-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_9517760-9699806

-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.52651_t
Valid prediction for snap_scaffold_12-snap.1842-T1
Valid prediction for snap_scaffold_12-snap.1827-T1
Valid prediction for GeneMark_model.52677_t
Valid prediction for GeneMark_model.52670_t
Valid prediction for GlimmerHMM_glimmerT_30466-T1
Valid prediction for GlimmerHMM_glimmerT_30483-T1
Valid prediction for GeneMark_model.52638_t
Valid prediction for GeneMark_model.52642_t
Valid prediction for GeneMark_model.52648_t
Valid prediction for Augustus_model.g20322.t1
Valid prediction for snap_scaffold_12-snap.1824-T1
Valid prediction for GlimmerHMM_glimmerT_30471-T1
Valid prediction for GeneMark_model.52675_t
Valid prediction for Augustus_model.g20310.t1
Valid prediction for Augustus_model.g20320.t1
Valid prediction for GeneMark_model.52665_t
Valid prediction for snap_scaffold_12-snap.1814-T1
Valid prediction for snap_scaffold_12-snap.1816-T1
Valid prediction for GlimmerHMM_glimmerT_30468-T1
Valid prediction for snap_scaffold_12-snap.1811-T1
Valid prediction for GlimmerHMM_glimmerT_30474-T1
Valid prediction for GeneMark_model.52662_t
Valid prediction for GlimmerHMM_glimmerT_30478-T1
Valid prediction for CodingQuarry_transcript_10310-T1
Valid prediction for GlimmerHMM_glimmerT_30490-T1
Valid prediction for snap_scaffold_12-snap.1815-T1
Valid prediction for GeneMark_model.52679_t
Valid prediction for GeneMark_model.52644_t
Valid prediction for GlimmerHMM_glimmerT_30488-T1
Valid prediction for Augustus_model.g20323.t1
Valid prediction for GlimmerHMM_glimmerT_30480-T1
Valid prediction for GeneMark_model.52658_t
Valid prediction for GeneMark_model.52656_t
Valid prediction for Augustus_model.g20313.t1
Valid prediction for snap_scaffold_12-snap.1826-T1
Valid prediction for snap_scaffold_12-snap.1840-T1
Valid prediction for snap_scaffold_12-snap.1844-T1
Valid prediction for snap_scaffold_12-snap.1841-T1
Valid prediction for snap_scaffold_12-snap.1821-T1
Valid prediction for GeneMark_model.52667_t
Valid prediction for GlimmerHMM_glimmerT_30479-T1
Valid prediction for GlimmerHMM_glimmerT_30487-T1
Valid prediction for GlimmerHMM_glimmerT_30473-T1
Valid prediction for GeneMark_model.52660_t
Valid prediction for CodingQuarry_transcript_10311-T1
Valid prediction for GeneMark_model.52663_t
Valid prediction for snap_scaffold_12-snap.1833-T1
Valid prediction for GeneMark_model.52639_t
Valid prediction for snap_scaffold_12-snap.1839-T1
Valid prediction for GeneMark_model.52649_t
Valid prediction for GeneMark_model.52646_t
Valid prediction for Augustus_model.g20318.t1
Valid prediction for Augustus_model.g20308.t1
Valid prediction for Augustus_model.g20319.t1
Valid prediction for snap_scaffold_12-snap.1818-T1
Valid prediction for snap_scaffold_12-snap.1820-T1
Valid prediction for GlimmerHMM_glimmerT_30460-T1
Valid prediction for Augustus_model.g20300.t1
Valid prediction for GlimmerHMM_glimmerT_30486-T1
Valid prediction for GeneMark_model.52653_t
Valid prediction for snap_scaffold_12-snap.1837-T1
Valid prediction for GeneMark_model.52673_t
Valid prediction for GeneMark_model.52655_t
Valid prediction for pasa_asmbl_8832.p1

-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 Augustus_model.g20303.t1
Couldn't classify 160334, 160419
Couldn't classify 160905, 160975
Sorry, prediction pasa_asmbl_7807.p1 fails validation.
(GTG)	 AC	160334-160419	GT	AAG
(GTA)	 AG	160568-160639	GT	GTG
(GTA)	 AG	160738-160811	GT	AGG
(GTG)	 AG	160905-160975	AG	AGA
-recovered pasa_asmbl_7807.p1, internal, 160568, 160639
-recovered pasa_asmbl_7807.p1, internal, 160738, 160811
Valid prediction for GeneMark_model.52641_t
Valid prediction for snap_scaffold_12-snap.1831-T1
Valid prediction for snap_scaffold_12-snap.1810-T1
Valid prediction for GlimmerHMM_glimmerT_30465-T1
Valid prediction for GeneMark_model.52666_t
Valid prediction for GlimmerHMM_glimmerT_30467-T1
Valid prediction for GlimmerHMM_glimmerT_30475-T1
Valid prediction for snap_scaffold_12-snap.1813-T1
Valid prediction for GlimmerHMM_glimmerT_30484-T1
Valid prediction for Augustus_model.g20311.t1
Valid prediction for GlimmerHMM_glimmerT_30463-T1
Valid prediction for snap_scaffold_12-snap.1817-T1
Valid prediction for GlimmerHMM_glimmerT_30476-T1
Valid prediction for snap_scaffold_12-snap.1835-T1
Valid prediction for GeneMark_model.52643_t
Valid prediction for GlimmerHMM_glimmerT_30482-T1
Valid prediction for Augustus_model.g20315.t1
Valid prediction for CodingQuarry_transcript_10312-T1
Valid prediction for snap_scaffold_12-snap.1846-T1
Couldn't classify 55662, 56411
Sorry, prediction pasa_asmbl_7811.p1 fails validation.
(GCC)	 CT	55662-56411	GT	AGG
(ATG)	 AG	56521-56636	GT	AGG
(TGG)	 AG	56729-56822	CC	GAC
-recovered pasa_asmbl_7811.p1, initial, 56521, 56636
-recovered pasa_asmbl_7811.p1, terminal, 56729, 56822
-recovered pasa_asmbl_7811.p1, internal, 56521, 56636
Valid prediction for GeneMark_model.52672_t
Valid prediction for snap_scaffold_12-snap.1832-T1
Valid prediction for GeneMark_model.52640_t
Valid prediction for GeneMark_model.52657_t
Valid prediction for GeneMark_model.52669_t
Valid prediction for GlimmerHMM_glimmerT_30464-T1
Valid prediction for Augustus_model.g20306.t1
Valid prediction for GlimmerHMM_glimmerT_30485-T1
Valid prediction for GlimmerHMM_glimmerT_30477-T1
Valid prediction for Augustus_model.g20304.t1
Couldn't classify 61870, 62283
Sorry, prediction pasa_asmbl_7809.p1 fails validation.
(CGG)	 GT	61870-62283	AA	AGA
Couldn't classify 61159, 61821
Sorry, prediction pasa_asmbl_7810.p1 fails validation.
(ATG)	 GG	61159-61821	TT	CCT
Valid prediction for GeneMark_model.52676_t
Valid prediction for GeneMark_model.52652_t
Valid prediction for CodingQuarry_transcript_10313-T1
Valid prediction for snap_scaffold_12-snap.1819-T1
Valid prediction for HiQ_model.g20321.t1
Valid prediction for GlimmerHMM_glimmerT_30481-T1
Valid prediction for Augustus_model.g20305.t1
Valid prediction for GlimmerHMM_glimmerT_30470-T1
Valid prediction for snap_scaffold_12-snap.1829-T1
Valid prediction for Augustus_model.g20301.t1
Valid prediction for GeneMark_model.52674_t
Valid prediction for GeneMark_model.52678_t
Valid prediction for snap_scaffold_12-snap.1830-T1
Valid prediction for GlimmerHMM_glimmerT_30472-T1
Couldn't classify 50117, 50191
Couldn't classify 51128, 51228
Sorry, prediction pasa_asmbl_7814.p1 fails validation.
(GAC)	 TC	50117-50191	GT	AGG
(AAC)	 AG	50446-50535	GT	GGG
(GTG)	 AG	50648-50776	GT	AGG
(GTA)	 AG	50929-51043	GT	CAG
(TTC)	 AG	51128-51228	GT	GAG
-recovered pasa_asmbl_7814.p1, internal, 50446, 50535
-recovered pasa_asmbl_7814.p1, internal, 50648, 50776
-recovered pasa_asmbl_7814.p1, internal, 50929, 51043
-recovered pasa_asmbl_7814.p1, internal, 51128, 51228
Valid prediction for Augustus_model.g20309.t1
Valid prediction for Augustus_model.g20302.t1
Valid prediction for GeneMark_model.52671_t
Valid prediction for GeneMark_model.52647_t
Valid prediction for Augustus_model.g20317.t1
Valid prediction for snap_scaffold_12-snap.1836-T1
Valid prediction for snap_scaffold_12-snap.1823-T1
Valid prediction for Augustus_model.g20307.t1
Valid prediction for snap_scaffold_12-snap.1828-T1
Valid prediction for GeneMark_model.52659_t
Valid prediction for GeneMark_model.52645_t
Valid prediction for Augustus_model.g20316.t1
Valid prediction for GlimmerHMM_glimmerT_30489-T1
Valid prediction for GeneMark_model.52664_t
Valid prediction for snap_scaffold_12-snap.1838-T1
Couldn't classify 161186, 161322
Couldn't classify 161963, 162008
Sorry, prediction pasa_asmbl_7805.p1 fails validation.
(GAG)	 TG	161186-161322	GT	AGG
(GCT)	 AG	161508-161774	GT	AGG
(GAG)	 AG	161963-162008	GC	GGG
-recovered pasa_asmbl_7805.p1, internal, 161508, 161774
-recovered pasa_asmbl_7805.p1, internal, 161963, 162008
Valid prediction for snap_scaffold_12-snap.1843-T1
Valid prediction for GlimmerHMM_glimmerT_30462-T1
Valid prediction for GlimmerHMM_glimmerT_30469-T1
Valid prediction for Augustus_model.g20314.t1
Valid prediction for Augustus_model.g20312.t1
Valid prediction for snap_scaffold_12-snap.1834-T1
Valid prediction for snap_scaffold_12-snap.1822-T1
Valid prediction for GeneMark_model.52654_t
Couldn't classify 51830, 51913
Couldn't classify 54892, 55076
Sorry, prediction pasa_asmbl_7812.p1 fails validation.
(CAG)	 CC	51830-51913	GT	AGG
(GTG)	 AG	52085-52202	GT	GGG
(GAA)	 AG	52360-52456	GT	AGG
(GAG)	 AG	52696-52934	GT	CAG
(AGG)	 AG	53080-53168	GT	GGG
(GTG)	 AG	53667-53748	GT	CGG
(GTT)	 AG	54110-54199	GT	AGG
(ATC)	 AG	54306-54419	GT	AGG
(AGA)	 AG	54519-54607	GT	AAG
(CTT)	 AG	54692-54779	GT	CGG
(GTG)	 AG	54892-55076	CC	CTC
add_exon() Sorry, pasa_asmbl_7812.p1 52360-52456-terminal-3 is invalid.
-recovered pasa_asmbl_7812.p1, terminal, 52360, 52456
add_exon() Sorry, pasa_asmbl_7812.p1 54110-54199-terminal-1 is invalid.
-recovered pasa_asmbl_7812.p1, terminal, 54110, 54199
-recovered pasa_asmbl_7812.p1, internal, 52085, 52202
-recovered pasa_asmbl_7812.p1, internal, 52360, 52456
-recovered pasa_asmbl_7812.p1, internal, 52696, 52934
-recovered pasa_asmbl_7812.p1, internal, 53080, 53168
-recovered pasa_asmbl_7812.p1, internal, 53667, 53748
-recovered pasa_asmbl_7812.p1, internal, 54110, 54199
-recovered pasa_asmbl_7812.p1, internal, 54306, 54419
-recovered pasa_asmbl_7812.p1, internal, 54519, 54607
-recovered pasa_asmbl_7812.p1, internal, 54692, 54779
Valid prediction for GeneMark_model.52680_t
Valid prediction for snap_scaffold_12-snap.1812-T1
Valid prediction for GeneMark_model.52661_t
Valid prediction for GeneMark_model.52650_t
Valid prediction for GlimmerHMM_glimmerT_30461-T1
Valid prediction for snap_scaffold_12-snap.1825-T1
Valid prediction for pasa_asmbl_7815.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11309, rend_intergenic: 6146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33243, rend_intergenic: 17787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40459, rend_intergenic: 33610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41356, rend_intergenic: 41206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51869, rend_intergenic: 42497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72360, rend_intergenic: 65715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77799, rend_intergenic: 74248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90548, rend_intergenic: 85379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136734, rend_intergenic: 136041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139921, rend_intergenic: 136862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182047
-exon list size: 734


building trellis

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81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 11309, rend_intergenic: 6146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33243, rend_intergenic: 17787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40459, rend_intergenic: 33610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41356, rend_intergenic: 41206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51869, rend_intergenic: 42497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72360, rend_intergenic: 65715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77799, rend_intergenic: 74248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90548, rend_intergenic: 85379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136734, rend_intergenic: 136041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139921, rend_intergenic: 136862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support