-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_9404006-9649752

-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_4323-T1
Valid prediction for GlimmerHMM_glimmerT_4311-T1
Valid prediction for snap_scaffold_2-snap.1870-T1
Valid prediction for snap_scaffold_2-snap.1896-T1
Valid prediction for GlimmerHMM_glimmerT_4305-T1
Valid prediction for snap_scaffold_2-snap.1884-T1
Valid prediction for GlimmerHMM_glimmerT_4327-T1
Valid prediction for snap_scaffold_2-snap.1878-T1
Valid prediction for Augustus_model.g2905.t1
Valid prediction for GlimmerHMM_glimmerT_4316-T1
Valid prediction for snap_scaffold_2-snap.1887-T1
Valid prediction for snap_scaffold_2-snap.1888-T1
Valid prediction for Augustus_model.g2906.t1
Couldn't classify 89060, 89368
Sorry, prediction pasa_asmbl_24684.p1 fails validation.
(CCT)	 CT	89060-89368	CT	AGC
Valid prediction for snap_scaffold_2-snap.1880-T1
Valid prediction for Augustus_model.g2897.t1
Valid prediction for Augustus_model.g2904.t1
Valid prediction for Augustus_model.g2903.t1
Valid prediction for GlimmerHMM_glimmerT_4319-T1
Valid prediction for snap_scaffold_2-snap.1866-T1
Valid prediction for snap_scaffold_2-snap.1882-T1
Valid prediction for snap_scaffold_2-snap.1889-T1
Valid prediction for Augustus_model.g2899.t1
Valid prediction for Augustus_model.g2901.t1
Valid prediction for GlimmerHMM_glimmerT_4326-T1
Valid prediction for GlimmerHMM_glimmerT_4308-T1
Valid prediction for Augustus_model.g2907.t1
Valid prediction for Augustus_model.g2909.t1
Valid prediction for GlimmerHMM_glimmerT_4315-T1
Valid prediction for snap_scaffold_2-snap.1890-T1
Valid prediction for Augustus_model.g2902.t1
Valid prediction for snap_scaffold_2-snap.1885-T1
Valid prediction for snap_scaffold_2-snap.1872-T1
Valid prediction for GlimmerHMM_glimmerT_4314-T1
Valid prediction for snap_scaffold_2-snap.1860-T1
Valid prediction for snap_scaffold_2-snap.1875-T1
Valid prediction for snap_scaffold_2-snap.1883-T1
Valid prediction for snap_scaffold_2-snap.1894-T1
Valid prediction for GlimmerHMM_glimmerT_4307-T1
Valid prediction for GlimmerHMM_glimmerT_4318-T1
Valid prediction for snap_scaffold_2-snap.1893-T1
Valid prediction for snap_scaffold_2-snap.1874-T1
Valid prediction for snap_scaffold_2-snap.1869-T1
Valid prediction for snap_scaffold_2-snap.1891-T1
Valid prediction for snap_scaffold_2-snap.1900-T1
Valid prediction for Augustus_model.g2900.t1
Valid prediction for GlimmerHMM_glimmerT_4328-T1
Valid prediction for snap_scaffold_2-snap.1886-T1
Valid prediction for snap_scaffold_2-snap.1901-T1
Valid prediction for snap_scaffold_2-snap.1898-T1
Couldn't classify 76708, 76758
Couldn't classify 88398, 88454
Sorry, prediction pasa_asmbl_24682.p1 fails validation.
(GCC)	 CG	76708-76758	GT	TGG
(AGG)	 AG	79685-79804	GT	AGG
(GAC)	 AG	80497-80587	GT	TGG
(ACG)	 AG	81456-81575	GT	CGG
(ACC)	 AG	81992-82134	GT	AGG
(AAC)	 AG	83174-83288	GT	GCG
(AGG)	 AG	83379-83448	GT	AGG
(TAA)	 AG	83692-83836	GT	CGG
(TGC)	 AG	83938-84157	GT	AGG
(ATG)	 AG	84272-84363	GT	GAG
(GAA)	 AG	84449-84490	GT	AGG
(CAA)	 AG	85421-85578	GT	AGG
(GAG)	 AG	86789-86856	GT	TGG
(AGG)	 AG	88132-88277	GT	AGG
(ATC)	 AG	88398-88454	AC	TGA
add_exon() Sorry, pasa_asmbl_24682.p1 84272-84363-initial-1 is invalid.
-recovered pasa_asmbl_24682.p1, initial, 84272, 84363
-recovered pasa_asmbl_24682.p1, internal, 79685, 79804
-recovered pasa_asmbl_24682.p1, internal, 80497, 80587
-recovered pasa_asmbl_24682.p1, internal, 81456, 81575
-recovered pasa_asmbl_24682.p1, internal, 81992, 82134
-recovered pasa_asmbl_24682.p1, internal, 83174, 83288
-recovered pasa_asmbl_24682.p1, internal, 83379, 83448
-recovered pasa_asmbl_24682.p1, internal, 83692, 83836
-recovered pasa_asmbl_24682.p1, internal, 83938, 84157
-recovered pasa_asmbl_24682.p1, internal, 84272, 84363
-recovered pasa_asmbl_24682.p1, internal, 84449, 84490
-recovered pasa_asmbl_24682.p1, internal, 85421, 85578
-recovered pasa_asmbl_24682.p1, internal, 86789, 86856
-recovered pasa_asmbl_24682.p1, internal, 88132, 88277
Valid prediction for snap_scaffold_2-snap.1858-T1
Valid prediction for Augustus_model.g2908.t1
Valid prediction for GlimmerHMM_glimmerT_4320-T1
Valid prediction for GlimmerHMM_glimmerT_4313-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_2-snap.1868-T1
Valid prediction for GlimmerHMM_glimmerT_4321-T1
Valid prediction for GlimmerHMM_glimmerT_4306-T1
Valid prediction for snap_scaffold_2-snap.1871-T1
Valid prediction for snap_scaffold_2-snap.1903-T1
Valid prediction for Augustus_model.g2898.t1
Valid prediction for snap_scaffold_2-snap.1895-T1
Valid prediction for snap_scaffold_2-snap.1873-T1
Valid prediction for snap_scaffold_2-snap.1892-T1
Valid prediction for GlimmerHMM_glimmerT_4312-T1
Valid prediction for snap_scaffold_2-snap.1862-T1
Valid prediction for snap_scaffold_2-snap.1904-T1
Valid prediction for GlimmerHMM_glimmerT_4304-T1
Valid prediction for snap_scaffold_2-snap.1863-T1
Valid prediction for snap_scaffold_2-snap.1876-T1
Valid prediction for snap_scaffold_2-snap.1881-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1859-T1
Valid prediction for GlimmerHMM_glimmerT_4325-T1
Valid prediction for snap_scaffold_2-snap.1867-T1
Valid prediction for snap_scaffold_2-snap.1877-T1
Valid prediction for snap_scaffold_2-snap.1899-T1
Valid prediction for snap_scaffold_2-snap.1861-T1
Valid prediction for snap_scaffold_2-snap.1902-T1
Valid prediction for snap_scaffold_2-snap.1864-T1
Valid prediction for GlimmerHMM_glimmerT_4310-T1
Valid prediction for GlimmerHMM_glimmerT_4317-T1
Valid prediction for GlimmerHMM_glimmerT_4324-T1
Valid prediction for snap_scaffold_2-snap.1905-T1
Valid prediction for GlimmerHMM_glimmerT_4322-T1
Valid prediction for snap_scaffold_2-snap.1865-T1
Valid prediction for GlimmerHMM_glimmerT_4309-T1
Valid prediction for snap_scaffold_2-snap.1897-T1
Valid prediction for snap_scaffold_2-snap.1879-T1
Valid prediction for Augustus_model.g2896.t1
Valid prediction for snap_scaffold_2-snap.1906-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9221, rend_intergenic: 7644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32927, rend_intergenic: 13028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56569, rend_intergenic: 40760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68759, rend_intergenic: 63942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74067, rend_intergenic: 70417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88982, rend_intergenic: 77587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96385, rend_intergenic: 91833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105063, rend_intergenic: 98947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127398, rend_intergenic: 107860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165706, rend_intergenic: 161813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190578, rend_intergenic: 179414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201803, rend_intergenic: 198537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205812, rend_intergenic: 202678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239299, rend_intergenic: 209990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 245747
-exon list size: 469


building trellis

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84.3    
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88.3    
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90.0    
90.2    
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90.7    
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91.3    
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92.6    
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97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 9221, rend_intergenic: 7644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32927, rend_intergenic: 13028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56569, rend_intergenic: 40760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68759, rend_intergenic: 63942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74067, rend_intergenic: 70417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88982, rend_intergenic: 77587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96385, rend_intergenic: 91833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105063, rend_intergenic: 98947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127398, rend_intergenic: 107860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165706, rend_intergenic: 161813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190578, rend_intergenic: 179414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201803, rend_intergenic: 198537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205812, rend_intergenic: 202678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239299, rend_intergenic: 209990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support