-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_10068103-10247456

-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_6-snap.2193-T1
Valid prediction for snap_scaffold_6-snap.2213-T1
Valid prediction for Augustus_model.g10228.t1
Valid prediction for Augustus_model.g10216.t1
Valid prediction for snap_scaffold_6-snap.2216-T1
Couldn't classify 107617, 107712
Couldn't classify 108224, 108283
Sorry, prediction pasa_asmbl_48002.p1 fails validation.
(GCC)	 GT	107617-107712	GT	AGG
(GTG)	 AG	107827-107976	GT	AGG
(GAG)	 AG	108224-108283	TT	ACT
-recovered pasa_asmbl_48002.p1, internal, 107827, 107976
Valid prediction for snap_scaffold_6-snap.2188-T1
Valid prediction for snap_scaffold_6-snap.2217-T1
Valid prediction for GlimmerHMM_glimmerT_15375-T1
Valid prediction for GlimmerHMM_glimmerT_15366-T1
Valid prediction for Augustus_model.g10213.t1
Valid prediction for snap_scaffold_6-snap.2184-T1
Valid prediction for GlimmerHMM_glimmerT_15355-T1
Valid prediction for snap_scaffold_6-snap.2186-T1
Valid prediction for Augustus_model.g10224.t1
Valid prediction for snap_scaffold_6-snap.2208-T1
Valid prediction for snap_scaffold_6-snap.2195-T1
Valid prediction for Augustus_model.g10215.t1
Valid prediction for snap_scaffold_6-snap.2214-T1
Valid prediction for snap_scaffold_6-snap.2201-T1
Valid prediction for pasa_asmbl_47274.p1
Valid prediction for snap_scaffold_6-snap.2198-T1
Valid prediction for CodingQuarry_transcript_55196-T1
Valid prediction for GlimmerHMM_glimmerT_15353-T1
Valid prediction for GlimmerHMM_glimmerT_15350-T1
Valid prediction for GlimmerHMM_glimmerT_15367-T1
Valid prediction for snap_scaffold_6-snap.2194-T1
Valid prediction for snap_scaffold_6-snap.2211-T1
Valid prediction for Augustus_model.g10232.t1
Valid prediction for HiQ_model.g10231.t1
Valid prediction for snap_scaffold_6-snap.2182-T1
Valid prediction for GlimmerHMM_glimmerT_15352-T1
Valid prediction for GlimmerHMM_glimmerT_15368-T1
Valid prediction for snap_scaffold_6-snap.2204-T1
Valid prediction for GlimmerHMM_glimmerT_15356-T1
Valid prediction for snap_scaffold_6-snap.2190-T1
Valid prediction for GlimmerHMM_glimmerT_15362-T1
Valid prediction for snap_scaffold_6-snap.2189-T1
Couldn't classify 108389, 108432
Sorry, prediction pasa_asmbl_47265.p2 fails validation.
(CCA)	 TC	108389-108432	GT	AGG
(CTC)	 AG	108658-108811	GT	AGG
(TTT)	 AG	108931-108976	GT	AGG
(AAG)	 AG	109065-109222	GC	GAG
-recovered pasa_asmbl_47265.p2, terminal, 109065, 109222
-recovered pasa_asmbl_47265.p2, internal, 108658, 108811
-recovered pasa_asmbl_47265.p2, internal, 108931, 108976
-recovered pasa_asmbl_47265.p2, internal, 109065, 109222
Valid prediction for GlimmerHMM_glimmerT_15354-T1
Couldn't classify 130463, 130590
Sorry, prediction pasa_asmbl_47269.p1 fails validation.
(GTG)	 AG	130463-130590	GT	AAG
(AGT)	 AG	130729-130887	GT	CGG
(ATT)	 AG	131039-131117	AC	GAA
-recovered pasa_asmbl_47269.p1, terminal, 131039, 131117
-recovered pasa_asmbl_47269.p1, internal, 130463, 130590
-recovered pasa_asmbl_47269.p1, internal, 130729, 130887
Valid prediction for GlimmerHMM_glimmerT_15370-T1
Valid prediction for GlimmerHMM_glimmerT_15371-T1
Valid prediction for Augustus_model.g10217.t1
Valid prediction for snap_scaffold_6-snap.2209-T1
Valid prediction for Augustus_model.g10229.t1
Valid prediction for Augustus_model.g10219.t1
Valid prediction for Augustus_model.g10227.t1
Valid prediction for Augustus_model.g10226.t1
Valid prediction for snap_scaffold_6-snap.2205-T1
Valid prediction for GlimmerHMM_glimmerT_15373-T1
Valid prediction for Augustus_model.g10211.t1
Valid prediction for snap_scaffold_6-snap.2210-T1
Valid prediction for GlimmerHMM_glimmerT_15359-T1
Valid prediction for GlimmerHMM_glimmerT_15363-T1
Valid prediction for GlimmerHMM_glimmerT_15369-T1
Couldn't classify 145602, 145662
Sorry, prediction pasa_asmbl_47271.p1 fails validation.
(ATG)	 AA	136085-136121	GT	GCG
(CAA)	 AG	137482-137540	GT	AGG
(GTT)	 AG	137812-137893	GT	AGG
(AAG)	 AG	138041-138084	GT	AGG
(GCG)	 AG	138167-138220	GT	AGG
(GTG)	 AG	138454-138506	GT	AGG
(GGT)	 AG	139213-139321	GT	AGG
(TGT)	 AG	140574-140675	GT	AGG
(ATG)	 AG	140811-140909	GT	AGG
(AGG)	 AG	141180-141288	GT	AGG
(GGT)	 AG	141592-141712	GT	CTG
(AAT)	 AG	141866-141950	GT	AAG
(GAC)	 AG	142037-142182	GT	ACG
(GCT)	 AG	142629-142729	GT	AGG
(TGA)	 AG	142865-142995	GT	AGG
(AAA)	 AG	143439-143522	GT	TGG
(CTC)	 AG	144091-144213	GT	AGG
(CAA)	 AG	144328-144530	GT	CCG
(CCA)	 AG	145602-145662	AT	ACA
-recovered pasa_asmbl_47271.p1, initial, 136085, 136121
-recovered pasa_asmbl_47271.p1, initial, 140811, 140909
-recovered pasa_asmbl_47271.p1, internal, 137482, 137540
-recovered pasa_asmbl_47271.p1, internal, 137812, 137893
-recovered pasa_asmbl_47271.p1, internal, 138041, 138084
-recovered pasa_asmbl_47271.p1, internal, 138167, 138220
-recovered pasa_asmbl_47271.p1, internal, 138454, 138506
-recovered pasa_asmbl_47271.p1, internal, 139213, 139321
-recovered pasa_asmbl_47271.p1, internal, 140574, 140675
-recovered pasa_asmbl_47271.p1, internal, 140811, 140909
-recovered pasa_asmbl_47271.p1, internal, 141180, 141288
-recovered pasa_asmbl_47271.p1, internal, 141592, 141712
-recovered pasa_asmbl_47271.p1, internal, 141866, 141950
-recovered pasa_asmbl_47271.p1, internal, 142037, 142182
-recovered pasa_asmbl_47271.p1, internal, 142629, 142729
-recovered pasa_asmbl_47271.p1, internal, 142865, 142995
-recovered pasa_asmbl_47271.p1, internal, 143439, 143522
-recovered pasa_asmbl_47271.p1, internal, 144091, 144213
-recovered pasa_asmbl_47271.p1, internal, 144328, 144530

-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 CodingQuarry_transcript_55188-T1
Valid prediction for Augustus_model.g10212.t1
Valid prediction for snap_scaffold_6-snap.2180-T1
Valid prediction for snap_scaffold_6-snap.2207-T1
Valid prediction for snap_scaffold_6-snap.2179-T1
Valid prediction for snap_scaffold_6-snap.2215-T1
Valid prediction for Augustus_model.g10230.t1
Valid prediction for snap_scaffold_6-snap.2200-T1
Valid prediction for snap_scaffold_6-snap.2181-T1
Valid prediction for snap_scaffold_6-snap.2185-T1
Valid prediction for snap_scaffold_6-snap.2196-T1
Valid prediction for pasa_asmbl_48668.p1
Couldn't classify 105954, 106223
Sorry, prediction pasa_asmbl_48658.p1 fails validation.
(CGC)	 CC	105954-106223	GT	AGG
(GTG)	 AG	106450-106515	GT	GGG
(CTG)	 AG	106639-106713	GG	AAG
-recovered pasa_asmbl_48658.p1, terminal, 106639, 106713
-recovered pasa_asmbl_48658.p1, internal, 106450, 106515
Valid prediction for GlimmerHMM_glimmerT_15372-T1
Valid prediction for snap_scaffold_6-snap.2202-T1
Valid prediction for GlimmerHMM_glimmerT_15351-T1
Valid prediction for snap_scaffold_6-snap.2191-T1
Couldn't classify 23058, 23172
Sorry, prediction pasa_asmbl_48675.p1 fails validation.
(GGT)	 AG	23058-23172	GT	CGG
(TCA)	 AG	23365-23468	GT	AGG
(GCC)	 AG	23607-23831	CC	AGC
-recovered pasa_asmbl_48675.p1, terminal, 23607, 23831
-recovered pasa_asmbl_48675.p1, internal, 23058, 23172
-recovered pasa_asmbl_48675.p1, internal, 23365, 23468
Valid prediction for HiQ_model.g10223.t1
Valid prediction for CodingQuarry_transcript_55189-T1
Valid prediction for snap_scaffold_6-snap.2203-T1
Couldn't classify 21757, 21885
Couldn't classify 22022, 22049
Sorry, prediction pasa_asmbl_48676.p1 fails validation.
(ATG)	 TA	20420-20556	GT	AGG
(ATC)	 AG	21026-21100	GT	AGG
(TCT)	 AG	21408-21533	GT	AGG
(TGT)	 AG	21757-21885	AT	CTA
(ATT)	 AC	22022-22049	CA	TGC
-recovered pasa_asmbl_48676.p1, initial, 20420, 20556
add_exon() Sorry, pasa_asmbl_48676.p1 21026-21100-terminal-1 is invalid.
-recovered pasa_asmbl_48676.p1, terminal, 21026, 21100
-recovered pasa_asmbl_48676.p1, internal, 21026, 21100
-recovered pasa_asmbl_48676.p1, internal, 21408, 21533
Valid prediction for GlimmerHMM_glimmerT_15358-T1
Valid prediction for snap_scaffold_6-snap.2183-T1
Valid prediction for snap_scaffold_6-snap.2197-T1
Valid prediction for GlimmerHMM_glimmerT_15360-T1
Valid prediction for pasa_asmbl_48678.p1
Couldn't classify 95353, 95381
Sorry, prediction pasa_asmbl_48663.p1 fails validation.
(AAC)	 GC	95353-95381	GT	AGG
(TGC)	 AG	95752-95923	GT	CGG
(GAG)	 AG	96038-96124	GT	AGG
(TGT)	 AG	96213-96320	GT	TGG
(ATG)	 AG	96464-96622	GT	AGG
(GAC)	 AG	97054-97141	GT	TGG
(CTG)	 AG	97338-97436	GT	GGG
(GCA)	 AG	97861-97896	GT	AGG
(GTG)	 AG	98090-98185	GT	AGG
(CCA)	 AG	98428-98503	GT	TGG
(GTG)	 AG	98668-98767	GT	AGG
(GAC)	 AG	99245-99319	GT	AGG
(ATC)	 AG	99569-99676	CC	AGC
-recovered pasa_asmbl_48663.p1, initial, 96464, 96622
-recovered pasa_asmbl_48663.p1, terminal, 99569, 99676
-recovered pasa_asmbl_48663.p1, internal, 95752, 95923
-recovered pasa_asmbl_48663.p1, internal, 96038, 96124
-recovered pasa_asmbl_48663.p1, internal, 96213, 96320
-recovered pasa_asmbl_48663.p1, internal, 96464, 96622
-recovered pasa_asmbl_48663.p1, internal, 97054, 97141
-recovered pasa_asmbl_48663.p1, internal, 97338, 97436
-recovered pasa_asmbl_48663.p1, internal, 97861, 97896
-recovered pasa_asmbl_48663.p1, internal, 98090, 98185
-recovered pasa_asmbl_48663.p1, internal, 98428, 98503
-recovered pasa_asmbl_48663.p1, internal, 98668, 98767
-recovered pasa_asmbl_48663.p1, internal, 99245, 99319
Valid prediction for GlimmerHMM_glimmerT_15357-T1
Valid prediction for pasa_asmbl_48666.p1
Valid prediction for Augustus_model.g10210.t1
Valid prediction for pasa_asmbl_48670.p1
Valid prediction for HiQ_model.g10225.t1
Valid prediction for GlimmerHMM_glimmerT_15348-T1
Couldn't classify 92128, 92180
Couldn't classify 92719, 92835
Sorry, prediction pasa_asmbl_49430.p2 fails validation.
(ATC)	 AC	92128-92180	GT	AGG
(ATC)	 AG	92304-92385	GT	AGG
(AGT)	 AG	92490-92612	GT	AGG
(TAC)	 AG	92719-92835	CA	TGC
-recovered pasa_asmbl_49430.p2, internal, 92304, 92385
-recovered pasa_asmbl_49430.p2, internal, 92490, 92612
Valid prediction for CodingQuarry_transcript_55191-T1
Valid prediction for snap_scaffold_6-snap.2206-T1
Valid prediction for snap_scaffold_6-snap.2212-T1
Valid prediction for GlimmerHMM_glimmerT_15374-T1
Valid prediction for GlimmerHMM_glimmerT_15365-T1
Valid prediction for HiQ_model.g10222.t1
Valid prediction for GlimmerHMM_glimmerT_15361-T1
Valid prediction for snap_scaffold_6-snap.2199-T1
Valid prediction for CodingQuarry_transcript_55195-T1
Valid prediction for Augustus_model.g10214.t1
Valid prediction for pasa_asmbl_48655.p1
Couldn't classify 104593, 105057
Sorry, prediction pasa_asmbl_48659.p1 fails validation.
(ATG)	 GA	104082-104203	GT	TGG
(GCT)	 AG	104296-104443	GT	AGG
(GTG)	 AG	104593-105057	GC	AGG
-recovered pasa_asmbl_48659.p1, initial, 104082, 104203
-recovered pasa_asmbl_48659.p1, internal, 104296, 104443
-recovered pasa_asmbl_48659.p1, internal, 104593, 105057
Valid prediction for snap_scaffold_6-snap.2192-T1
Valid prediction for Augustus_model.g10209.t1
Valid prediction for CodingQuarry_transcript_55192-T1
Valid prediction for snap_scaffold_6-snap.2187-T1
Valid prediction for CodingQuarry_transcript_55187-T1
Valid prediction for CodingQuarry_transcript_55190-T1
Valid prediction for GlimmerHMM_glimmerT_15349-T1
Valid prediction for HiQ_model.g10220.t1
Valid prediction for Augustus_model.g10221.t1
Valid prediction for GlimmerHMM_glimmerT_15364-T1
Valid prediction for HiQ_model.g10218.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13773, rend_intergenic: 12663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30888, rend_intergenic: 25875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61717, rend_intergenic: 47637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66392, rend_intergenic: 62905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89325, rend_intergenic: 80046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110019, rend_intergenic: 106411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144249, rend_intergenic: 138037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179354
-exon list size: 450


building trellis

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98.9    
99.1    
99.3    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 13773, rend_intergenic: 12663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30888, rend_intergenic: 25875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61717, rend_intergenic: 47637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66392, rend_intergenic: 62905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89325, rend_intergenic: 80046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110019, rend_intergenic: 106411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144249, rend_intergenic: 138037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support