, 29238
-recovered pasa_asmbl_13971.p1, internal, 27494, 27648
-recovered pasa_asmbl_13971.p1, internal, 27749, 27857
-recovered pasa_asmbl_13971.p1, internal, 28251, 28400
-recovered pasa_asmbl_13971.p1, internal, 28636, 28836
Valid prediction for Augustus_model.g23775.t1
Valid prediction for GlimmerHMM_glimmerT_35617-T1
Valid prediction for CodingQuarry_transcript_17912-T1
Valid prediction for snap_scaffold_15-snap.344-T1
Valid prediction for snap_scaffold_15-snap.318-T1
Valid prediction for snap_scaffold_15-snap.319-T1
Valid prediction for snap_scaffold_15-snap.316-T1
Valid prediction for GlimmerHMM_glimmerT_35622-T1
Valid prediction for GlimmerHMM_glimmerT_35615-T1
Valid prediction for Augustus_model.g23767.t1
Valid prediction for snap_scaffold_15-snap.330-T1
Valid prediction for snap_scaffold_15-snap.328-T1
Valid prediction for HiQ_model.g23777.t1
Valid prediction for GlimmerHMM_glimmerT_35624-T1
Valid prediction for snap_scaffold_15-snap.325-T1
Valid prediction for snap_scaffold_15-snap.335-T1
Valid prediction for snap_scaffold_15-snap.326-T1
Valid prediction for pasa_asmbl_13960.p1
Valid prediction for GlimmerHMM_glimmerT_35611-T1
Valid prediction for snap_scaffold_15-snap.350-T1
Valid prediction for Augustus_model.g23778.t1
Valid prediction for GlimmerHMM_glimmerT_35616-T1
Valid prediction for Augustus_model.g23780.t1
Valid prediction for Augustus_model.g23784.t1
Valid prediction for snap_scaffold_15-snap.310-T1
Valid prediction for Augustus_model.g23776.t1
Valid prediction for CodingQuarry_transcript_17911-T1
Couldn't classify 127029, 127198
Couldn't classify 128416, 128481
Sorry, prediction pasa_asmbl_13966.p1 fails validation.
(GAG)	 TT	127029-127198	GT	AGG
(TTC)	 AG	127496-127595	GC	AGG
(GAG)	 AG	127963-128070	GT	TGG
(ATG)	 AG	128416-128481	TC	GCT
-recovered pasa_asmbl_13966.p1, internal, 127496, 127595
-recovered pasa_asmbl_13966.p1, internal, 127963, 128070
Valid prediction for GlimmerHMM_glimmerT_35614-T1
Valid prediction for GlimmerHMM_glimmerT_35633-T1
Valid prediction for GlimmerHMM_glimmerT_35632-T1
Valid prediction for snap_scaffold_15-snap.352-T1
Valid prediction for snap_scaffold_15-snap.314-T1
Valid prediction for snap_scaffold_15-snap.340-T1
Valid prediction for snap_scaffold_15-snap.327-T1
Valid prediction for Augustus_model.g23779.t1
Valid prediction for CodingQuarry_transcript_17917-T1
Valid prediction for Augustus_model.g23783.t1
Valid prediction for snap_scaffold_15-snap.333-T1
Valid prediction for Augustus_model.g23769.t1
Valid prediction for GlimmerHMM_glimmerT_35631-T1
Couldn't classify 128632, 129060
Sorry, prediction pasa_asmbl_13965.p1 fails validation.
(CTG)	 TC	128632-129060	GT	CAG
Couldn't classify 130063, 130146
Couldn't classify 131080, 131174
Sorry, prediction pasa_asmbl_14893.p1 fails validation.
(TCT)	 GT	130063-130146	GT	AGG
(GAA)	 AG	130235-130363	GT	AGG
(ATA)	 AG	130729-130921	GT	AGG
(GTG)	 AG	131080-131174	GG	CAG
-recovered pasa_asmbl_14893.p1, internal, 130235, 130363
-recovered pasa_asmbl_14893.p1, internal, 130729, 130921

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25831, rend_intergenic: 24288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36428, rend_intergenic: 32679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44529, rend_intergenic: 38285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47313, rend_intergenic: 45570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107927, rend_intergenic: 102717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108561, rend_intergenic: 108034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140698, rend_intergenic: 138595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170434, rend_intergenic: 168979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173481, rend_intergenic: 171683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175445, rend_intergenic: 174301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209856, rend_intergenic: 207403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212458
-exon list size: 401


building trellis

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32.5    
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41.9    
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98.0    
98.3    
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99.0    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 25831, rend_intergenic: 24288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36428, rend_intergenic: 32679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44529, rend_intergenic: 38285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47313, rend_intergenic: 45570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107927, rend_intergenic: 102717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108561, rend_intergenic: 108034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140698, rend_intergenic: 138595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170434, rend_intergenic: 168979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173481, rend_intergenic: 171683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175445, rend_intergenic: 174301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209856, rend_intergenic: 207403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support