-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_10818756-11027959

-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_1496-T1
Valid prediction for GeneMark_model.1972_t
Valid prediction for CodingQuarry_transcript_2751-T1
Valid prediction for snap_scaffold_1-snap.1883-T1
Valid prediction for GlimmerHMM_glimmerT_1492-T1
Couldn't classify 175468, 175719
Sorry, prediction pasa_asmbl_2039.p1 fails validation.
(AAG)	 AC	175468-175719	GT	AGG
(GCC)	 AG	175913-176108	GT	AGG
(ACG)	 AG	177422-177660	GT	AGG
(ATC)	 AG	177757-177840	GT	AGG
(ATC)	 AG	178166-178342	GT	AGG
(CTG)	 AG	178820-178949	GT	TGG
(GCA)	 AG	179624-179780	GT	AGG
(GTC)	 AG	180993-181125	GT	AGG
(GCT)	 AG	181472-181585	GT	TGG
(TTG)	 AG	181690-181804	GT	AGG
(GAA)	 AG	182090-182224	GT	AGG
(GTG)	 AG	182450-182637	AA	GAA
-recovered pasa_asmbl_2039.p1, terminal, 182450, 182637
-recovered pasa_asmbl_2039.p1, internal, 175913, 176108
-recovered pasa_asmbl_2039.p1, internal, 177422, 177660
-recovered pasa_asmbl_2039.p1, internal, 177757, 177840
-recovered pasa_asmbl_2039.p1, internal, 178166, 178342
-recovered pasa_asmbl_2039.p1, internal, 178820, 178949
-recovered pasa_asmbl_2039.p1, internal, 179624, 179780
-recovered pasa_asmbl_2039.p1, internal, 180993, 181125
-recovered pasa_asmbl_2039.p1, internal, 181472, 181585
-recovered pasa_asmbl_2039.p1, internal, 181690, 181804
-recovered pasa_asmbl_2039.p1, internal, 182090, 182224
Valid prediction for GeneMark_model.1993_t
Valid prediction for snap_scaffold_1-snap.1910-T1
Valid prediction for Augustus_model.g1089.t1
Valid prediction for GlimmerHMM_glimmerT_1512-T1
Valid prediction for GeneMark_model.1947_t
Valid prediction for HiQ_model.g1087.t1
Valid prediction for snap_scaffold_1-snap.1905-T1
Couldn't classify 35888, 36053
Sorry, prediction pasa_asmbl_2022.p1 fails validation.
(GTG)	 CA	35888-36053	GT	AGG
(GTC)	 AG	36534-36618	GT	AGG
(GTA)	 AG	36697-36843	GT	GAG
(ACC)	 AG	39719-39767	TA	AGT
-recovered pasa_asmbl_2022.p1, terminal, 39719, 39767
-recovered pasa_asmbl_2022.p1, internal, 36534, 36618
-recovered pasa_asmbl_2022.p1, internal, 36697, 36843
Valid prediction for GeneMark_model.1995_t
Valid prediction for snap_scaffold_1-snap.1893-T1
Valid prediction for GlimmerHMM_glimmerT_1499-T1
Valid prediction for GeneMark_model.1981_t
Valid prediction for GeneMark_model.1983_t
Valid prediction for GeneMark_model.1949_t
Valid prediction for GlimmerHMM_glimmerT_1511-T1
Valid prediction for snap_scaffold_1-snap.1898-T1
Valid prediction for Augustus_model.g1068.t1
Valid prediction for GeneMark_model.1961_t
Valid prediction for GeneMark_model.1985_t
Valid prediction for snap_scaffold_1-snap.1896-T1
Valid prediction for GlimmerHMM_glimmerT_1489-T1
Valid prediction for GlimmerHMM_glimmerT_1485-T1
Couldn't classify 11439, 12899
Sorry, prediction pasa_asmbl_2016.p1 fails validation.
(GTG)	 AT	11439-12899	GG	GAG
Valid prediction for pasa_asmbl_2027.p1
Valid prediction for GeneMark_model.1956_t
Valid prediction for snap_scaffold_1-snap.1879-T1
Valid prediction for Augustus_model.g1077.t1
Valid prediction for HiQ_model.g1081.t1
Valid prediction for Augustus_model.g1071.t1
Valid prediction for GlimmerHMM_glimmerT_1509-T1
Valid prediction for Augustus_model.g1074.t1
Valid prediction for GeneMark_model.1975_t
Valid prediction for snap_scaffold_1-snap.1904-T1
Valid prediction for snap_scaffold_1-snap.1899-T1
Valid prediction for GeneMark_model.1987_t
Valid prediction for snap_scaffold_1-snap.1881-T1
Valid prediction for GeneMark_model.1954_t
Couldn't classify 19459, 19476
Sorry, prediction pasa_asmbl_2019.p1 fails validation.
(GTT)	 CT	19459-19476	GT	AGG
(CTC)	 AG	19653-19803	GT	CGG
(AGA)	 AG	19985-20102	GT	AGG
(TGC)	 AG	20199-20274	GT	CTG
(GCG)	 AG	20397-20537	GT	AGG
(GAG)	 AG	20652-21266	TA	GAT
-recovered pasa_asmbl_2019.p1, terminal, 20652, 21266
-recovered pasa_asmbl_2019.p1, internal, 19653, 19803
-recovered pasa_asmbl_2019.p1, internal, 19985, 20102
-recovered pasa_asmbl_2019.p1, internal, 20199, 20274
-recovered pasa_asmbl_2019.p1, internal, 20397, 20537
Valid prediction for CodingQuarry_transcript_2755-T1
Valid prediction for GlimmerHMM_glimmerT_1505-T1
Valid prediction for Augustus_model.g1072.t1
Valid prediction for snap_scaffold_1-snap.1912-T1
Valid prediction for pasa_asmbl_2032.p1
Valid prediction for GeneMark_model.1980_t
Valid prediction for snap_scaffold_1-snap.1884-T1
Valid prediction for GeneMark_model.1958_t
Valid prediction for GlimmerHMM_glimmerT_1488-T1
Valid prediction for GeneMark_model.1965_t
Valid prediction for GeneMark_model.1982_t
Valid prediction for snap_scaffold_1-snap.1871-T1
Valid prediction for snap_scaffold_1-snap.1887-T1
Valid prediction for Augustus_model.g1091.t1
Valid prediction for Augustus_model.g1083.t1
Couldn't classify 172082, 172225
Couldn't classify 175219, 175413
Sorry, prediction pasa_asmbl_2038.p1 fails validation.
(TAC)	 AG	172082-172225	GT	AGG
(GAG)	 AG	175219-175413	AC	GCA
-recovered pasa_asmbl_2038.p1, internal, 172082, 172225
Valid prediction for Augustus_model.g1073.t1
Valid prediction for snap_scaffold_1-snap.1902-T1
Valid prediction for CodingQuarry_transcript_2753-T1
Valid prediction for GeneMark_model.1951_t
Valid prediction for GeneMark_model.1992_t
Valid prediction for Augustus_model.g1084.t1
Valid prediction for snap_scaffold_1-snap.1891-T1
Couldn't classify 10121, 10315
Sorry, prediction pasa_asmbl_2722.p1 fails validation.
(ATG)	 CG	9864-10004	GT	AGG
(ATC)	 AG	10121-10315	GC	GTG
-recovered pasa_asmbl_2722.p1, initial, 9864, 10004
-recovered pasa_asmbl_2722.p1, internal, 10121, 10315
Valid prediction for snap_scaffold_1-snap.1895-T1
Valid prediction for GlimmerHMM_glimmerT_1508-T1
Valid prediction for snap_scaffold_1-snap.1874-T1
Valid prediction for Augustus_model.g1082.t1
Valid prediction for GeneMark_model.1953_t
Valid prediction for GeneMark_model.1997_t
Valid prediction for snap_scaffold_1-snap.1888-T1
Valid prediction for snap_scaffold_1-snap.1909-T1
Valid prediction for pasa_asmbl_2034.p1
Valid prediction for CodingQuarry_transcript_2752-T1
Valid prediction for GeneMark_model.1991_t
Valid prediction for snap_scaffold_1-snap.1897-T1
Valid prediction for GeneMark_model.1989_t
Couldn't classify 18968, 19076
Sorry, prediction pasa_asmbl_2018.p1 fails validation.
(ATG)	 AC	17454-17543	GT	TGG
(GCC)	 AG	17671-17860	GT	TGG
(AGC)	 AG	18146-18277	GT	CAG
(GTG)	 AG	18373-18512	GT	AGG
(GTG)	 AG	18602-18691	GT	CGG
(GAT)	 AG	18779-18831	GT	AAG
(GGC)	 AG	18968-19076	AT	AGA
-recovered pasa_asmbl_2018.p1, initial, 17454, 17543
-recovered pasa_asmbl_2018.p1, internal, 17671, 17860
-recovered pasa_asmbl_2018.p1, internal, 18146, 18277
-recovered pasa_asmbl_2018.p1, internal, 18373, 18512
-recovered pasa_asmbl_2018.p1, internal, 18602, 18691
-recovered pasa_asmbl_2018.p1, internal, 18779, 18831
Valid prediction for snap_scaffold_1-snap.1885-T1
Valid prediction for Augustus_model.g1069.t1
Valid prediction for GlimmerHMM_glimmerT_1504-T1
Valid prediction for GlimmerHMM_glimmerT_1486-T1
Valid prediction for GeneMark_model.1970_t
Valid prediction for GeneMark_model.1963_t
Valid prediction for snap_scaffold_1-snap.1907-T1
Valid prediction for GlimmerHMM_glimmerT_1500-T1
Valid prediction for snap_scaffold_1-snap.1872-T1
Valid prediction for GlimmerHMM_glimmerT_1503-T1
Valid prediction for HiQ_model.g1090.t1
Valid prediction for GeneMark_model.1968_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 GlimmerHMM_glimmerT_1490-T1
Valid prediction for snap_scaffold_1-snap.1890-T1
Couldn't classify 47580, 47601
Sorry, prediction pasa_asmbl_613.p1 fails validation.
(CGC)	 AT	47580-47601	GT	AGG
(ATG)	 AG	47737-48779	GA	GAG
-recovered pasa_asmbl_613.p1, terminal, 47737, 48779
Valid prediction for snap_scaffold_1-snap.1906-T1
Valid prediction for Augustus_model.g1085.t1
Valid prediction for GeneMark_model.1978_t
Valid prediction for snap_scaffold_1-snap.1875-T1
Valid prediction for GeneMark_model.1999_t
Valid prediction for GeneMark_model.1952_t
Valid prediction for snap_scaffold_1-snap.1873-T1
Valid prediction for snap_scaffold_1-snap.1878-T1
Valid prediction for snap_scaffold_1-snap.1894-T1
Valid prediction for GlimmerHMM_glimmerT_1502-T1
Valid prediction for GeneMark_model.1976_t
Valid prediction for snap_scaffold_1-snap.1908-T1
Valid prediction for Augustus_model.g1088.t1
Valid prediction for snap_scaffold_1-snap.1889-T1
Valid prediction for snap_scaffold_1-snap.1901-T1
Valid prediction for Augustus_model.g1076.t1
Valid prediction for pasa_asmbl_612.p1
Valid prediction for Augustus_model.g1075.t1
Valid prediction for GeneMark_model.1979_t
Valid prediction for GeneMark_model.1966_t
Valid prediction for Augustus_model.g1080.t1
Valid prediction for HiQ_model.g1070.t1
Valid prediction for Augustus_model.g1093.t1
Valid prediction for snap_scaffold_1-snap.1882-T1
Valid prediction for snap_scaffold_1-snap.1903-T1
Valid prediction for GeneMark_model.1990_t
Valid prediction for GeneMark_model.1950_t
Valid prediction for GeneMark_model.1988_t
Valid prediction for GeneMark_model.1969_t
Valid prediction for CodingQuarry_transcript_2754-T1
Valid prediction for GeneMark_model.1984_t
Valid prediction for GeneMark_model.1967_t
Valid prediction for GeneMark_model.1973_t
Valid prediction for GlimmerHMM_glimmerT_1507-T1
Valid prediction for Augustus_model.g1092.t1
Valid prediction for CodingQuarry_transcript_2749-T1
Valid prediction for GeneMark_model.1977_t
Valid prediction for snap_scaffold_1-snap.1892-T1
Valid prediction for GlimmerHMM_glimmerT_1495-T1
Valid prediction for GeneMark_model.1974_t
Valid prediction for snap_scaffold_1-snap.1911-T1
Valid prediction for GlimmerHMM_glimmerT_1513-T1
Valid prediction for GeneMark_model.1971_t
Valid prediction for GeneMark_model.1998_t
Valid prediction for Augustus_model.g1078.t1
Valid prediction for GlimmerHMM_glimmerT_1501-T1
Valid prediction for pasa_asmbl_610.p1
Valid prediction for GeneMark_model.1948_t
Valid prediction for GeneMark_model.1957_t
Valid prediction for HiQ_model.g1086.t1
Valid prediction for GeneMark_model.1986_t
Valid prediction for snap_scaffold_1-snap.1876-T1
Valid prediction for GeneMark_model.1962_t
Valid prediction for snap_scaffold_1-snap.1880-T1
Valid prediction for GlimmerHMM_glimmerT_1493-T1
Valid prediction for snap_scaffold_1-snap.1877-T1
Valid prediction for GeneMark_model.1955_t
Valid prediction for GlimmerHMM_glimmerT_1510-T1
Valid prediction for GlimmerHMM_glimmerT_1498-T1
Valid prediction for GlimmerHMM_glimmerT_1494-T1
Valid prediction for GeneMark_model.1996_t
Valid prediction for Augustus_model.g1079.t1
Valid prediction for GlimmerHMM_glimmerT_1491-T1
Valid prediction for snap_scaffold_1-snap.1886-T1
Valid prediction for GlimmerHMM_glimmerT_1506-T1
Valid prediction for GeneMark_model.1994_t
Valid prediction for GlimmerHMM_glimmerT_1497-T1
Valid prediction for snap_scaffold_1-snap.1900-T1
Valid prediction for GeneMark_model.1959_t
Valid prediction for GeneMark_model.1960_t
Valid prediction for GlimmerHMM_glimmerT_1487-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 58632, rend_intergenic: 42658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84468, rend_intergenic: 64001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92894, rend_intergenic: 85681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99225, rend_intergenic: 96142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105946, rend_intergenic: 102888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108146, rend_intergenic: 106336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182637, rend_intergenic: 178046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197785, rend_intergenic: 190684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209204
-exon list size: 652


building trellis

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80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 58632, rend_intergenic: 42658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84468, rend_intergenic: 64001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92894, rend_intergenic: 85681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99225, rend_intergenic: 96142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105946, rend_intergenic: 102888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108146, rend_intergenic: 106336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182637, rend_intergenic: 178046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197785, rend_intergenic: 190684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support