-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_9277467-9465743

-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 GeneMark_model.7051_t
Valid prediction for GeneMark_model.7022_t
Valid prediction for snap_scaffold_2-snap.1902-T1
Valid prediction for Augustus_model.g2959.t1
Valid prediction for snap_scaffold_2-snap.1898-T1
Couldn't classify 18362, 18639
Sorry, prediction pasa_asmbl_24713.p1 fails validation.
(ATG)	 AA	17352-17579	GT	TGG
(GAT)	 AG	17711-18266	GT	CTG
(CTA)	 AG	18362-18639	AC	GCA
-recovered pasa_asmbl_24713.p1, initial, 17352, 17579
-recovered pasa_asmbl_24713.p1, internal, 17711, 18266
Valid prediction for GlimmerHMM_glimmerT_4398-T1
Valid prediction for GeneMark_model.7032_t
Valid prediction for GeneMark_model.7009_t
Valid prediction for GeneMark_model.7008_t
Valid prediction for GeneMark_model.7049_t
Valid prediction for CodingQuarry_transcript_28594-T1
Valid prediction for snap_scaffold_2-snap.1881-T1
Valid prediction for snap_scaffold_2-snap.1890-T1
Valid prediction for snap_scaffold_2-snap.1876-T1
Valid prediction for GlimmerHMM_glimmerT_4400-T1
Valid prediction for snap_scaffold_2-snap.1878-T1
Valid prediction for GlimmerHMM_glimmerT_4408-T1
Valid prediction for Augustus_model.g2958.t1
Valid prediction for GlimmerHMM_glimmerT_4406-T1
Valid prediction for snap_scaffold_2-snap.1893-T1
Valid prediction for Augustus_model.g2956.t1
Valid prediction for Augustus_model.g2960.t1
Valid prediction for GeneMark_model.7035_t
Valid prediction for GlimmerHMM_glimmerT_4387-T1
Valid prediction for snap_scaffold_2-snap.1871-T1
Valid prediction for Augustus_model.g2954.t1
Valid prediction for snap_scaffold_2-snap.1858-T1
Valid prediction for GlimmerHMM_glimmerT_4410-T1
Valid prediction for snap_scaffold_2-snap.1891-T1
Valid prediction for snap_scaffold_2-snap.1856-T1
Valid prediction for GeneMark_model.7038_t
Couldn't classify 18967, 19008
Sorry, prediction pasa_asmbl_24716.p1 fails validation.
(CTG)	 AG	18967-19008	GT	TGG
(ATT)	 AG	19134-19218	GT	CGG
(GTG)	 AG	19353-19585	GC	AGG
(GCT)	 AG	19771-19965	GT	AGG
(GAC)	 AG	20049-20274	GT	GGG
(GCG)	 AG	20420-20958	GC	GAG
-recovered pasa_asmbl_24716.p1, terminal, 20420, 20958
-recovered pasa_asmbl_24716.p1, internal, 18967, 19008
-recovered pasa_asmbl_24716.p1, internal, 19134, 19218
-recovered pasa_asmbl_24716.p1, internal, 19353, 19585
-recovered pasa_asmbl_24716.p1, internal, 19771, 19965
-recovered pasa_asmbl_24716.p1, internal, 20049, 20274
-recovered pasa_asmbl_24716.p1, internal, 20420, 20958
Valid prediction for GlimmerHMM_glimmerT_4403-T1
Valid prediction for snap_scaffold_2-snap.1884-T1
Valid prediction for GlimmerHMM_glimmerT_4399-T1
Valid prediction for GeneMark_model.7045_t
Valid prediction for GeneMark_model.7020_t
Valid prediction for GeneMark_model.7017_t
Valid prediction for GlimmerHMM_glimmerT_4389-T1
Valid prediction for GeneMark_model.7011_t
Valid prediction for snap_scaffold_2-snap.1873-T1
Valid prediction for Augustus_model.g2950.t1
Valid prediction for GeneMark_model.7007_t
Valid prediction for GeneMark_model.7014_t
Valid prediction for GeneMark_model.7031_t
Valid prediction for GlimmerHMM_glimmerT_4394-T1
Valid prediction for snap_scaffold_2-snap.1870-T1
Valid prediction for GlimmerHMM_glimmerT_4383-T1
Valid prediction for snap_scaffold_2-snap.1865-T1
Valid prediction for GeneMark_model.7041_t
Valid prediction for snap_scaffold_2-snap.1862-T1
Valid prediction for snap_scaffold_2-snap.1886-T1
Valid prediction for GlimmerHMM_glimmerT_4405-T1
Valid prediction for GeneMark_model.7043_t
Valid prediction for GeneMark_model.7027_t
Valid prediction for GeneMark_model.7019_t
Valid prediction for snap_scaffold_2-snap.1885-T1
Valid prediction for snap_scaffold_2-snap.1854-T1
Valid prediction for GeneMark_model.7029_t
Valid prediction for GlimmerHMM_glimmerT_4386-T1
Valid prediction for GeneMark_model.7004_t
Valid prediction for GlimmerHMM_glimmerT_4390-T1
Valid prediction for Augustus_model.g2963.t1
Valid prediction for Augustus_model.g2961.t1
Valid prediction for GeneMark_model.7047_t
Valid prediction for CodingQuarry_transcript_28593-T1
Valid prediction for GeneMark_model.7024_t
Valid prediction for GeneMark_model.7026_t
Valid prediction for snap_scaffold_2-snap.1888-T1
Valid prediction for GeneMark_model.7053_t

-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 snap_scaffold_2-snap.1863-T1
Valid prediction for GeneMark_model.7002_t
Valid prediction for GlimmerHMM_glimmerT_4402-T1
Valid prediction for snap_scaffold_2-snap.1874-T1
Valid prediction for GeneMark_model.7048_t
Valid prediction for Augustus_model.g2949.t1
Valid prediction for GeneMark_model.7054_t
Valid prediction for snap_scaffold_2-snap.1855-T1
Valid prediction for snap_scaffold_2-snap.1875-T1
Valid prediction for pasa_asmbl_23392.p1
Valid prediction for snap_scaffold_2-snap.1895-T1
Valid prediction for GlimmerHMM_glimmerT_4385-T1
Valid prediction for GeneMark_model.7050_t
Valid prediction for snap_scaffold_2-snap.1883-T1
Valid prediction for GeneMark_model.7018_t
Valid prediction for snap_scaffold_2-snap.1867-T1
Valid prediction for GeneMark_model.7039_t
Valid prediction for GlimmerHMM_glimmerT_4397-T1
Valid prediction for snap_scaffold_2-snap.1864-T1
Valid prediction for GeneMark_model.7012_t
Valid prediction for GlimmerHMM_glimmerT_4392-T1
Valid prediction for GeneMark_model.7013_t
Valid prediction for GlimmerHMM_glimmerT_4388-T1
Valid prediction for snap_scaffold_2-snap.1869-T1
Valid prediction for pasa_asmbl_23393.p2
Valid prediction for GeneMark_model.7036_t
Valid prediction for snap_scaffold_2-snap.1860-T1
Valid prediction for Augustus_model.g2957.t1
Valid prediction for Augustus_model.g2955.t1
Valid prediction for Augustus_model.g2964.t1
Valid prediction for GeneMark_model.7023_t
Valid prediction for snap_scaffold_2-snap.1887-T1
Valid prediction for Augustus_model.g2965.t1
Valid prediction for snap_scaffold_2-snap.1879-T1
Valid prediction for snap_scaffold_2-snap.1866-T1
Valid prediction for HiQ_model.g2952.t1
Valid prediction for GlimmerHMM_glimmerT_4382-T1
Valid prediction for GlimmerHMM_glimmerT_4396-T1
Valid prediction for Augustus_model.g2953.t1
Valid prediction for GlimmerHMM_glimmerT_4381-T1
Valid prediction for GlimmerHMM_glimmerT_4404-T1
Valid prediction for snap_scaffold_2-snap.1892-T1
Valid prediction for snap_scaffold_2-snap.1896-T1
Valid prediction for snap_scaffold_2-snap.1872-T1
Valid prediction for GeneMark_model.7033_t
Valid prediction for GeneMark_model.7005_t
Valid prediction for GlimmerHMM_glimmerT_4401-T1
Valid prediction for GeneMark_model.7046_t
Valid prediction for GeneMark_model.7003_t
Valid prediction for snap_scaffold_2-snap.1882-T1
Valid prediction for snap_scaffold_2-snap.1861-T1
Valid prediction for GeneMark_model.7025_t
Valid prediction for GeneMark_model.7010_t
Valid prediction for snap_scaffold_2-snap.1880-T1
Valid prediction for GeneMark_model.7015_t
Valid prediction for GeneMark_model.7044_t
Valid prediction for Augustus_model.g2962.t1
Valid prediction for snap_scaffold_2-snap.1899-T1
Valid prediction for GeneMark_model.7030_t
Valid prediction for snap_scaffold_2-snap.1859-T1
Valid prediction for GeneMark_model.7042_t
Valid prediction for snap_scaffold_2-snap.1900-T1
Valid prediction for Augustus_model.g2948.t1
Valid prediction for CodingQuarry_transcript_28595-T1
Valid prediction for GeneMark_model.7052_t
Valid prediction for GlimmerHMM_glimmerT_4384-T1
Valid prediction for GlimmerHMM_glimmerT_4407-T1
Valid prediction for GeneMark_model.7034_t
Valid prediction for GeneMark_model.7040_t
Valid prediction for snap_scaffold_2-snap.1894-T1
Valid prediction for GeneMark_model.7021_t
Valid prediction for GeneMark_model.7016_t
Valid prediction for snap_scaffold_2-snap.1897-T1
Valid prediction for snap_scaffold_2-snap.1877-T1
Valid prediction for GeneMark_model.7037_t
Valid prediction for snap_scaffold_2-snap.1889-T1
Valid prediction for HiQ_model.g2951.t1
Valid prediction for GeneMark_model.7028_t
Valid prediction for GeneMark_model.7006_t
Valid prediction for CodingQuarry_transcript_28596-T1
Valid prediction for snap_scaffold_2-snap.1901-T1
Valid prediction for snap_scaffold_2-snap.1857-T1
Valid prediction for GlimmerHMM_glimmerT_4395-T1
Valid prediction for GlimmerHMM_glimmerT_4391-T1
Valid prediction for GlimmerHMM_glimmerT_4409-T1
Valid prediction for GlimmerHMM_glimmerT_4393-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11138, rend_intergenic: 8284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14869, rend_intergenic: 14029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47111, rend_intergenic: 39705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63575, rend_intergenic: 52863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77221, rend_intergenic: 72894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77875, rend_intergenic: 77257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82242, rend_intergenic: 80883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86331, rend_intergenic: 82365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91575, rend_intergenic: 88629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94825, rend_intergenic: 93717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98215, rend_intergenic: 94939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104561, rend_intergenic: 98319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105526, rend_intergenic: 104834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107697, rend_intergenic: 106064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112602, rend_intergenic: 108382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116788, rend_intergenic: 113866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118640, rend_intergenic: 116901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121012, rend_intergenic: 118985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126311, rend_intergenic: 121983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135760, rend_intergenic: 134183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157053, rend_intergenic: 139567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180884, rend_intergenic: 167403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188277
-exon list size: 712


building trellis

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84.3    
84.5    
84.6    
84.7    
84.9    
85.0    
85.2    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 11138, rend_intergenic: 8284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14869, rend_intergenic: 14029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47111, rend_intergenic: 39705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63575, rend_intergenic: 52863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77221, rend_intergenic: 72894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77875, rend_intergenic: 77257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82242, rend_intergenic: 80883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86331, rend_intergenic: 82365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91575, rend_intergenic: 88629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94825, rend_intergenic: 93717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98215, rend_intergenic: 94939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104561, rend_intergenic: 98319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105526, rend_intergenic: 104834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107697, rend_intergenic: 106064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112602, rend_intergenic: 108382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116788, rend_intergenic: 113866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118640, rend_intergenic: 116901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121012, rend_intergenic: 118985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126311, rend_intergenic: 121983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135760, rend_intergenic: 134183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157053, rend_intergenic: 139567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180884, rend_intergenic: 167403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support