-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_8929894-9115777

-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_54740-T1
Valid prediction for snap_scaffold_25-snap.1959-T1
Valid prediction for GlimmerHMM_glimmerT_54748-T1
Valid prediction for snap_scaffold_25-snap.1967-T1
Valid prediction for snap_scaffold_25-snap.1964-T1
Valid prediction for snap_scaffold_25-snap.1941-T1
Valid prediction for GlimmerHMM_glimmerT_54753-T1
Valid prediction for snap_scaffold_25-snap.1950-T1
Valid prediction for snap_scaffold_25-snap.1968-T1
Valid prediction for snap_scaffold_25-snap.1949-T1
Valid prediction for snap_scaffold_25-snap.1935-T1
Valid prediction for snap_scaffold_25-snap.1946-T1
Valid prediction for snap_scaffold_25-snap.1962-T1
Valid prediction for snap_scaffold_25-snap.1960-T1
Valid prediction for snap_scaffold_25-snap.1969-T1
Valid prediction for snap_scaffold_25-snap.1943-T1
Couldn't classify 89196, 89318
Couldn't classify 93152, 93215
Sorry, prediction pasa_asmbl_33883.p1 fails validation.
(ACG)	 CC	89196-89318	GT	AGG
(ACT)	 AG	89578-89646	GT	AAG
(AAA)	 AG	89771-89928	GT	AGG
(GAT)	 AG	90183-90304	GT	AGG
(ATG)	 AG	92128-92189	GT	TTG
(CCA)	 AG	92298-92378	GT	ATG
(GTG)	 AG	92686-92745	GT	AGG
(GTG)	 AG	92893-92954	GT	CAG
(TAT)	 AG	93152-93215	GT	AGG
add_exon() Sorry, pasa_asmbl_33883.p1 92128-92189-initial-1 is invalid.
-recovered pasa_asmbl_33883.p1, initial, 92128, 92189
-recovered pasa_asmbl_33883.p1, internal, 89578, 89646
-recovered pasa_asmbl_33883.p1, internal, 89771, 89928
-recovered pasa_asmbl_33883.p1, internal, 90183, 90304
-recovered pasa_asmbl_33883.p1, internal, 92128, 92189
-recovered pasa_asmbl_33883.p1, internal, 92298, 92378
-recovered pasa_asmbl_33883.p1, internal, 92686, 92745
-recovered pasa_asmbl_33883.p1, internal, 92893, 92954
-recovered pasa_asmbl_33883.p1, internal, 93152, 93215
Valid prediction for GlimmerHMM_glimmerT_54739-T1
Couldn't classify 156464, 159709
Sorry, prediction pasa_asmbl_33778.p1 fails validation.
(AAG)	 TG	156464-159709	GA	AAG
Valid prediction for GlimmerHMM_glimmerT_54747-T1
Valid prediction for snap_scaffold_25-snap.1937-T1
Valid prediction for GlimmerHMM_glimmerT_54757-T1
Valid prediction for HiQ_model.g36328.t1
Couldn't classify 154732, 155124
Sorry, prediction pasa_asmbl_33777.p1 fails validation.
(AAC)	 AG	154732-155124	AC	GGA
Valid prediction for snap_scaffold_25-snap.1933-T1
Valid prediction for pasa_asmbl_33772.p2
Valid prediction for Augustus_model.g36322.t1
Valid prediction for Augustus_model.g36316.t1
Valid prediction for snap_scaffold_25-snap.1945-T1
Valid prediction for GlimmerHMM_glimmerT_54728-T1
Valid prediction for GlimmerHMM_glimmerT_54751-T1
Valid prediction for snap_scaffold_25-snap.1963-T1
Valid prediction for Augustus_model.g36318.t1
Valid prediction for GlimmerHMM_glimmerT_54732-T1
Valid prediction for HiQ_model.g36323.t1
Valid prediction for GlimmerHMM_glimmerT_54744-T1
Valid prediction for snap_scaffold_25-snap.1932-T1
Couldn't classify 152866, 152934
Couldn't classify 153847, 154314
Sorry, prediction pasa_asmbl_33776.p1 fails validation.
(CAG)	 CA	152866-152934	GT	AGG
(GCA)	 AG	153129-153212	GT	AGG
(AAC)	 AG	153318-153425	GT	AGG
(GCT)	 AG	153526-153624	GT	AGG
(ATG)	 AG	153847-154314	AT	GGA
-recovered pasa_asmbl_33776.p1, internal, 153129, 153212
-recovered pasa_asmbl_33776.p1, internal, 153318, 153425
-recovered pasa_asmbl_33776.p1, internal, 153526, 153624
Valid prediction for pasa_asmbl_33775.p1
Valid prediction for snap_scaffold_25-snap.1965-T1
Valid prediction for GlimmerHMM_glimmerT_54733-T1
Valid prediction for Augustus_model.g36314.t1
Valid prediction for GlimmerHMM_glimmerT_54726-T1
Couldn't classify 82717, 82860
Couldn't classify 84696, 84813
Sorry, prediction pasa_asmbl_33769.p1 fails validation.
(GCG)	 GA	82717-82860	GT	AGG
(GGA)	 AG	83282-83363	GT	AGG
(TGT)	 AG	83609-83711	GT	AGG
(GTA)	 AG	84696-84813	GG	GAG
-recovered pasa_asmbl_33769.p1, internal, 83282, 83363
-recovered pasa_asmbl_33769.p1, internal, 83609, 83711
Valid prediction for GlimmerHMM_glimmerT_54754-T1
Valid prediction for Augustus_model.g36317.t1
Valid prediction for GlimmerHMM_glimmerT_54737-T1
Valid prediction for pasa_asmbl_33779.p1
Valid prediction for snap_scaffold_25-snap.1956-T1
Valid prediction for GlimmerHMM_glimmerT_54752-T1
Valid prediction for GlimmerHMM_glimmerT_54743-T1
Valid prediction for GlimmerHMM_glimmerT_54736-T1
Valid prediction for snap_scaffold_25-snap.1938-T1
Valid prediction for Augustus_model.g36327.t1
Valid prediction for CodingQuarry_transcript_38825-T1
Valid prediction for CodingQuarry_transcript_38826-T1
Valid prediction for CodingQuarry_transcript_38827-T1
Valid prediction for GlimmerHMM_glimmerT_54750-T1
Valid prediction for snap_scaffold_25-snap.1958-T1
Valid prediction for GlimmerHMM_glimmerT_54734-T1
Valid prediction for Augustus_model.g36326.t1
Valid prediction for snap_scaffold_25-snap.1953-T1
Couldn't classify 69209, 69386
Couldn't classify 72901, 73024
Sorry, prediction pasa_asmbl_33877.p1 fails validation.
(GGC)	 CA	69209-69386	GT	CGG
(GTA)	 AG	69771-69897	GT	AAG
(GGG)	 AG	72583-72696	GT	AGG
(TTT)	 AG	72901-73024	GG	CAG
-recovered pasa_asmbl_33877.p1, internal, 69771, 69897
-recovered pasa_asmbl_33877.p1, internal, 72583, 72696

-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_25-snap.1952-T1
Valid prediction for GlimmerHMM_glimmerT_54755-T1
Valid prediction for CodingQuarry_transcript_38824-T1
Valid prediction for snap_scaffold_25-snap.1939-T1
Valid prediction for Augustus_model.g36330.t1
Valid prediction for Augustus_model.g36329.t1
Valid prediction for Augustus_model.g36320.t1
Valid prediction for Augustus_model.g36315.t1
Valid prediction for GlimmerHMM_glimmerT_54758-T1
Valid prediction for GlimmerHMM_glimmerT_54735-T1
Valid prediction for Augustus_model.g36319.t1
Valid prediction for GlimmerHMM_glimmerT_54746-T1
Valid prediction for snap_scaffold_25-snap.1972-T1
Valid prediction for GlimmerHMM_glimmerT_54741-T1
Valid prediction for GlimmerHMM_glimmerT_54730-T1
Valid prediction for GlimmerHMM_glimmerT_54756-T1
Valid prediction for snap_scaffold_25-snap.1942-T1
Valid prediction for pasa_asmbl_34475.p1
Valid prediction for snap_scaffold_25-snap.1955-T1
Valid prediction for snap_scaffold_25-snap.1944-T1
Valid prediction for snap_scaffold_25-snap.1966-T1
Valid prediction for GlimmerHMM_glimmerT_54729-T1
Valid prediction for snap_scaffold_25-snap.1954-T1
Valid prediction for GlimmerHMM_glimmerT_54742-T1
Valid prediction for snap_scaffold_25-snap.1957-T1
Valid prediction for GlimmerHMM_glimmerT_54727-T1
Valid prediction for snap_scaffold_25-snap.1961-T1
Valid prediction for Augustus_model.g36313.t1
Valid prediction for Augustus_model.g36325.t1
Valid prediction for GlimmerHMM_glimmerT_54745-T1
Valid prediction for HiQ_model.g36321.t1
Valid prediction for GlimmerHMM_glimmerT_54749-T1
Valid prediction for snap_scaffold_25-snap.1951-T1
Valid prediction for snap_scaffold_25-snap.1931-T1
Valid prediction for snap_scaffold_25-snap.1934-T1
Valid prediction for Augustus_model.g36324.t1
Valid prediction for snap_scaffold_25-snap.1936-T1
Valid prediction for snap_scaffold_25-snap.1947-T1
Valid prediction for snap_scaffold_25-snap.1971-T1
Valid prediction for snap_scaffold_25-snap.1948-T1
Valid prediction for GlimmerHMM_glimmerT_54731-T1
Valid prediction for snap_scaffold_25-snap.1970-T1
Valid prediction for snap_scaffold_25-snap.1940-T1
Valid prediction for GlimmerHMM_glimmerT_54738-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10287, rend_intergenic: 3285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17465, rend_intergenic: 14398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18947, rend_intergenic: 18255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20816, rend_intergenic: 19021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31918, rend_intergenic: 24626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41529, rend_intergenic: 37285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45020, rend_intergenic: 42925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48740, rend_intergenic: 45204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74105, rend_intergenic: 48815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78970, rend_intergenic: 75998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102724, rend_intergenic: 81781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110053, rend_intergenic: 106302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138805, rend_intergenic: 126919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146130, rend_intergenic: 140951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176381, rend_intergenic: 168033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185884
-exon list size: 388


building trellis

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48.5    
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80.8    
81.0    
81.3    
81.5    
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82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
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85.4    
85.6    
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86.4    
86.7    
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87.2    
87.4    
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88.2    
88.5    
88.7    
89.0    
89.2    
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90.3    
90.5    
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91.0    
91.3    
91.5    
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92.1    
92.3    
92.6    
92.8    
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93.3    
93.6    
93.8    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 10287, rend_intergenic: 3285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17465, rend_intergenic: 14398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18947, rend_intergenic: 18255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20816, rend_intergenic: 19021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31918, rend_intergenic: 24626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41529, rend_intergenic: 37285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45020, rend_intergenic: 42925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48740, rend_intergenic: 45204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74105, rend_intergenic: 48815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78970, rend_intergenic: 75998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102724, rend_intergenic: 81781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110053, rend_intergenic: 106302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138805, rend_intergenic: 126919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146130, rend_intergenic: 140951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176381, rend_intergenic: 168033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13795
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support