-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_15538949-15705125

-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_12-snap.2985-T1
Valid prediction for CodingQuarry_transcript_10506-T1
Valid prediction for GlimmerHMM_glimmerT_30683-T1
Valid prediction for pasa_asmbl_8134.p1
Valid prediction for GlimmerHMM_glimmerT_30693-T1
Valid prediction for snap_scaffold_12-snap.2984-T1
Valid prediction for GlimmerHMM_glimmerT_30677-T1
Valid prediction for snap_scaffold_12-snap.2994-T1
Valid prediction for GlimmerHMM_glimmerT_30699-T1
Valid prediction for snap_scaffold_12-snap.2980-T1
Valid prediction for Augustus_model.g20308.t1
Valid prediction for snap_scaffold_12-snap.2972-T1
Valid prediction for snap_scaffold_12-snap.3002-T1
Valid prediction for snap_scaffold_12-snap.2975-T1
Valid prediction for GlimmerHMM_glimmerT_30680-T1
Valid prediction for Augustus_model.g20303.t1
Valid prediction for snap_scaffold_12-snap.2974-T1
Valid prediction for snap_scaffold_12-snap.2981-T1
Valid prediction for snap_scaffold_12-snap.2970-T1
Valid prediction for HiQ_model.g20315.t1
Valid prediction for GlimmerHMM_glimmerT_30681-T1
Valid prediction for snap_scaffold_12-snap.2995-T1
Valid prediction for GlimmerHMM_glimmerT_30679-T1
Valid prediction for snap_scaffold_12-snap.3001-T1
Valid prediction for GlimmerHMM_glimmerT_30688-T1
Valid prediction for Augustus_model.g20302.t1
Valid prediction for GlimmerHMM_glimmerT_30696-T1
Valid prediction for GlimmerHMM_glimmerT_30687-T1
Couldn't classify 106138, 106338
Sorry, prediction pasa_asmbl_8129.p1 fails validation.
(ATG)	 AA	104413-105057	GT	AGG
(GTG)	 AG	106138-106338	GA	GAG
-recovered pasa_asmbl_8129.p1, initial, 104413, 105057
Valid prediction for GlimmerHMM_glimmerT_30682-T1
Valid prediction for snap_scaffold_12-snap.2990-T1
Valid prediction for GlimmerHMM_glimmerT_30685-T1
Valid prediction for snap_scaffold_12-snap.2967-T1
Valid prediction for snap_scaffold_12-snap.2982-T1
Valid prediction for GlimmerHMM_glimmerT_30678-T1
Valid prediction for snap_scaffold_12-snap.2983-T1
Valid prediction for HiQ_model.g20311.t1
Valid prediction for pasa_asmbl_8131.p1
Valid prediction for Augustus_model.g20304.t1
Valid prediction for snap_scaffold_12-snap.2976-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 snap_scaffold_12-snap.2999-T1
Valid prediction for GlimmerHMM_glimmerT_30698-T1
Valid prediction for GlimmerHMM_glimmerT_30690-T1
Valid prediction for snap_scaffold_12-snap.2968-T1
Valid prediction for Augustus_model.g20309.t1
Valid prediction for CodingQuarry_transcript_10503-T1
Valid prediction for snap_scaffold_12-snap.2998-T1
Valid prediction for snap_scaffold_12-snap.3003-T1
Valid prediction for GlimmerHMM_glimmerT_30694-T1
Valid prediction for snap_scaffold_12-snap.2978-T1
Valid prediction for HiQ_model.g20312.t1
Valid prediction for GlimmerHMM_glimmerT_30684-T1
Valid prediction for HiQ_model.g20314.t1
Couldn't classify 43538, 43585
Sorry, prediction pasa_asmbl_9216.p1 fails validation.
(CTG)	 AG	43538-43585	GT	AGG
(TTG)	 AG	43696-43910	GT	AGG
(ACT)	 AG	44335-44502	GT	AGG
(GCT)	 AG	44632-44767	GT	AGG
(GTC)	 AG	45357-45517	GT	AGG
(ATT)	 AG	45613-45742	GT	CCG
(GAC)	 AG	45882-45992	GT	AGG
(GTG)	 AG	46111-46383	GT	AGG
(GTG)	 AG	46598-46798	GT	ATG
(ATT)	 AG	47037-47154	GT	CGG
(GAA)	 AG	47298-47462	GT	GGG
(GCT)	 AG	47728-47828	AC	GAA
add_exon() Sorry, pasa_asmbl_9216.p1 43696-43910-terminal-2 is invalid.
-recovered pasa_asmbl_9216.p1, terminal, 43696, 43910
-recovered pasa_asmbl_9216.p1, terminal, 47728, 47828
-recovered pasa_asmbl_9216.p1, internal, 43538, 43585
-recovered pasa_asmbl_9216.p1, internal, 43696, 43910
-recovered pasa_asmbl_9216.p1, internal, 44335, 44502
-recovered pasa_asmbl_9216.p1, internal, 44632, 44767
-recovered pasa_asmbl_9216.p1, internal, 45357, 45517
-recovered pasa_asmbl_9216.p1, internal, 45613, 45742
-recovered pasa_asmbl_9216.p1, internal, 45882, 45992
-recovered pasa_asmbl_9216.p1, internal, 46111, 46383
-recovered pasa_asmbl_9216.p1, internal, 46598, 46798
-recovered pasa_asmbl_9216.p1, internal, 47037, 47154
-recovered pasa_asmbl_9216.p1, internal, 47298, 47462
Valid prediction for pasa_asmbl_9096.p1
Valid prediction for snap_scaffold_12-snap.2989-T1
Valid prediction for snap_scaffold_12-snap.2991-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for HiQ_model.g20306.t1
Valid prediction for snap_scaffold_12-snap.2996-T1
Valid prediction for snap_scaffold_12-snap.2973-T1
Valid prediction for CodingQuarry_transcript_10500-T1
Valid prediction for snap_scaffold_12-snap.2992-T1
Couldn't classify 14995, 15081
Couldn't classify 15169, 15194
Sorry, prediction CodingQuarry_transcript_10505-T1 fails validation.
(ATG)	 CC	13839-13930	GT	AGG
(ATT)	 AG	14081-14165	GT	AGG
(GTG)	 AG	14378-14478	GT	CGG
(GTT)	 AG	14656-14731	GT	ATG
(TTT)	 AG	14995-15081	AT	ATA
(GGA)	 AT	15169-15194	GT	ATG
(TCG)	 AG	15284-15422	GT	ATG
(ATG)	 AG	15567-15656	GT	CAG
(GGT)	 AG	15779-15880	GT	GGG
(ACG)	 AG	16146-16509	GT	AGG
(TTC)	 AG	16761-16923	GT	AGG
(GAA)	 AG	17012-17066	CT	AAC
-recovered CodingQuarry_transcript_10505-T1, initial, 13839, 13930
-recovered CodingQuarry_transcript_10505-T1, initial, 15567, 15656
add_exon() Sorry, CodingQuarry_transcript_10505-T1 16761-16923-terminal-3 is invalid.
-recovered CodingQuarry_transcript_10505-T1, terminal, 16761, 16923
-recovered CodingQuarry_transcript_10505-T1, terminal, 17012, 17066
-recovered CodingQuarry_transcript_10505-T1, internal, 14081, 14165
-recovered CodingQuarry_transcript_10505-T1, internal, 14378, 14478
-recovered CodingQuarry_transcript_10505-T1, internal, 14656, 14731
-recovered CodingQuarry_transcript_10505-T1, internal, 15284, 15422
-recovered CodingQuarry_transcript_10505-T1, internal, 15567, 15656
-recovered CodingQuarry_transcript_10505-T1, internal, 15779, 15880
-recovered CodingQuarry_transcript_10505-T1, internal, 16146, 16509
-recovered CodingQuarry_transcript_10505-T1, internal, 16761, 16923
Valid prediction for pasa_asmbl_9091.p1
Valid prediction for GlimmerHMM_glimmerT_30691-T1
Valid prediction for snap_scaffold_12-snap.2977-T1
Valid prediction for GlimmerHMM_glimmerT_30695-T1
Valid prediction for snap_scaffold_12-snap.2971-T1
Valid prediction for snap_scaffold_12-snap.2993-T1
Valid prediction for GlimmerHMM_glimmerT_30689-T1
Valid prediction for CodingQuarry_transcript_10499-T1
Valid prediction for snap_scaffold_12-snap.2988-T1
Valid prediction for HiQ_model.g20313.t1
Valid prediction for snap_scaffold_12-snap.3004-T1
Valid prediction for GlimmerHMM_glimmerT_30697-T1
Valid prediction for CodingQuarry_transcript_10502-T1
Valid prediction for CodingQuarry_transcript_10501-T1
Couldn't classify 66520, 66623
Sorry, prediction pasa_asmbl_9090.p1 fails validation.
(ACG)	 AG	66520-66623	GT	AGG
(AAA)	 AG	67372-67503	GT	AGG
(CTT)	 AG	67731-67835	GT	CGG
(TTA)	 AG	67944-68006	GT	AGG
(CTC)	 AG	68146-68280	GT	AGG
(ACA)	 AG	68561-68710	GT	ATG
(AGA)	 AG	69046-69145	GT	AGG
(GAG)	 AG	69314-69376	CT	AGC
add_exon() Sorry, pasa_asmbl_9090.p1 66520-66623-terminal-2 is invalid.
-recovered pasa_asmbl_9090.p1, terminal, 66520, 66623
-recovered pasa_asmbl_9090.p1, terminal, 69314, 69376
-recovered pasa_asmbl_9090.p1, internal, 66520, 66623
-recovered pasa_asmbl_9090.p1, internal, 67372, 67503
-recovered pasa_asmbl_9090.p1, internal, 67731, 67835
-recovered pasa_asmbl_9090.p1, internal, 67944, 68006
-recovered pasa_asmbl_9090.p1, internal, 68146, 68280
-recovered pasa_asmbl_9090.p1, internal, 68561, 68710
-recovered pasa_asmbl_9090.p1, internal, 69046, 69145
Valid prediction for Augustus_model.g20305.t1
Valid prediction for snap_scaffold_12-snap.2969-T1
Valid prediction for GlimmerHMM_glimmerT_30692-T1
Valid prediction for GlimmerHMM_glimmerT_30686-T1
Valid prediction for snap_scaffold_12-snap.2997-T1
Valid prediction for CodingQuarry_transcript_10504-T1
Valid prediction for snap_scaffold_12-snap.2979-T1
Valid prediction for Augustus_model.g20310.t1
Valid prediction for pasa_asmbl_9092.p1
Valid prediction for snap_scaffold_12-snap.3000-T1
Valid prediction for snap_scaffold_12-snap.2986-T1
Valid prediction for CodingQuarry_transcript_10497-T1
Valid prediction for Augustus_model.g20307.t1
Valid prediction for snap_scaffold_12-snap.2987-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23622, rend_intergenic: 23476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25303, rend_intergenic: 23779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28468, rend_intergenic: 26215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43252, rend_intergenic: 30569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63316, rend_intergenic: 43283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72384, rend_intergenic: 64697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95034, rend_intergenic: 86125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109948, rend_intergenic: 105613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129993, rend_intergenic: 119401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135675, rend_intergenic: 130871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164174, rend_intergenic: 158443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166177
-exon list size: 433


building trellis

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27.8    
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28.3    
28.5    
28.7    
29.0    
29.2    
29.4    
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29.9    
30.1    
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31.0    
31.3    
31.5    
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32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
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34.9    
35.2    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.5    
37.7    
37.9    
38.2    
38.4    
38.6    
38.9    
39.1    
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39.5    
39.8    
40.0    
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40.7    
40.9    
41.1    
41.4    
41.6    
41.8    
42.1    
42.3    
42.5    
42.8    
43.0    
43.2    
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43.7    
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44.1    
44.4    
44.6    
44.8    
45.1    
45.3    
45.5    
45.7    
46.0    
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47.1    
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47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
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49.2    
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49.7    
49.9    
50.1    
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50.6    
50.8    
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81.8    
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84.6    
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88.3    
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90.6    
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91.0    
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91.5    
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92.2    
92.4    
92.6    
92.9    
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93.3    
93.6    
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96.8    
97.0    
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97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 23622, rend_intergenic: 23476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25303, rend_intergenic: 23779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28468, rend_intergenic: 26215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43252, rend_intergenic: 30569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63316, rend_intergenic: 43283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72384, rend_intergenic: 64697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95034, rend_intergenic: 86125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109948, rend_intergenic: 105613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129993, rend_intergenic: 119401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135675, rend_intergenic: 130871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164174, rend_intergenic: 158443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support