-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_8478753-8682191

-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_49442-T1
Valid prediction for GeneMark_model.85620_t
Valid prediction for GlimmerHMM_glimmerT_49454-T1
Valid prediction for snap_scaffold_21-snap.1823-T1
Valid prediction for snap_scaffold_21-snap.1820-T1
Valid prediction for GlimmerHMM_glimmerT_49441-T1
Valid prediction for GeneMark_model.85605_t
Couldn't classify 101926, 101958
Sorry, prediction pasa_asmbl_28840.p1 fails validation.
(TAC)	 AC	101926-101958	GT	CAG
(GTC)	 AG	102215-102473	GT	CGG
(AGG)	 AG	102682-102806	GT	GGG
(GTC)	 AG	103265-103401	GT	GCG
(AAC)	 AG	103799-104127	GT	AGG
(GCC)	 AG	104306-104383	GT	TGG
(TGA)	 AG	104694-104864	GT	AGG
(GAC)	 AG	105002-105132	CC	AAC
-recovered pasa_asmbl_28840.p1, terminal, 105002, 105132
-recovered pasa_asmbl_28840.p1, internal, 102215, 102473
-recovered pasa_asmbl_28840.p1, internal, 102682, 102806
-recovered pasa_asmbl_28840.p1, internal, 103265, 103401
-recovered pasa_asmbl_28840.p1, internal, 103799, 104127
-recovered pasa_asmbl_28840.p1, internal, 104306, 104383
-recovered pasa_asmbl_28840.p1, internal, 104694, 104864
Valid prediction for GeneMark_model.85614_t
Valid prediction for snap_scaffold_21-snap.1846-T1
Couldn't classify 91103, 91146
Couldn't classify 91671, 91825
Sorry, prediction pasa_asmbl_28836.p1 fails validation.
(TCC)	 CC	91103-91146	GT	CGG
(GTA)	 AG	91319-91437	GT	AGG
(ATC)	 AG	91671-91825	GA	GCG
-recovered pasa_asmbl_28836.p1, internal, 91319, 91437
Valid prediction for snap_scaffold_21-snap.1842-T1
Valid prediction for GeneMark_model.85598_t
Valid prediction for snap_scaffold_21-snap.1851-T1
Valid prediction for GeneMark_model.85616_t
Valid prediction for Augustus_model.g33179.t1
Valid prediction for snap_scaffold_21-snap.1830-T1
Valid prediction for GlimmerHMM_glimmerT_49438-T1
Valid prediction for snap_scaffold_21-snap.1814-T1
Valid prediction for snap_scaffold_21-snap.1811-T1
Valid prediction for snap_scaffold_21-snap.1829-T1
Valid prediction for GeneMark_model.85595_t
Couldn't classify 66739, 66799
Sorry, prediction pasa_asmbl_28833.p1 fails validation.
(GTG)	 AG	66739-66799	GT	AGG
(GTT)	 AG	66931-66975	GT	AGG
(CTG)	 AG	67186-67328	GT	GGG
(CTT)	 AG	67435-68118	AC	AAA
-recovered pasa_asmbl_28833.p1, terminal, 67435, 68118
-recovered pasa_asmbl_28833.p1, internal, 66739, 66799
-recovered pasa_asmbl_28833.p1, internal, 66931, 66975
-recovered pasa_asmbl_28833.p1, internal, 67186, 67328
Valid prediction for Augustus_model.g33177.t1
Valid prediction for GeneMark_model.85588_t
Valid prediction for GeneMark_model.85602_t
Valid prediction for snap_scaffold_21-snap.1817-T1
Valid prediction for Augustus_model.g33165.t1
Valid prediction for Augustus_model.g33185.t1
Valid prediction for GlimmerHMM_glimmerT_49450-T1
Valid prediction for snap_scaffold_21-snap.1838-T1
Valid prediction for GeneMark_model.85597_t
Valid prediction for GeneMark_model.85631_t
Valid prediction for GeneMark_model.85577_t
Valid prediction for GeneMark_model.85581_t
Valid prediction for GeneMark_model.85623_t
Valid prediction for snap_scaffold_21-snap.1813-T1
Valid prediction for GeneMark_model.85607_t
Valid prediction for GeneMark_model.85592_t
Valid prediction for snap_scaffold_21-snap.1833-T1
Valid prediction for Augustus_model.g33166.t1
Valid prediction for GeneMark_model.85600_t
Valid prediction for snap_scaffold_21-snap.1839-T1
Valid prediction for GeneMark_model.85585_t
Valid prediction for GlimmerHMM_glimmerT_49459-T1
Valid prediction for GlimmerHMM_glimmerT_49468-T1
Valid prediction for pasa_asmbl_28828.p1
Valid prediction for GeneMark_model.85625_t
Valid prediction for GlimmerHMM_glimmerT_49445-T1
Valid prediction for GeneMark_model.85593_t
Valid prediction for GeneMark_model.85579_t
Valid prediction for snap_scaffold_21-snap.1853-T1
Valid prediction for Augustus_model.g33186.t1
Valid prediction for GeneMark_model.85608_t
Valid prediction for GlimmerHMM_glimmerT_49448-T1
Valid prediction for GeneMark_model.85604_t
Valid prediction for GlimmerHMM_glimmerT_49461-T1
Valid prediction for snap_scaffold_21-snap.1854-T1
Valid prediction for snap_scaffold_21-snap.1841-T1
Valid prediction for GeneMark_model.85618_t
Valid prediction for GlimmerHMM_glimmerT_49462-T1
Valid prediction for GlimmerHMM_glimmerT_49456-T1
Valid prediction for GeneMark_model.85627_t
Valid prediction for GeneMark_model.85629_t
Valid prediction for Augustus_model.g33176.t1
Valid prediction for snap_scaffold_21-snap.1856-T1
Valid prediction for GlimmerHMM_glimmerT_49437-T1
Valid prediction for GlimmerHMM_glimmerT_49449-T1
Valid prediction for snap_scaffold_21-snap.1844-T1
Valid prediction for GlimmerHMM_glimmerT_49465-T1
Valid prediction for HiQ_model.g33172.t1
Valid prediction for Augustus_model.g33167.t1
Valid prediction for GeneMark_model.85612_t
Valid prediction for GeneMark_model.85583_t
Valid prediction for Augustus_model.g33175.t1
Valid prediction for GeneMark_model.85587_t
Valid prediction for snap_scaffold_21-snap.1815-T1
Valid prediction for snap_scaffold_21-snap.1849-T1
Couldn't classify 87628, 87835
Couldn't classify 88119, 88222
Sorry, prediction pasa_asmbl_28965.p2 fails validation.
(AGC)	 AC	87628-87835	GT	AGG
(CAA)	 AG	88119-88222	TA	AAT
Valid prediction for GeneMark_model.85610_t
Valid prediction for Augustus_model.g33169.t1
Couldn't classify 93640, 93828
Couldn't classify 94783, 94900
Sorry, prediction pasa_asmbl_28838.p1 fails validation.
(CTC)	 CT	93640-93828	GT	ACG
(GCT)	 AG	94013-94250	GT	CCG
(GAA)	 AG	94411-94585	GT	AGG
(GGA)	 AG	94783-94900	AC	GGA
-recovered pasa_asmbl_28838.p1, internal, 94013, 94250
-recovered pasa_asmbl_28838.p1, internal, 94411, 94585
Valid prediction for GlimmerHMM_glimmerT_49470-T1
Valid prediction for GeneMark_model.85576_t
Valid prediction for GlimmerHMM_glimmerT_49452-T1
Valid prediction for GlimmerHMM_glimmerT_49435-T1
Valid prediction for GeneMark_model.85622_t
Valid prediction for Augustus_model.g33182.t1
Valid prediction for GeneMark_model.85589_t
Valid prediction for snap_scaffold_21-snap.1827-T1
Sorry, intron length (6) is less than minimum required (10)

-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 GeneMark_model.85621_t
Couldn't classify 90835, 91161
Sorry, prediction pasa_asmbl_27955.p4 fails validation.
(AGC)	 AC	90835-91161	GT	CAG
(AAC)	 AG	92260-92271	TC	GAT
-recovered pasa_asmbl_27955.p4, terminal, 92260, 92271
Valid prediction for GeneMark_model.85603_t
Valid prediction for snap_scaffold_21-snap.1835-T1
Valid prediction for CodingQuarry_transcript_32617-T1
Valid prediction for CodingQuarry_transcript_32619-T1
Valid prediction for snap_scaffold_21-snap.1824-T1
Valid prediction for snap_scaffold_21-snap.1825-T1
Valid prediction for GlimmerHMM_glimmerT_49444-T1
Valid prediction for Augustus_model.g33187.t1
Valid prediction for GeneMark_model.85624_t
Valid prediction for GlimmerHMM_glimmerT_49464-T1
Valid prediction for Augustus_model.g33170.t1
Valid prediction for GlimmerHMM_glimmerT_49460-T1
Valid prediction for snap_scaffold_21-snap.1831-T1
Valid prediction for GlimmerHMM_glimmerT_49471-T1
Valid prediction for GlimmerHMM_glimmerT_49463-T1
Valid prediction for Augustus_model.g33183.t1
Valid prediction for GeneMark_model.85606_t
Valid prediction for GeneMark_model.85590_t
Valid prediction for GlimmerHMM_glimmerT_49447-T1
Valid prediction for GeneMark_model.85609_t
Valid prediction for GlimmerHMM_glimmerT_49467-T1
Valid prediction for HiQ_model.g33173.t1
Valid prediction for pasa_asmbl_27948.p1
Valid prediction for HiQ_model.g33174.t1
Valid prediction for GeneMark_model.85613_t
Valid prediction for snap_scaffold_21-snap.1850-T1
Valid prediction for GlimmerHMM_glimmerT_49458-T1
Valid prediction for GlimmerHMM_glimmerT_49466-T1
Valid prediction for GlimmerHMM_glimmerT_49469-T1
Valid prediction for GeneMark_model.85580_t
Valid prediction for snap_scaffold_21-snap.1855-T1
Valid prediction for GlimmerHMM_glimmerT_49455-T1
Valid prediction for GlimmerHMM_glimmerT_49451-T1
Valid prediction for GeneMark_model.85596_t
Valid prediction for snap_scaffold_21-snap.1822-T1
Valid prediction for GeneMark_model.85615_t
Valid prediction for GeneMark_model.85582_t
Valid prediction for GeneMark_model.85611_t
Valid prediction for snap_scaffold_21-snap.1848-T1
Valid prediction for GeneMark_model.85626_t
Valid prediction for Augustus_model.g33178.t1
Valid prediction for GeneMark_model.85578_t
Valid prediction for GlimmerHMM_glimmerT_49443-T1
Valid prediction for pasa_asmbl_27951.p1
Valid prediction for GeneMark_model.85619_t
Valid prediction for Augustus_model.g33184.t1
Valid prediction for snap_scaffold_21-snap.1840-T1
Valid prediction for snap_scaffold_21-snap.1819-T1
Valid prediction for GlimmerHMM_glimmerT_49446-T1
Valid prediction for GeneMark_model.85601_t
Valid prediction for GeneMark_model.85617_t
Valid prediction for GlimmerHMM_glimmerT_49439-T1
Valid prediction for snap_scaffold_21-snap.1816-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.1847-T1
Valid prediction for Augustus_model.g33171.t1
Valid prediction for CodingQuarry_transcript_32618-T1
Valid prediction for snap_scaffold_21-snap.1836-T1
Valid prediction for GeneMark_model.85628_t
Valid prediction for snap_scaffold_21-snap.1834-T1
Valid prediction for GlimmerHMM_glimmerT_49453-T1
Valid prediction for GeneMark_model.85584_t
Valid prediction for GlimmerHMM_glimmerT_49457-T1
Valid prediction for GlimmerHMM_glimmerT_49436-T1
Valid prediction for snap_scaffold_21-snap.1826-T1
Valid prediction for Augustus_model.g33180.t1
Valid prediction for GeneMark_model.85599_t
Valid prediction for Augustus_model.g33189.t1
Valid prediction for GlimmerHMM_glimmerT_49440-T1
Valid prediction for GeneMark_model.85594_t
Valid prediction for snap_scaffold_21-snap.1843-T1
Valid prediction for snap_scaffold_21-snap.1818-T1
Valid prediction for snap_scaffold_21-snap.1832-T1
Valid prediction for snap_scaffold_21-snap.1812-T1
Valid prediction for GeneMark_model.85630_t
Valid prediction for snap_scaffold_21-snap.1821-T1
Valid prediction for snap_scaffold_21-snap.1845-T1
Valid prediction for GeneMark_model.85591_t
Valid prediction for HiQ_model.g33181.t1
Valid prediction for snap_scaffold_21-snap.1837-T1
Valid prediction for Augustus_model.g33168.t1
Valid prediction for snap_scaffold_21-snap.1828-T1
Valid prediction for snap_scaffold_21-snap.1852-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g33188.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11833, rend_intergenic: 7644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95454, rend_intergenic: 92713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99798, rend_intergenic: 97085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105132, rend_intergenic: 100553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114854, rend_intergenic: 112459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125549, rend_intergenic: 116735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137770, rend_intergenic: 126179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140679, rend_intergenic: 139187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148224, rend_intergenic: 140763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148613, rend_intergenic: 148460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151742, rend_intergenic: 149403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160845, rend_intergenic: 152222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166841, rend_intergenic: 162643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171037, rend_intergenic: 167442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190391, rend_intergenic: 173567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192490, rend_intergenic: 191214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203439
-exon list size: 829


building trellis

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61.4    
61.5    
61.6    
61.7    
61.9    
62.0    
62.1    
62.2    
62.3    
62.5    
62.6    
62.7    
62.8    
62.9    
63.1    
63.2    
63.3    
63.4    
63.5    
63.7    
63.8    
63.9    
64.0    
64.1    
64.3    
64.4    
64.5    
64.6    
64.7    
64.9    
65.0    
65.1    
65.2    
65.3    
65.5    
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    
67.1    
67.3    
67.4    
67.5    
67.6    
67.7    
67.9    
68.0    
68.1    
68.2    
68.4    
68.5    
68.6    
68.7    
68.8    
69.0    
69.1    
69.2    
69.3    
69.4    
69.6    
69.7    
69.8    
69.9    
70.0    
70.2    
70.3    
70.4    
70.5    
70.6    
70.8    
70.9    
71.0    
71.1    
71.2    
71.4    
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    
73.6    
73.8    
73.9    
74.0    
74.1    
74.2    
74.4    
74.5    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.3    
75.5    
75.6    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.0    
77.1    
77.3    
77.4    
77.5    
77.6    
77.7    
77.9    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
78.9    
79.1    
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    
80.7    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
81.9    
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    
83.6    
83.8    
83.9    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.3    
85.4    
85.6    
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    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.0    
90.1    
90.3    
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    
91.9    
92.1    
92.2    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 48 predictions from path traversal
Error with prediction: snap lend_intergenic: 11833, rend_intergenic: 7644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95454, rend_intergenic: 92713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99798, rend_intergenic: 97085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105132, rend_intergenic: 100553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114854, rend_intergenic: 112459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125549, rend_intergenic: 116735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137770, rend_intergenic: 126179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140679, rend_intergenic: 139187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148224, rend_intergenic: 140763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148613, rend_intergenic: 148460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151742, rend_intergenic: 149403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160845, rend_intergenic: 152222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166841, rend_intergenic: 162643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171037, rend_intergenic: 167442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190391, rend_intergenic: 173567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192490, rend_intergenic: 191214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support