-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_8343510-8555954

-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 snap_scaffold_3-snap.1719-T1
Valid prediction for GeneMark_model.11739_t
Valid prediction for GlimmerHMM_glimmerT_7120-T1
Valid prediction for Augustus_model.g4677.t1
Valid prediction for GlimmerHMM_glimmerT_7123-T1
Valid prediction for GeneMark_model.11746_t
Valid prediction for GeneMark_model.11785_t
Valid prediction for snap_scaffold_3-snap.1707-T1
Valid prediction for snap_scaffold_3-snap.1725-T1
Valid prediction for GlimmerHMM_glimmerT_7090-T1
Valid prediction for snap_scaffold_3-snap.1716-T1
Valid prediction for GlimmerHMM_glimmerT_7085-T1
Valid prediction for HiQ_model.g4682.t1
Valid prediction for GeneMark_model.11782_t
Valid prediction for snap_scaffold_3-snap.1735-T1
Valid prediction for snap_scaffold_3-snap.1744-T1
Valid prediction for Augustus_model.g4679.t1
Valid prediction for snap_scaffold_3-snap.1727-T1
Valid prediction for Augustus_model.g4665.t1
Valid prediction for GlimmerHMM_glimmerT_7100-T1
Valid prediction for Augustus_model.g4667.t1
Valid prediction for GlimmerHMM_glimmerT_7099-T1
Valid prediction for snap_scaffold_3-snap.1717-T1
Valid prediction for GeneMark_model.11783_t
Valid prediction for GlimmerHMM_glimmerT_7121-T1
Valid prediction for GeneMark_model.11776_t
Valid prediction for GeneMark_model.11762_t
Valid prediction for Augustus_model.g4672.t1
Valid prediction for pasa_asmbl_40177.p1
Valid prediction for snap_scaffold_3-snap.1740-T1
Valid prediction for GeneMark_model.11757_t
Valid prediction for Augustus_model.g4678.t1
Valid prediction for Augustus_model.g4683.t1
Valid prediction for GlimmerHMM_glimmerT_7098-T1
Valid prediction for GeneMark_model.11734_t
Valid prediction for GeneMark_model.11764_t
Valid prediction for Augustus_model.g4668.t1
Valid prediction for CodingQuarry_transcript_46122-T1
Couldn't classify 77978, 78023
Sorry, prediction pasa_asmbl_40171.p1 fails validation.
(TGC)	 CC	77978-78023	GT	AGG
(TAA)	 AG	79042-79086	GT	AGG
(CAT)	 AG	79620-79825	GT	AGG
(ACC)	 AG	80910-81086	GA	GAG
-recovered pasa_asmbl_40171.p1, terminal, 80910, 81086
-recovered pasa_asmbl_40171.p1, internal, 79042, 79086
-recovered pasa_asmbl_40171.p1, internal, 79620, 79825
Valid prediction for GeneMark_model.11749_t
Valid prediction for GeneMark_model.11743_t
Valid prediction for GeneMark_model.11747_t
Valid prediction for GlimmerHMM_glimmerT_7096-T1
Valid prediction for Augustus_model.g4658.t1
Valid prediction for snap_scaffold_3-snap.1700-T1
Valid prediction for GeneMark_model.11781_t
Valid prediction for GlimmerHMM_glimmerT_7116-T1
Valid prediction for GeneMark_model.11759_t
Valid prediction for GeneMark_model.11767_t
Valid prediction for GlimmerHMM_glimmerT_7097-T1
Valid prediction for snap_scaffold_3-snap.1739-T1
Valid prediction for Augustus_model.g4684.t1
Couldn't classify 64498, 64693
Couldn't classify 64967, 65079
Sorry, prediction pasa_asmbl_40796.p1 fails validation.
(GAT)	 TC	64498-64693	GT	AGG
(AGT)	 AG	64967-65079	CA	TAC
Valid prediction for Augustus_model.g4663.t1
Valid prediction for snap_scaffold_3-snap.1746-T1
Valid prediction for GlimmerHMM_glimmerT_7095-T1
Valid prediction for GlimmerHMM_glimmerT_7115-T1
Valid prediction for snap_scaffold_3-snap.1712-T1
Valid prediction for GlimmerHMM_glimmerT_7103-T1
Valid prediction for GlimmerHMM_glimmerT_7101-T1
Valid prediction for GeneMark_model.11741_t
Valid prediction for GeneMark_model.11733_t
Couldn't classify 123857, 123913
Sorry, prediction pasa_asmbl_40175.p1 fails validation.
(AGG)	 GG	123857-123913	GT	AGG
(GTG)	 AG	124823-124906	GT	TGG
(GAA)	 AG	125364-125474	GT	AGG
(GAA)	 AG	125967-126503	AC	GAA
-recovered pasa_asmbl_40175.p1, terminal, 125967, 126503
-recovered pasa_asmbl_40175.p1, internal, 124823, 124906
-recovered pasa_asmbl_40175.p1, internal, 125364, 125474
Valid prediction for GlimmerHMM_glimmerT_7087-T1
Valid prediction for GlimmerHMM_glimmerT_7117-T1
Valid prediction for GlimmerHMM_glimmerT_7106-T1
Valid prediction for GeneMark_model.11736_t
Valid prediction for CodingQuarry_transcript_46117-T1
Valid prediction for snap_scaffold_3-snap.1743-T1
Valid prediction for GeneMark_model.11789_t
Valid prediction for GeneMark_model.11751_t
Valid prediction for GeneMark_model.11773_t
Valid prediction for snap_scaffold_3-snap.1705-T1
Valid prediction for GeneMark_model.11774_t
Valid prediction for Augustus_model.g4659.t1
Valid prediction for snap_scaffold_3-snap.1714-T1
Valid prediction for snap_scaffold_3-snap.1737-T1
Valid prediction for GeneMark_model.11787_t
Valid prediction for snap_scaffold_3-snap.1699-T1
Valid prediction for snap_scaffold_3-snap.1702-T1
Valid prediction for GeneMark_model.11753_t
Valid prediction for GeneMark_model.11778_t
Valid prediction for Augustus_model.g4686.t1
Valid prediction for Augustus_model.g4664.t1
Valid prediction for snap_scaffold_3-snap.1710-T1
Valid prediction for GeneMark_model.11766_t
Valid prediction for GeneMark_model.11755_t
Valid prediction for snap_scaffold_3-snap.1709-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_3-snap.1711-T1
Valid prediction for Augustus_model.g4673.t1
Valid prediction for GlimmerHMM_glimmerT_7124-T1
Valid prediction for snap_scaffold_3-snap.1723-T1
Valid prediction for snap_scaffold_3-snap.1742-T1
Valid prediction for snap_scaffold_3-snap.1715-T1
Valid prediction for GlimmerHMM_glimmerT_7092-T1
Valid prediction for GlimmerHMM_glimmerT_7111-T1
Valid prediction for Augustus_model.g4660.t1
Valid prediction for snap_scaffold_3-snap.1718-T1
Valid prediction for snap_scaffold_3-snap.1713-T1
Valid prediction for GeneMark_model.11738_t
Valid prediction for snap_scaffold_3-snap.1722-T1
Valid prediction for snap_scaffold_3-snap.1749-T1
Valid prediction for Augustus_model.g4661.t1
Valid prediction for GlimmerHMM_glimmerT_7122-T1
Valid prediction for GeneMark_model.11768_t
Valid prediction for GlimmerHMM_glimmerT_7108-T1
Valid prediction for GeneMark_model.11742_t
Valid prediction for snap_scaffold_3-snap.1708-T1
Valid prediction for snap_scaffold_3-snap.1704-T1
Valid prediction for snap_scaffold_3-snap.1734-T1
Valid prediction for HiQ_model.g4675.t1
Valid prediction for GlimmerHMM_glimmerT_7109-T1
Valid prediction for GeneMark_model.11761_t
Valid prediction for GeneMark_model.11760_t
Valid prediction for GlimmerHMM_glimmerT_7112-T1
Valid prediction for Augustus_model.g4676.t1
Valid prediction for GeneMark_model.11758_t
Valid prediction for snap_scaffold_3-snap.1728-T1
Valid prediction for Augustus_model.g4670.t1
Valid prediction for GeneMark_model.11765_t
Valid prediction for GlimmerHMM_glimmerT_7119-T1
Valid prediction for snap_scaffold_3-snap.1720-T1
Valid prediction for snap_scaffold_3-snap.1732-T1
Valid prediction for pasa_asmbl_38997.p1
Valid prediction for GeneMark_model.11780_t
Valid prediction for GeneMark_model.11756_t
Valid prediction for GeneMark_model.11784_t
Valid prediction for GeneMark_model.11754_t
Valid prediction for snap_scaffold_3-snap.1726-T1
Valid prediction for GeneMark_model.11770_t
Valid prediction for GlimmerHMM_glimmerT_7113-T1
Valid prediction for GeneMark_model.11748_t
Valid prediction for snap_scaffold_3-snap.1741-T1
Valid prediction for GlimmerHMM_glimmerT_7114-T1
Valid prediction for Augustus_model.g4671.t1
Valid prediction for GeneMark_model.11788_t
Valid prediction for Augustus_model.g4681.t1
Valid prediction for HiQ_model.g4680.t1
Valid prediction for GlimmerHMM_glimmerT_7093-T1
Valid prediction for GlimmerHMM_glimmerT_7086-T1
Valid prediction for GlimmerHMM_glimmerT_7104-T1
Valid prediction for GeneMark_model.11771_t
Valid prediction for snap_scaffold_3-snap.1745-T1
Valid prediction for Augustus_model.g4662.t1
Valid prediction for Augustus_model.g4669.t1
Valid prediction for GeneMark_model.11735_t
Valid prediction for GlimmerHMM_glimmerT_7091-T1
Valid prediction for GeneMark_model.11737_t
Valid prediction for GeneMark_model.11744_t
Valid prediction for GeneMark_model.11769_t
Valid prediction for snap_scaffold_3-snap.1706-T1
Valid prediction for snap_scaffold_3-snap.1703-T1
Valid prediction for GeneMark_model.11752_t
Valid prediction for GeneMark_model.11775_t
Valid prediction for GeneMark_model.11732_t
Valid prediction for snap_scaffold_3-snap.1738-T1
Valid prediction for snap_scaffold_3-snap.1724-T1
Valid prediction for GeneMark_model.11786_t
Valid prediction for snap_scaffold_3-snap.1748-T1
Valid prediction for GlimmerHMM_glimmerT_7110-T1
Valid prediction for GeneMark_model.11763_t
Valid prediction for GlimmerHMM_glimmerT_7118-T1
Valid prediction for snap_scaffold_3-snap.1731-T1
Valid prediction for GlimmerHMM_glimmerT_7094-T1
Valid prediction for GlimmerHMM_glimmerT_7107-T1
Valid prediction for GlimmerHMM_glimmerT_7105-T1
Valid prediction for GeneMark_model.11745_t
Valid prediction for GlimmerHMM_glimmerT_7089-T1
Valid prediction for pasa_asmbl_38998.p1
Valid prediction for GeneMark_model.11777_t
Valid prediction for GeneMark_model.11731_t
Valid prediction for snap_scaffold_3-snap.1701-T1
Valid prediction for snap_scaffold_3-snap.1736-T1
Valid prediction for snap_scaffold_3-snap.1729-T1
Valid prediction for GlimmerHMM_glimmerT_7102-T1
Valid prediction for GeneMark_model.11772_t
Valid prediction for GeneMark_model.11779_t
Valid prediction for CodingQuarry_transcript_46120-T1
Valid prediction for GlimmerHMM_glimmerT_7088-T1
Valid prediction for CodingQuarry_transcript_46121-T1
Couldn't classify 72806, 72901
Sorry, prediction pasa_asmbl_38995.p1 fails validation.
(GGG)	 AA	72806-72901	GT	CGG
(ACG)	 AG	73010-73176	GT	CGG
(AAT)	 AG	73361-73442	GT	ATG
(ACC)	 AG	73557-73760	GT	GGG
(TTG)	 AG	74586-74747	TA	AGT
-recovered pasa_asmbl_38995.p1, terminal, 74586, 74747
-recovered pasa_asmbl_38995.p1, internal, 73010, 73176
-recovered pasa_asmbl_38995.p1, internal, 73361, 73442
-recovered pasa_asmbl_38995.p1, internal, 73557, 73760
Valid prediction for snap_scaffold_3-snap.1733-T1
Valid prediction for snap_scaffold_3-snap.1730-T1
Valid prediction for Augustus_model.g4666.t1
Valid prediction for Augustus_model.g4685.t1
Couldn't classify 99943, 100210
Sorry, prediction pasa_asmbl_38993.p1 fails validation.
(TTT)	 GG	99943-100210	GT	AGG
(AGT)	 AG	101148-101332	GC	AGG
-recovered pasa_asmbl_38993.p1, terminal, 101148, 101332
-recovered pasa_asmbl_38993.p1, internal, 101148, 101332
Valid prediction for snap_scaffold_3-snap.1721-T1
Valid prediction for CodingQuarry_transcript_46118-T1
Valid prediction for GeneMark_model.11750_t
Valid prediction for GeneMark_model.11740_t
Valid prediction for GlimmerHMM_glimmerT_7125-T1
Valid prediction for Augustus_model.g4674.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 105544, rend_intergenic: 105541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17224, rend_intergenic: 14671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18758, rend_intergenic: 17254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36480, rend_intergenic: 29539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48816, rend_intergenic: 46700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59128, rend_intergenic: 53358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60365, rend_intergenic: 59261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66721, rend_intergenic: 61334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71540, rend_intergenic: 70499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113439, rend_intergenic: 105449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166318, rend_intergenic: 155675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171520, rend_intergenic: 168213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197090, rend_intergenic: 194996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199106, rend_intergenic: 197539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212445
-exon list size: 818


building trellis

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64.0    
64.1    
64.3    
64.4    
64.5    
64.6    
64.8    
64.9    
65.0    
65.1    
65.2    
65.4    
65.5    
65.6    
65.7    
65.9    
66.0    
66.1    
66.2    
66.3    
66.5    
66.6    
66.7    
66.8    
67.0    
67.1    
67.2    
67.3    
67.4    
67.6    
67.7    
67.8    
67.9    
68.0    
68.2    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.0    
69.1    
69.3    
69.4    
69.5    
69.6    
69.8    
69.9    
70.0    
70.1    
70.2    
70.4    
70.5    
70.6    
70.7    
70.9    
71.0    
71.1    
71.2    
71.3    
71.5    
71.6    
71.7    
71.8    
72.0    
72.1    
72.2    
72.3    
72.4    
72.6    
72.7    
72.8    
72.9    
73.0    
73.2    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.6    
74.8    
74.9    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.6    
79.8    
79.9    
80.0    
80.1    
80.2    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.0    
99.1    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 45 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 105544, rend_intergenic: 105541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17224, rend_intergenic: 14671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18758, rend_intergenic: 17254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36480, rend_intergenic: 29539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48816, rend_intergenic: 46700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59128, rend_intergenic: 53358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60365, rend_intergenic: 59261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66721, rend_intergenic: 61334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71540, rend_intergenic: 70499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113439, rend_intergenic: 105449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166318, rend_intergenic: 155675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171520, rend_intergenic: 168213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197090, rend_intergenic: 194996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199106, rend_intergenic: 197539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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