-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_411527-588289

-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 Augustus_model.g23695.t1
Couldn't classify 78185, 78214
Sorry, prediction pasa_asmbl_14980.p1 fails validation.
(GAG)	 CC	78185-78214	GT	GTG
(ATG)	 AG	78419-78511	GT	ACG
(GGA)	 AG	78635-78790	GT	AGG
(AGC)	 AG	78914-79057	GG	GAG
-recovered pasa_asmbl_14980.p1, initial, 78419, 78511
-recovered pasa_asmbl_14980.p1, terminal, 78914, 79057
-recovered pasa_asmbl_14980.p1, internal, 78419, 78511
-recovered pasa_asmbl_14980.p1, internal, 78635, 78790
Valid prediction for snap_scaffold_15-snap.106-T1
Valid prediction for GlimmerHMM_glimmerT_35486-T1
Valid prediction for snap_scaffold_15-snap.109-T1
Valid prediction for GlimmerHMM_glimmerT_35493-T1
Valid prediction for snap_scaffold_15-snap.99-T1
Valid prediction for Augustus_model.g23697.t1
Valid prediction for Augustus_model.g23698.t1
Valid prediction for snap_scaffold_15-snap.96-T1
Valid prediction for CodingQuarry_transcript_17895-T1
Valid prediction for snap_scaffold_15-snap.91-T1
Valid prediction for snap_scaffold_15-snap.123-T1
Valid prediction for snap_scaffold_15-snap.89-T1
Valid prediction for snap_scaffold_15-snap.113-T1
Valid prediction for snap_scaffold_15-snap.122-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.105-T1
Valid prediction for snap_scaffold_15-snap.86-T1
Valid prediction for Augustus_model.g23700.t1
Valid prediction for snap_scaffold_15-snap.117-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.119-T1
Valid prediction for snap_scaffold_15-snap.108-T1
Couldn't classify 86152, 86484
Sorry, prediction pasa_asmbl_14981.p2 fails validation.
(ATG)	 AA	86152-86484	GG	CAG
Valid prediction for Augustus_model.g23699.t1
Valid prediction for snap_scaffold_15-snap.97-T1
Valid prediction for snap_scaffold_15-snap.103-T1
Valid prediction for GlimmerHMM_glimmerT_35496-T1
Valid prediction for GlimmerHMM_glimmerT_35479-T1
Valid prediction for GlimmerHMM_glimmerT_35488-T1
Valid prediction for snap_scaffold_15-snap.104-T1
Couldn't classify 114410, 114958
Sorry, prediction pasa_asmbl_14986.p1 fails validation.
(TAC)	 TG	114410-114958	CT	TGC
Valid prediction for snap_scaffold_15-snap.115-T1
Valid prediction for GlimmerHMM_glimmerT_35490-T1
Valid prediction for snap_scaffold_15-snap.124-T1
Valid prediction for GlimmerHMM_glimmerT_35492-T1
Valid prediction for HiQ_model.g23701.t1
Valid prediction for snap_scaffold_15-snap.110-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35497-T1
Valid prediction for snap_scaffold_15-snap.121-T1
Valid prediction for pasa_asmbl_14985.p1
Valid prediction for snap_scaffold_15-snap.98-T1
Valid prediction for snap_scaffold_15-snap.107-T1
Valid prediction for GlimmerHMM_glimmerT_35495-T1
Valid prediction for CodingQuarry_transcript_17892-T1
Valid prediction for GlimmerHMM_glimmerT_35491-T1
Valid prediction for pasa_asmbl_14977.p1
Valid prediction for snap_scaffold_15-snap.126-T1
Valid prediction for CodingQuarry_transcript_17893-T1
Valid prediction for snap_scaffold_15-snap.116-T1
Couldn't classify 98583, 98731
Couldn't classify 99407, 99782
Sorry, prediction pasa_asmbl_15878.p1 fails validation.
(ACA)	 CT	98583-98731	GT	ACG
(GTC)	 AG	99407-99782	GC	GGG
-recovered pasa_asmbl_15878.p1, internal, 99407, 99782
Valid prediction for snap_scaffold_15-snap.92-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g23696.t1
Valid prediction for snap_scaffold_15-snap.120-T1
Valid prediction for snap_scaffold_15-snap.102-T1
Valid prediction for snap_scaffold_15-snap.112-T1
Valid prediction for snap_scaffold_15-snap.87-T1
Valid prediction for pasa_asmbl_14987.p1
Valid prediction for GlimmerHMM_glimmerT_35481-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_35494-T1
Valid prediction for snap_scaffold_15-snap.94-T1
Valid prediction for snap_scaffold_15-snap.125-T1
Valid prediction for GlimmerHMM_glimmerT_35489-T1
Couldn't classify 46964, 47088
Sorry, prediction pasa_asmbl_13926.p1 fails validation.
(CCT)	 AG	46964-47088	GT	ACG
(GTC)	 AG	47446-47554	GT	AGG
(CCG)	 AG	47972-48178	GT	AGG
(GTG)	 AG	48440-48549	GT	AGG
(CAT)	 AG	49083-49197	GT	AGG
(GTG)	 AG	49739-49876	GT	AGG
(ATC)	 AG	50033-50223	GT	AGG
(GCG)	 AG	51487-51733	GT	GGG
(GTC)	 AG	52349-52564	GT	AGG
(ATC)	 AG	53215-53355	AC	GAA
-recovered pasa_asmbl_13926.p1, terminal, 53215, 53355
-recovered pasa_asmbl_13926.p1, internal, 46964, 47088
-recovered pasa_asmbl_13926.p1, internal, 47446, 47554
-recovered pasa_asmbl_13926.p1, internal, 47972, 48178
-recovered pasa_asmbl_13926.p1, internal, 48440, 48549
-recovered pasa_asmbl_13926.p1, internal, 49083, 49197
-recovered pasa_asmbl_13926.p1, internal, 49739, 49876
-recovered pasa_asmbl_13926.p1, internal, 50033, 50223
-recovered pasa_asmbl_13926.p1, internal, 51487, 51733
-recovered pasa_asmbl_13926.p1, internal, 52349, 52564
Couldn't classify 29942, 30006
Sorry, prediction pasa_asmbl_14925.p1 fails validation.
(ATG)	 AC	26365-26410	GT	AGG
(ATC)	 AG	28264-28396	GT	TGG
(CTC)	 AG	28711-28805	GT	GAG
(ATC)	 AG	29942-30006	TT	AGT
-recovered pasa_asmbl_14925.p1, initial, 26365, 26410
-recovered pasa_asmbl_14925.p1, internal, 28264, 28396
-recovered pasa_asmbl_14925.p1, internal, 28711, 28805
Valid prediction for GlimmerHMM_glimmerT_35482-T1
Valid prediction for GlimmerHMM_glimmerT_35483-T1
Couldn't classify 39849, 40605
Sorry, prediction pasa_asmbl_13928.p1 fails validation.
(ATG)	 AG	39291-39355	GT	AGG
(GGA)	 AG	39849-40605	GA	GGG
-recovered pasa_asmbl_13928.p1, initial, 39291, 39355
-recovered pasa_asmbl_13928.p1, internal, 39291, 39355
Valid prediction for Augustus_model.g23691.t1
Valid prediction for Augustus_model.g23702.t1
Valid prediction for GlimmerHMM_glimmerT_35498-T1
Valid prediction for GlimmerHMM_glimmerT_35484-T1
Valid prediction for GlimmerHMM_glimmerT_35501-T1
Valid prediction for Augustus_model.g23703.t1
Valid prediction for snap_scaffold_15-snap.90-T1
Valid prediction for GlimmerHMM_glimmerT_35499-T1
Valid prediction for GlimmerHMM_glimmerT_35487-T1
Valid prediction for GlimmerHMM_glimmerT_35485-T1
Valid prediction for snap_scaffold_15-snap.118-T1
Couldn't classify 42806, 42909
Couldn't classify 46844, 46858
Sorry, prediction pasa_asmbl_13927.p1 fails validation.
(GAA)	 GA	42806-42909	GT	AAG
(GTA)	 AG	43706-43821	GT	AGG
(GAG)	 AG	44251-44369	GT	AGG
(GCG)	 AG	44491-44609	GT	AGG
(GTG)	 AG	45048-45189	GT	AGG
(TAC)	 AG	46844-46858	AT	CCA
-recovered pasa_asmbl_13927.p1, internal, 43706, 43821
-recovered pasa_asmbl_13927.p1, internal, 44251, 44369
-recovered pasa_asmbl_13927.p1, internal, 44491, 44609
-recovered pasa_asmbl_13927.p1, internal, 45048, 45189
Valid prediction for Augustus_model.g23689.t1
Couldn't classify 36495, 36974
Sorry, prediction pasa_asmbl_13930.p1 fails validation.
(GAC)	 CG	36495-36974	AT	ACA
Valid prediction for snap_scaffold_15-snap.95-T1
Couldn't classify 38331, 39095
Sorry, prediction pasa_asmbl_13929.p1 fails validation.
(TCA)	 TG	38331-39095	GG	AAG
Valid prediction for snap_scaffold_15-snap.100-T1
Valid prediction for Augustus_model.g23690.t1
Valid prediction for Augustus_model.g23694.t1
Valid prediction for snap_scaffold_15-snap.93-T1
Valid prediction for snap_scaffold_15-snap.114-T1
Valid prediction for GlimmerHMM_glimmerT_35480-T1
Valid prediction for GlimmerHMM_glimmerT_35502-T1
Valid prediction for CodingQuarry_transcript_17891-T1
Valid prediction for Augustus_model.g23692.t1
Valid prediction for snap_scaffold_15-snap.101-T1
Couldn't classify 168349, 169998
Sorry, prediction pasa_asmbl_13922.p1 fails validation.
(ATG)	 GA	167877-167978	GT	AGG
(AAC)	 AG	168349-169998	GG	AGG
-recovered pasa_asmbl_13922.p1, initial, 167877, 167978
Valid prediction for GlimmerHMM_glimmerT_35500-T1
Valid prediction for Augustus_model.g23693.t1
Valid prediction for snap_scaffold_15-snap.111-T1
Valid prediction for GlimmerHMM_glimmerT_35478-T1
Valid prediction for snap_scaffold_15-snap.88-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19874, rend_intergenic: 9855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28708, rend_intergenic: 25336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48876, rend_intergenic: 44093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60876, rend_intergenic: 57963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108836, rend_intergenic: 107230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136990, rend_intergenic: 123911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162420, rend_intergenic: 141602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167701, rend_intergenic: 166422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173814, rend_intergenic: 168196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176763
-exon list size: 335


building trellis

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27.9    
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29.4    
29.7    
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30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
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33.2    
33.5    
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36.2    
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38.6    
38.9    
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40.4    
40.7    
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43.6    
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44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
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51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
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53.4    
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54.0    
54.3    
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56.1    
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57.3    
57.6    
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64.1    
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65.6    
65.9    
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81.0    
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84.3    
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86.4    
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87.2    
87.5    
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88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
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91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
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94.1    
94.4    
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95.3    
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96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 19874, rend_intergenic: 9855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28708, rend_intergenic: 25336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48876, rend_intergenic: 44093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60876, rend_intergenic: 57963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108836, rend_intergenic: 107230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136990, rend_intergenic: 123911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162420, rend_intergenic: 141602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167701, rend_intergenic: 166422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173814, rend_intergenic: 168196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support