-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_9083613-9255163

-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_54384-T1
Valid prediction for GeneMark_model.94788_t
Valid prediction for snap_scaffold_24-snap.1888-T1
Valid prediction for snap_scaffold_24-snap.1894-T1
Valid prediction for GeneMark_model.94766_t
Valid prediction for GlimmerHMM_glimmerT_54381-T1
Valid prediction for Augustus_model.g36413.t1
Valid prediction for CodingQuarry_transcript_37332-T1
Valid prediction for GeneMark_model.94764_t
Valid prediction for CodingQuarry_transcript_37328-T1
Valid prediction for GlimmerHMM_glimmerT_54380-T1
Valid prediction for GeneMark_model.94801_t
Valid prediction for GeneMark_model.94795_t
Valid prediction for Augustus_model.g36424.t1
Valid prediction for snap_scaffold_24-snap.1914-T1
Valid prediction for CodingQuarry_transcript_37333-T1
Couldn't classify 49873, 50571
Sorry, prediction pasa_asmbl_32523.p1 fails validation.
(CTT)	 GA	49873-50571	CC	GAC
Valid prediction for GeneMark_model.94803_t
Valid prediction for snap_scaffold_24-snap.1876-T1
Valid prediction for snap_scaffold_24-snap.1908-T1
Valid prediction for pasa_asmbl_32505.p1
Valid prediction for GlimmerHMM_glimmerT_54404-T1
Valid prediction for snap_scaffold_24-snap.1910-T1
Valid prediction for snap_scaffold_24-snap.1906-T1
Valid prediction for GeneMark_model.94802_t
Valid prediction for CodingQuarry_transcript_37329-T1
Valid prediction for snap_scaffold_24-snap.1873-T1
Valid prediction for pasa_asmbl_32509.p1
Valid prediction for GlimmerHMM_glimmerT_54387-T1
Valid prediction for GlimmerHMM_glimmerT_54386-T1
Valid prediction for GeneMark_model.94770_t
Valid prediction for snap_scaffold_24-snap.1882-T1
Valid prediction for HiQ_model.g36411.t1
Valid prediction for snap_scaffold_24-snap.1890-T1
Valid prediction for GlimmerHMM_glimmerT_54398-T1
Valid prediction for GeneMark_model.94773_t
Valid prediction for HiQ_model.g36409.t1
Valid prediction for GeneMark_model.94777_t
Valid prediction for snap_scaffold_24-snap.1874-T1
Valid prediction for GeneMark_model.94775_t
Valid prediction for snap_scaffold_24-snap.1875-T1
Valid prediction for GeneMark_model.94769_t
Valid prediction for snap_scaffold_24-snap.1903-T1
Valid prediction for Augustus_model.g36425.t1
Valid prediction for GeneMark_model.94779_t
Valid prediction for GeneMark_model.94792_t
Valid prediction for GeneMark_model.94789_t
Valid prediction for snap_scaffold_24-snap.1896-T1
Valid prediction for snap_scaffold_24-snap.1880-T1
Valid prediction for GeneMark_model.94808_t
Valid prediction for Augustus_model.g36412.t1
Valid prediction for GeneMark_model.94799_t
Valid prediction for GeneMark_model.94806_t
Valid prediction for snap_scaffold_24-snap.1881-T1
Valid prediction for GlimmerHMM_glimmerT_54379-T1
Valid prediction for GlimmerHMM_glimmerT_54405-T1
Valid prediction for snap_scaffold_24-snap.1883-T1
Valid prediction for CodingQuarry_transcript_37330-T1
Couldn't classify 38605, 38692
Sorry, prediction pasa_asmbl_32517.p1 fails validation.
(ATG)	 CT	37556-37606	GT	GGG
(CAC)	 AG	37885-37934	GT	AGG
(GAC)	 AG	38242-38379	GT	GGG
(CCA)	 AG	38605-38692	CT	CAC
-recovered pasa_asmbl_32517.p1, initial, 37556, 37606
-recovered pasa_asmbl_32517.p1, internal, 37885, 37934
-recovered pasa_asmbl_32517.p1, internal, 38242, 38379
Valid prediction for snap_scaffold_24-snap.1901-T1
Valid prediction for pasa_asmbl_32512.p1
Valid prediction for GeneMark_model.94783_t
Valid prediction for GeneMark_model.94781_t
Valid prediction for Augustus_model.g36422.t1
Valid prediction for GeneMark_model.94791_t
Valid prediction for snap_scaffold_24-snap.1909-T1
Valid prediction for GlimmerHMM_glimmerT_54390-T1
Valid prediction for GeneMark_model.94785_t
Couldn't classify 39497, 39578
Sorry, prediction pasa_asmbl_32521.p1 fails validation.
(TCT)	 CC	39497-39578	GT	GGG
(ACA)	 AG	39885-40016	GT	CAG
(GTG)	 AG	40944-41318	GT	TGG
(ATC)	 AG	41849-41968	GT	GGG
(AAA)	 AG	42067-42192	GT	AGG
(GAG)	 AG	42774-42945	GT	AGG
(GAT)	 AG	43099-43314	GT	GGG
(TCT)	 AG	43510-43628	GT	AGG
(ATG)	 AG	43871-44010	GT	AGG
(GGA)	 AG	44142-44283	GT	AGG
(AAT)	 AG	44543-44617	GT	CGG
(TGT)	 AG	44763-44921	GT	AGG
(GAC)	 AG	45195-45247	CA	AGC
add_exon() Sorry, pasa_asmbl_32521.p1 43871-44010-initial-1 is invalid.
-recovered pasa_asmbl_32521.p1, initial, 43871, 44010
add_exon() Sorry, pasa_asmbl_32521.p1 43510-43628-terminal-2 is invalid.
-recovered pasa_asmbl_32521.p1, terminal, 43510, 43628
-recovered pasa_asmbl_32521.p1, terminal, 45195, 45247
-recovered pasa_asmbl_32521.p1, internal, 39885, 40016
-recovered pasa_asmbl_32521.p1, internal, 40944, 41318
-recovered pasa_asmbl_32521.p1, internal, 41849, 41968
-recovered pasa_asmbl_32521.p1, internal, 42067, 42192
-recovered pasa_asmbl_32521.p1, internal, 42774, 42945
-recovered pasa_asmbl_32521.p1, internal, 43099, 43314
-recovered pasa_asmbl_32521.p1, internal, 43510, 43628
-recovered pasa_asmbl_32521.p1, internal, 43871, 44010
-recovered pasa_asmbl_32521.p1, internal, 44142, 44283
-recovered pasa_asmbl_32521.p1, internal, 44543, 44617
-recovered pasa_asmbl_32521.p1, internal, 44763, 44921
Valid prediction for GeneMark_model.94796_t
Valid prediction for GeneMark_model.94798_t
Valid prediction for snap_scaffold_24-snap.1884-T1
Valid prediction for snap_scaffold_24-snap.1898-T1
Valid prediction for GeneMark_model.94768_t
Valid prediction for snap_scaffold_24-snap.1879-T1
Valid prediction for GlimmerHMM_glimmerT_54401-T1
Valid prediction for snap_scaffold_24-snap.1900-T1
Valid prediction for GlimmerHMM_glimmerT_54385-T1
Valid prediction for GlimmerHMM_glimmerT_54402-T1
Valid prediction for GeneMark_model.94762_t
Valid prediction for snap_scaffold_24-snap.1878-T1
Valid prediction for GlimmerHMM_glimmerT_54393-T1
Valid prediction for snap_scaffold_24-snap.1913-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_54395-T1
Valid prediction for snap_scaffold_24-snap.1889-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_54407-T1
Valid prediction for GlimmerHMM_glimmerT_54406-T1
Valid prediction for snap_scaffold_24-snap.1877-T1
Valid prediction for snap_scaffold_24-snap.1912-T1
Valid prediction for Augustus_model.g36415.t1
Valid prediction for GeneMark_model.94809_t
Valid prediction for GlimmerHMM_glimmerT_54388-T1
Valid prediction for Augustus_model.g36426.t1
Valid prediction for GeneMark_model.94780_t
Valid prediction for pasa_asmbl_33121.p1
Valid prediction for snap_scaffold_24-snap.1893-T1
Valid prediction for GlimmerHMM_glimmerT_54400-T1
Valid prediction for GlimmerHMM_glimmerT_54403-T1
Valid prediction for HiQ_model.g36410.t1
Valid prediction for GlimmerHMM_glimmerT_54408-T1
Valid prediction for GeneMark_model.94778_t
Valid prediction for snap_scaffold_24-snap.1904-T1
Valid prediction for snap_scaffold_24-snap.1902-T1
Valid prediction for Augustus_model.g36420.t1
Valid prediction for GlimmerHMM_glimmerT_54399-T1
Valid prediction for GeneMark_model.94804_t
Valid prediction for GeneMark_model.94787_t
Couldn't classify 115431, 115460
Couldn't classify 116636, 116707
Sorry, prediction pasa_asmbl_33127.p1 fails validation.
(CTG)	 GG	115431-115460	GT	AAG
(GGA)	 AG	115681-115853	GT	TGG
(GTA)	 AG	116200-116317	GT	AAG
(CTT)	 AG	116636-116707	GA	GAG
-recovered pasa_asmbl_33127.p1, internal, 115681, 115853
-recovered pasa_asmbl_33127.p1, internal, 116200, 116317
Valid prediction for GlimmerHMM_glimmerT_54396-T1
Valid prediction for snap_scaffold_24-snap.1916-T1
Valid prediction for snap_scaffold_24-snap.1887-T1
Valid prediction for Augustus_model.g36418.t1
Valid prediction for GeneMark_model.94784_t
Valid prediction for GeneMark_model.94771_t
Valid prediction for snap_scaffold_24-snap.1917-T1
Valid prediction for GeneMark_model.94790_t
Valid prediction for snap_scaffold_24-snap.1899-T1
Valid prediction for Augustus_model.g36423.t1
Valid prediction for GeneMark_model.94805_t
Valid prediction for GlimmerHMM_glimmerT_54394-T1
Valid prediction for snap_scaffold_24-snap.1905-T1
Valid prediction for GeneMark_model.94793_t
Valid prediction for GeneMark_model.94786_t
Valid prediction for GeneMark_model.94767_t
Valid prediction for snap_scaffold_24-snap.1915-T1
Valid prediction for Augustus_model.g36416.t1
Valid prediction for GeneMark_model.94765_t
Valid prediction for GeneMark_model.94774_t
Valid prediction for snap_scaffold_24-snap.1911-T1
Valid prediction for GeneMark_model.94772_t
Valid prediction for snap_scaffold_24-snap.1886-T1
Valid prediction for snap_scaffold_24-snap.1891-T1
Valid prediction for GeneMark_model.94797_t
Valid prediction for GlimmerHMM_glimmerT_54392-T1
Valid prediction for CodingQuarry_transcript_37331-T1
Valid prediction for Augustus_model.g36421.t1
Valid prediction for GeneMark_model.94763_t
Valid prediction for GeneMark_model.94800_t
Valid prediction for GeneMark_model.94776_t
Valid prediction for snap_scaffold_24-snap.1895-T1
Valid prediction for GlimmerHMM_glimmerT_54391-T1
Valid prediction for GlimmerHMM_glimmerT_54389-T1
Valid prediction for snap_scaffold_24-snap.1885-T1
Valid prediction for Augustus_model.g36414.t1
Valid prediction for snap_scaffold_24-snap.1907-T1
Valid prediction for snap_scaffold_24-snap.1897-T1
Valid prediction for GeneMark_model.94807_t
Valid prediction for GlimmerHMM_glimmerT_54397-T1
Valid prediction for GlimmerHMM_glimmerT_54382-T1
Valid prediction for Augustus_model.g36417.t1
Valid prediction for GlimmerHMM_glimmerT_54383-T1
Valid prediction for GeneMark_model.94794_t
Valid prediction for GeneMark_model.94782_t
Valid prediction for snap_scaffold_24-snap.1892-T1
Valid prediction for Augustus_model.g36419.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 67619, rend_intergenic: 66161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74335, rend_intergenic: 70235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77589, rend_intergenic: 76574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89535, rend_intergenic: 77707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108497, rend_intergenic: 105473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118423, rend_intergenic: 116743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124484, rend_intergenic: 121327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125200, rend_intergenic: 124703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129405, rend_intergenic: 126436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135572, rend_intergenic: 133990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145967, rend_intergenic: 142205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153836, rend_intergenic: 149754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165095, rend_intergenic: 161796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171551
-exon list size: 633


building trellis

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91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
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    
96.1    
96.2    
96.4    
96.5    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 67619, rend_intergenic: 66161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74335, rend_intergenic: 70235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77589, rend_intergenic: 76574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89535, rend_intergenic: 77707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108497, rend_intergenic: 105473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118423, rend_intergenic: 116743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124484, rend_intergenic: 121327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125200, rend_intergenic: 124703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129405, rend_intergenic: 126436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135572, rend_intergenic: 133990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145967, rend_intergenic: 142205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153836, rend_intergenic: 149754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165095, rend_intergenic: 161796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support