-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_8764950-8996236

-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.88789_t
Couldn't classify 167999, 168005
Sorry, prediction GeneMark_model.88829_t fails validation.
(GGC)	 AG	167999-168005	GT	CTG
(AGA)	 AG	170913-170963	GT	GCG
(AGA)	 AG	170987-171062	AT	AGA
-recovered GeneMark_model.88829_t, terminal, 170987, 171062
-recovered GeneMark_model.88829_t, internal, 167999, 168005
-recovered GeneMark_model.88829_t, internal, 170913, 170963
Valid prediction for snap_scaffold_22-snap.1841-T1
Valid prediction for snap_scaffold_22-snap.1861-T1
Valid prediction for GeneMark_model.88837_t
Valid prediction for GeneMark_model.88796_t
Valid prediction for Augustus_model.g34314.t1
Valid prediction for GeneMark_model.88840_t
Valid prediction for GeneMark_model.88779_t
Valid prediction for GlimmerHMM_glimmerT_51184-T1
Valid prediction for snap_scaffold_22-snap.1850-T1
Valid prediction for snap_scaffold_22-snap.1842-T1
Valid prediction for snap_scaffold_22-snap.1859-T1
Valid prediction for snap_scaffold_22-snap.1865-T1
Valid prediction for Augustus_model.g34321.t1
Valid prediction for GeneMark_model.88802_t
Valid prediction for GeneMark_model.88775_t
Valid prediction for GeneMark_model.88844_t
Valid prediction for GeneMark_model.88824_t
Valid prediction for GlimmerHMM_glimmerT_51174-T1
Valid prediction for snap_scaffold_22-snap.1847-T1
Valid prediction for snap_scaffold_22-snap.1846-T1
Valid prediction for GeneMark_model.88803_t
Valid prediction for GlimmerHMM_glimmerT_51186-T1
Valid prediction for GeneMark_model.88777_t
Valid prediction for GeneMark_model.88805_t
Valid prediction for GeneMark_model.88810_t
Valid prediction for GlimmerHMM_glimmerT_51176-T1
Valid prediction for GeneMark_model.88794_t
Valid prediction for snap_scaffold_22-snap.1832-T1
Valid prediction for snap_scaffold_22-snap.1853-T1
Valid prediction for snap_scaffold_22-snap.1871-T1
Valid prediction for GeneMark_model.88791_t
Valid prediction for snap_scaffold_22-snap.1875-T1
Valid prediction for GeneMark_model.88832_t
Valid prediction for snap_scaffold_22-snap.1833-T1
Valid prediction for GeneMark_model.88813_t
Valid prediction for Augustus_model.g34320.t1
Valid prediction for GeneMark_model.88807_t
Valid prediction for Augustus_model.g34318.t1
Valid prediction for GeneMark_model.88782_t
Valid prediction for snap_scaffold_22-snap.1868-T1
Valid prediction for GeneMark_model.88811_t
Valid prediction for GeneMark_model.88800_t
Valid prediction for GeneMark_model.88787_t
Valid prediction for snap_scaffold_22-snap.1834-T1
Valid prediction for Augustus_model.g34315.t1
Valid prediction for snap_scaffold_22-snap.1873-T1
Valid prediction for GeneMark_model.88798_t
Couldn't classify 53866, 54030
Sorry, prediction pasa_asmbl_29575.p2 fails validation.
(GGG)	 TA	53866-54030	GT	AGG
(GTG)	 AG	54242-54523	GG	AGG
-recovered pasa_asmbl_29575.p2, terminal, 54242, 54523
Valid prediction for GeneMark_model.88834_t
Valid prediction for GeneMark_model.88827_t
Valid prediction for GlimmerHMM_glimmerT_51187-T1
Valid prediction for GeneMark_model.88790_t
Valid prediction for snap_scaffold_22-snap.1851-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_51177-T1
Valid prediction for GeneMark_model.88781_t
Valid prediction for GeneMark_model.88785_t
Valid prediction for Augustus_model.g34322.t1
Valid prediction for GlimmerHMM_glimmerT_51179-T1
Valid prediction for GeneMark_model.88816_t
Valid prediction for GeneMark_model.88825_t
Valid prediction for snap_scaffold_22-snap.1836-T1
Valid prediction for GeneMark_model.88835_t
Valid prediction for snap_scaffold_22-snap.1864-T1
Valid prediction for GeneMark_model.88818_t
Valid prediction for GeneMark_model.88792_t
Valid prediction for GeneMark_model.88826_t
Valid prediction for GlimmerHMM_glimmerT_51173-T1
Valid prediction for GeneMark_model.88842_t
Valid prediction for GlimmerHMM_glimmerT_51183-T1
Valid prediction for snap_scaffold_22-snap.1844-T1
Valid prediction for snap_scaffold_22-snap.1855-T1
Valid prediction for snap_scaffold_22-snap.1840-T1
Valid prediction for snap_scaffold_22-snap.1831-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_51181-T1
Valid prediction for snap_scaffold_22-snap.1874-T1
Couldn't classify 217661, 217759
Couldn't classify 220932, 221068
Sorry, prediction pasa_asmbl_30267.p1 fails validation.
(GCA)	 AG	217661-217759	GT	AGG
(TCC)	 AG	218057-218203	GT	AGG
(GGC)	 AG	218618-218671	GT	AGG
(GAT)	 AG	218916-219038	GT	AGG
(GTC)	 AG	219415-219510	GT	AGG
(GTG)	 AG	219751-219858	GT	AGG
(GGT)	 AG	220019-220097	GT	AGG
(TGT)	 AG	220932-221068	AC	GTA
-recovered pasa_asmbl_30267.p1, internal, 217661, 217759
-recovered pasa_asmbl_30267.p1, internal, 218057, 218203
-recovered pasa_asmbl_30267.p1, internal, 218618, 218671
-recovered pasa_asmbl_30267.p1, internal, 218916, 219038
-recovered pasa_asmbl_30267.p1, internal, 219415, 219510
-recovered pasa_asmbl_30267.p1, internal, 219751, 219858
-recovered pasa_asmbl_30267.p1, internal, 220019, 220097
Valid prediction for snap_scaffold_22-snap.1866-T1
Valid prediction for snap_scaffold_22-snap.1839-T1
Valid prediction for GeneMark_model.88823_t
Valid prediction for GeneMark_model.88841_t
Valid prediction for snap_scaffold_22-snap.1843-T1
Valid prediction for snap_scaffold_22-snap.1854-T1
Valid prediction for Augustus_model.g34323.t1
Valid prediction for GeneMark_model.88797_t
Valid prediction for snap_scaffold_22-snap.1862-T1
Valid prediction for GeneMark_model.88843_t
Valid prediction for snap_scaffold_22-snap.1835-T1
Valid prediction for Augustus_model.g34311.t1
Valid prediction for snap_scaffold_22-snap.1848-T1
Valid prediction for snap_scaffold_22-snap.1863-T1
Valid prediction for GeneMark_model.88784_t
Valid prediction for snap_scaffold_22-snap.1857-T1
Valid prediction for snap_scaffold_22-snap.1856-T1
Valid prediction for GeneMark_model.88801_t
Valid prediction for snap_scaffold_22-snap.1837-T1
Valid prediction for GeneMark_model.88788_t
Valid prediction for GeneMark_model.88776_t
Valid prediction for Augustus_model.g34313.t1
Valid prediction for GeneMark_model.88839_t
Valid prediction for GeneMark_model.88795_t
Valid prediction for snap_scaffold_22-snap.1830-T1
Valid prediction for GeneMark_model.88786_t
Valid prediction for GeneMark_model.88845_t
Valid prediction for GlimmerHMM_glimmerT_51182-T1
Valid prediction for snap_scaffold_22-snap.1849-T1
Valid prediction for GeneMark_model.88804_t
Valid prediction for snap_scaffold_22-snap.1872-T1
Valid prediction for GeneMark_model.88799_t
Valid prediction for GeneMark_model.88778_t
Valid prediction for HiQ_model.g34312.t1
Valid prediction for GeneMark_model.88812_t
Valid prediction for GeneMark_model.88780_t
Valid prediction for snap_scaffold_22-snap.1858-T1
Valid prediction for GlimmerHMM_glimmerT_51185-T1
Valid prediction for GeneMark_model.88783_t
Valid prediction for GlimmerHMM_glimmerT_51180-T1
Valid prediction for Augustus_model.g34317.t1
Valid prediction for GeneMark_model.88836_t
Valid prediction for GlimmerHMM_glimmerT_51175-T1
Valid prediction for GeneMark_model.88808_t
Valid prediction for snap_scaffold_22-snap.1876-T1
Valid prediction for snap_scaffold_22-snap.1867-T1
Valid prediction for snap_scaffold_22-snap.1845-T1
Valid prediction for snap_scaffold_22-snap.1870-T1
Valid prediction for snap_scaffold_22-snap.1838-T1
Couldn't classify 223280, 223356
Couldn't classify 223738, 223910
Sorry, prediction pasa_asmbl_30491.p1 fails validation.
(GAG)	 CT	223280-223356	GT	AGG
(GGT)	 AG	223503-223651	GT	CGG
(AGA)	 AG	223738-223910	AG	AAA
-recovered pasa_asmbl_30491.p1, internal, 223503, 223651
Valid prediction for GeneMark_model.88817_t
Couldn't classify 224740, 224898
Sorry, prediction pasa_asmbl_30539.p1 fails validation.
(GCC)	 AG	224740-224898	GT	AGG
(GAG)	 AG	225340-225466	GC	TTG
(CAG)	 AG	225750-225854	GT	CGG
(TGC)	 AG	226022-226143	GT	TGG
(AGT)	 AG	227122-227166	GT	GGG
(AGG)	 AG	227545-227706	GT	AGG
(TGC)	 AG	228267-228320	GT	AGG
(ATG)	 AG	228682-228882	GT	AGG
(AAG)	 AG	229573-229746	AG	AAA
-recovered pasa_asmbl_30539.p1, initial, 228682, 228882
-recovered pasa_asmbl_30539.p1, terminal, 229573, 229746
-recovered pasa_asmbl_30539.p1, internal, 224740, 224898
-recovered pasa_asmbl_30539.p1, internal, 225340, 225466
-recovered pasa_asmbl_30539.p1, internal, 225750, 225854
-recovered pasa_asmbl_30539.p1, internal, 226022, 226143
-recovered pasa_asmbl_30539.p1, internal, 227122, 227166
-recovered pasa_asmbl_30539.p1, internal, 227545, 227706
-recovered pasa_asmbl_30539.p1, internal, 228267, 228320
-recovered pasa_asmbl_30539.p1, internal, 228682, 228882
Valid prediction for snap_scaffold_22-snap.1860-T1
Valid prediction for GeneMark_model.88815_t
Valid prediction for Augustus_model.g34319.t1
Valid prediction for GeneMark_model.88806_t
Valid prediction for GeneMark_model.88793_t
Valid prediction for GlimmerHMM_glimmerT_51178-T1
Valid prediction for CodingQuarry_transcript_34194-T1
Valid prediction for GlimmerHMM_glimmerT_51172-T1
Valid prediction for Augustus_model.g34316.t1
Valid prediction for GeneMark_model.88822_t
Valid prediction for GeneMark_model.88820_t
Valid prediction for GeneMark_model.88833_t
Valid prediction for snap_scaffold_22-snap.1852-T1
Valid prediction for snap_scaffold_22-snap.1869-T1
Valid prediction for GeneMark_model.88814_t
Valid prediction for GeneMark_model.88838_t
Valid prediction for GeneMark_model.88831_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18070, rend_intergenic: 2400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30366, rend_intergenic: 23120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47265, rend_intergenic: 34580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60485, rend_intergenic: 52161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76879, rend_intergenic: 76619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90876, rend_intergenic: 77005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99244, rend_intergenic: 93754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102841, rend_intergenic: 101900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106095, rend_intergenic: 103767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119716, rend_intergenic: 106174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133013, rend_intergenic: 124227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133322, rend_intergenic: 133205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135741, rend_intergenic: 133962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141593, rend_intergenic: 137661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174154, rend_intergenic: 141823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179018, rend_intergenic: 174802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188152, rend_intergenic: 179188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188898, rend_intergenic: 188473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200214, rend_intergenic: 194682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207654, rend_intergenic: 200765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210281, rend_intergenic: 209295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212398, rend_intergenic: 210970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222871, rend_intergenic: 221267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231287
-exon list size: 814


building trellis

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63.8    
64.0    
64.1    
64.2    
64.3    
64.5    
64.6    
64.7    
64.8    
65.0    
65.1    
65.2    
65.3    
65.4    
65.6    
65.7    
65.8    
65.9    
66.1    
66.2    
66.3    
66.4    
66.5    
66.7    
66.8    
66.9    
67.0    
67.2    
67.3    
67.4    
67.5    
67.6    
67.8    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.1    
69.2    
69.4    
69.5    
69.6    
69.7    
69.9    
70.0    
70.1    
70.2    
70.3    
70.5    
70.6    
70.7    
70.8    
71.0    
71.1    
71.2    
71.3    
71.4    
71.6    
71.7    
71.8    
71.9    
72.1    
72.2    
72.3    
72.4    
72.5    
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    
77.5    
77.6    
77.7    
77.8    
77.9    
78.1    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.5    
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 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 18070, rend_intergenic: 2400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30366, rend_intergenic: 23120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47265, rend_intergenic: 34580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60485, rend_intergenic: 52161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76879, rend_intergenic: 76619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90876, rend_intergenic: 77005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99244, rend_intergenic: 93754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102841, rend_intergenic: 101900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106095, rend_intergenic: 103767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119716, rend_intergenic: 106174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133013, rend_intergenic: 124227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133322, rend_intergenic: 133205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135741, rend_intergenic: 133962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141593, rend_intergenic: 137661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174154, rend_intergenic: 141823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179018, rend_intergenic: 174802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188152, rend_intergenic: 179188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188898, rend_intergenic: 188473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200214, rend_intergenic: 194682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207654, rend_intergenic: 200765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210281, rend_intergenic: 209295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212398, rend_intergenic: 210970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222871, rend_intergenic: 221267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support