-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_8465875-8682829

-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_25-snap.1905-T1
Valid prediction for snap_scaffold_25-snap.1911-T1
Couldn't classify 200617, 200642
Sorry, prediction pasa_asmbl_33736.p1 fails validation.
(ATC)	 AC	200617-200642	GT	AGG
(AGA)	 AG	200734-200830	GT	CTG
(ATC)	 AG	201328-201400	GT	TAG
(TGA)	 AG	201476-201653	GT	GAG
(TGC)	 AG	201769-201953	GT	CTG
(GGC)	 AG	202049-202137	GT	AGG
(ATC)	 AG	202236-202316	GT	AGG
(ACC)	 AG	202828-202923	GT	AGG
(AGT)	 AG	203677-203880	CA	AGC
-recovered pasa_asmbl_33736.p1, terminal, 203677, 203880
-recovered pasa_asmbl_33736.p1, internal, 200734, 200830
-recovered pasa_asmbl_33736.p1, internal, 201328, 201400
-recovered pasa_asmbl_33736.p1, internal, 201476, 201653
-recovered pasa_asmbl_33736.p1, internal, 201769, 201953
-recovered pasa_asmbl_33736.p1, internal, 202049, 202137
-recovered pasa_asmbl_33736.p1, internal, 202236, 202316
-recovered pasa_asmbl_33736.p1, internal, 202828, 202923
Valid prediction for GeneMark_model.97602_t
Valid prediction for snap_scaffold_25-snap.1889-T1
Valid prediction for Augustus_model.g37354.t1
Valid prediction for Augustus_model.g37352.t1
Valid prediction for GeneMark_model.97610_t
Valid prediction for GlimmerHMM_glimmerT_56006-T1
Valid prediction for GeneMark_model.97625_t
Valid prediction for CodingQuarry_transcript_38723-T1
Valid prediction for snap_scaffold_25-snap.1910-T1
Couldn't classify 198337, 198384
Couldn't classify 199633, 199793
Sorry, prediction pasa_asmbl_33900.p1 fails validation.
(AAA)	 CC	198337-198384	GT	TGG
(GAG)	 AG	198561-198578	GT	CGG
(TCG)	 AG	198681-198834	GT	GGG
(TTC)	 AG	199099-199219	GT	AGG
(GGA)	 AG	199303-199427	GT	TGG
(GCG)	 AG	199633-199793	GT	AGG
-recovered pasa_asmbl_33900.p1, internal, 198561, 198578
-recovered pasa_asmbl_33900.p1, internal, 198681, 198834
-recovered pasa_asmbl_33900.p1, internal, 199099, 199219
-recovered pasa_asmbl_33900.p1, internal, 199303, 199427
-recovered pasa_asmbl_33900.p1, internal, 199633, 199793
Valid prediction for GlimmerHMM_glimmerT_56013-T1
Valid prediction for snap_scaffold_25-snap.1903-T1
Valid prediction for snap_scaffold_25-snap.1913-T1
Valid prediction for Augustus_model.g37355.t1
Valid prediction for pasa_asmbl_33731.p1
Valid prediction for snap_scaffold_25-snap.1924-T1
Valid prediction for GeneMark_model.97616_t
Valid prediction for snap_scaffold_25-snap.1915-T1
Valid prediction for GlimmerHMM_glimmerT_56008-T1
Valid prediction for snap_scaffold_25-snap.1923-T1
Valid prediction for Augustus_model.g37361.t1
Valid prediction for GlimmerHMM_glimmerT_55994-T1
Valid prediction for GeneMark_model.97626_t
Valid prediction for snap_scaffold_25-snap.1892-T1
Valid prediction for snap_scaffold_25-snap.1920-T1
Valid prediction for GeneMark_model.97619_t
Valid prediction for GeneMark_model.97603_t
Valid prediction for GlimmerHMM_glimmerT_56010-T1
Valid prediction for GeneMark_model.97591_t
Valid prediction for snap_scaffold_25-snap.1914-T1
Valid prediction for GeneMark_model.97592_t
Valid prediction for snap_scaffold_25-snap.1918-T1
Couldn't classify 212446, 212531
Sorry, prediction pasa_asmbl_33741.p1 fails validation.
(GTC)	 CG	212446-212531	GT	AGG
(GAG)	 AG	213923-214095	GT	AGG
(GTG)	 AG	214505-214701	CC	AGC
-recovered pasa_asmbl_33741.p1, terminal, 214505, 214701
-recovered pasa_asmbl_33741.p1, internal, 213923, 214095
Valid prediction for snap_scaffold_25-snap.1893-T1
Valid prediction for snap_scaffold_25-snap.1901-T1
Valid prediction for GeneMark_model.97606_t
Valid prediction for GlimmerHMM_glimmerT_56011-T1
Valid prediction for GeneMark_model.97600_t
Valid prediction for GeneMark_model.97624_t
Valid prediction for Augustus_model.g37356.t1
Valid prediction for GeneMark_model.97615_t
Valid prediction for GeneMark_model.97597_t
Valid prediction for GeneMark_model.97594_t
Valid prediction for GlimmerHMM_glimmerT_56004-T1
Valid prediction for GeneMark_model.97604_t
Valid prediction for GlimmerHMM_glimmerT_56015-T1
Valid prediction for GlimmerHMM_glimmerT_56005-T1
Valid prediction for HiQ_model.g37344.t1
Valid prediction for Augustus_model.g37358.t1
Valid prediction for GeneMark_model.97611_t
Valid prediction for GlimmerHMM_glimmerT_56012-T1
Valid prediction for GlimmerHMM_glimmerT_55996-T1
Valid prediction for GeneMark_model.97613_t
Valid prediction for snap_scaffold_25-snap.1912-T1
Valid prediction for GeneMark_model.97612_t
Valid prediction for Augustus_model.g37360.t1
Valid prediction for snap_scaffold_25-snap.1887-T1
Valid prediction for snap_scaffold_25-snap.1885-T1
Valid prediction for GeneMark_model.97622_t
Valid prediction for snap_scaffold_25-snap.1922-T1
Valid prediction for snap_scaffold_25-snap.1921-T1
Valid prediction for GeneMark_model.97617_t
Valid prediction for Augustus_model.g37362.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 Augustus_model.g37357.t1
Couldn't classify 182355, 182435
Sorry, prediction pasa_asmbl_34422.p1 fails validation.
(ATG)	 TG	179398-179486	GT	AAG
(CTG)	 AG	179800-179865	GT	AGG
(TTT)	 AG	181256-181362	GT	TGG
(ACT)	 AG	181438-181523	GT	GAG
(ATC)	 AG	182355-182435	AA	AGA
-recovered pasa_asmbl_34422.p1, initial, 179398, 179486
-recovered pasa_asmbl_34422.p1, internal, 179800, 179865
-recovered pasa_asmbl_34422.p1, internal, 181256, 181362
-recovered pasa_asmbl_34422.p1, internal, 181438, 181523
Valid prediction for Augustus_model.g37353.t1
Valid prediction for Augustus_model.g37346.t1
Valid prediction for GlimmerHMM_glimmerT_56001-T1
Valid prediction for GlimmerHMM_glimmerT_56000-T1
Valid prediction for GeneMark_model.97605_t
Valid prediction for snap_scaffold_25-snap.1902-T1
Valid prediction for GlimmerHMM_glimmerT_55997-T1
Valid prediction for GeneMark_model.97593_t
Valid prediction for Augustus_model.g37351.t1
Valid prediction for snap_scaffold_25-snap.1909-T1
Valid prediction for Augustus_model.g37345.t1
Valid prediction for GeneMark_model.97607_t
Valid prediction for snap_scaffold_25-snap.1886-T1
Valid prediction for snap_scaffold_25-snap.1904-T1
Couldn't classify 160311, 160311
Sorry, prediction CodingQuarry_transcript_38725-T1 fails validation.
(ATG)	 AG	156151-156173	GT	CTG
(GGT)	 AG	157316-157369	GT	GGG
(GGG)	 AG	159285-159338	GT	AGG
(GGT)	 AG	159493-159537	GT	TAG
(GGC)	 AG	160311-160311	GC	GGG
-recovered CodingQuarry_transcript_38725-T1, initial, 156151, 156173
-recovered CodingQuarry_transcript_38725-T1, internal, 156151, 156173
-recovered CodingQuarry_transcript_38725-T1, internal, 157316, 157369
-recovered CodingQuarry_transcript_38725-T1, internal, 159285, 159338
-recovered CodingQuarry_transcript_38725-T1, internal, 159493, 159537
-recovered CodingQuarry_transcript_38725-T1, internal, 160311, 160311
Valid prediction for snap_scaffold_25-snap.1906-T1
Valid prediction for GeneMark_model.97601_t
Valid prediction for GlimmerHMM_glimmerT_56009-T1
Valid prediction for GeneMark_model.97621_t
Valid prediction for snap_scaffold_25-snap.1895-T1
Valid prediction for Augustus_model.g37349.t1
Valid prediction for snap_scaffold_25-snap.1899-T1
Valid prediction for Augustus_model.g37348.t1
Valid prediction for GlimmerHMM_glimmerT_55995-T1
Couldn't classify 154123, 154176
Couldn't classify 163891, 163944
Sorry, prediction pasa_asmbl_34516.p1 fails validation.
(GGT)	 AG	154123-154176	GT	AGG
(GGC)	 AG	155150-155203	GT	GGG
(GGG)	 AG	156120-156173	GT	CTG
(GGT)	 AG	157316-157369	GT	GGG
(GGG)	 AG	159285-159338	GT	AGG
(GGT)	 AG	159493-159537	GT	TAG
(GGC)	 AG	160311-160355	GT	CAG
(GGT)	 AG	162084-162137	GT	CAG
(GGG)	 AG	162781-162834	GT	AGG
(GGC)	 AG	162993-163046	GT	AGG
(GGC)	 AG	163340-163393	GT	GAG
(GGG)	 AG	163891-163944	GT	AGG
-recovered pasa_asmbl_34516.p1, internal, 154123, 154176
-recovered pasa_asmbl_34516.p1, internal, 155150, 155203
-recovered pasa_asmbl_34516.p1, internal, 156120, 156173
-recovered pasa_asmbl_34516.p1, internal, 157316, 157369
-recovered pasa_asmbl_34516.p1, internal, 159285, 159338
-recovered pasa_asmbl_34516.p1, internal, 159493, 159537
-recovered pasa_asmbl_34516.p1, internal, 160311, 160355
-recovered pasa_asmbl_34516.p1, internal, 162084, 162137
-recovered pasa_asmbl_34516.p1, internal, 162781, 162834
-recovered pasa_asmbl_34516.p1, internal, 162993, 163046
-recovered pasa_asmbl_34516.p1, internal, 163340, 163393
-recovered pasa_asmbl_34516.p1, internal, 163891, 163944
Valid prediction for Augustus_model.g37359.t1
Valid prediction for GeneMark_model.97614_t
Valid prediction for snap_scaffold_25-snap.1907-T1
Valid prediction for Augustus_model.g37347.t1
Valid prediction for Augustus_model.g37343.t1
Couldn't classify 164161, 164214
Sorry, prediction pasa_asmbl_34425.p1 fails validation.
(GGG)	 AG	164161-164214	GT	CTG
(GGA)	 AG	164562-164615	GT	AGG
(GGA)	 AG	164692-164799	GT	CGG
(GGT)	 AG	165584-165637	GT	CCG
(GGT)	 AG	166321-166374	GT	AGG
(GGT)	 AG	166609-166665	GT	CAG
(GGT)	 AG	167454-167507	GT	AGG
(GGT)	 AG	168208-168261	GT	CTG
(GGG)	 AG	168378-168431	GT	TGG
(GGA)	 AG	169479-169532	GT	AAG
(GGG)	 AG	169925-170032	GT	AGG
(GGT)	 AG	172110-172217	GT	AGG
(GGG)	 AG	172314-172421	GT	TAG
(GGG)	 AG	173483-173536	GT	AGG
(GGG)	 AG	173713-173775	GT	TGG
(GGC)	 AG	173859-173912	GT	CTG
(GGT)	 AG	174349-174384	GT	TGG
(GGA)	 AG	175109-175144	GT	GAG
(GGT)	 AG	175238-175264	GT	CTG
(AGA)	 AG	175742-175795	GT	AGG
(ACC)	 AG	175913-176081	GT	CGG
(GCT)	 AG	176204-176313	GT	AGG
(ATG)	 AG	176661-176885	GT	AGG
(ATC)	 AG	176977-177123	AT	GAA
-recovered pasa_asmbl_34425.p1, initial, 176661, 176885
-recovered pasa_asmbl_34425.p1, terminal, 176977, 177123
-recovered pasa_asmbl_34425.p1, internal, 164161, 164214
-recovered pasa_asmbl_34425.p1, internal, 164562, 164615
-recovered pasa_asmbl_34425.p1, internal, 164692, 164799
-recovered pasa_asmbl_34425.p1, internal, 165584, 165637
-recovered pasa_asmbl_34425.p1, internal, 166321, 166374
-recovered pasa_asmbl_34425.p1, internal, 166609, 166665
-recovered pasa_asmbl_34425.p1, internal, 167454, 167507
-recovered pasa_asmbl_34425.p1, internal, 168208, 168261
-recovered pasa_asmbl_34425.p1, internal, 168378, 168431
-recovered pasa_asmbl_34425.p1, internal, 169479, 169532
-recovered pasa_asmbl_34425.p1, internal, 169925, 170032
-recovered pasa_asmbl_34425.p1, internal, 172110, 172217
-recovered pasa_asmbl_34425.p1, internal, 172314, 172421
-recovered pasa_asmbl_34425.p1, internal, 173483, 173536
-recovered pasa_asmbl_34425.p1, internal, 173713, 173775
-recovered pasa_asmbl_34425.p1, internal, 173859, 173912
-recovered pasa_asmbl_34425.p1, internal, 174349, 174384
-recovered pasa_asmbl_34425.p1, internal, 175109, 175144
-recovered pasa_asmbl_34425.p1, internal, 175238, 175264
-recovered pasa_asmbl_34425.p1, internal, 175742, 175795
-recovered pasa_asmbl_34425.p1, internal, 175913, 176081
-recovered pasa_asmbl_34425.p1, internal, 176204, 176313
-recovered pasa_asmbl_34425.p1, internal, 176661, 176885
Valid prediction for GlimmerHMM_glimmerT_56014-T1
Valid prediction for snap_scaffold_25-snap.1896-T1
Valid prediction for GeneMark_model.97599_t
Valid prediction for GeneMark_model.97598_t
Couldn't classify 50953, 51240
Couldn't classify 51336, 51590
Sorry, prediction pasa_asmbl_34428.p1 fails validation.
(CTG)	 AC	50953-51240	GT	TGG
(TAT)	 AG	51336-51590	GA	AGG
Valid prediction for GeneMark_model.97620_t
Valid prediction for GlimmerHMM_glimmerT_55993-T1
Valid prediction for GlimmerHMM_glimmerT_55998-T1
Valid prediction for snap_scaffold_25-snap.1890-T1
Valid prediction for GeneMark_model.97618_t
Valid prediction for snap_scaffold_25-snap.1908-T1
Valid prediction for GlimmerHMM_glimmerT_55999-T1
Couldn't classify 196932, 197058
Sorry, prediction pasa_asmbl_34419.p1 fails validation.
(AGG)	 TC	196932-197058	GT	AGG
(CAG)	 AG	198473-198870	AC	AGA
-recovered pasa_asmbl_34419.p1, terminal, 198473, 198870
Valid prediction for snap_scaffold_25-snap.1891-T1
Valid prediction for snap_scaffold_25-snap.1898-T1
Valid prediction for GeneMark_model.97623_t
Valid prediction for snap_scaffold_25-snap.1916-T1
Valid prediction for snap_scaffold_25-snap.1897-T1
Valid prediction for GlimmerHMM_glimmerT_56002-T1
Valid prediction for GeneMark_model.97596_t
Valid prediction for GeneMark_model.97595_t
Valid prediction for GeneMark_model.97608_t
Valid prediction for snap_scaffold_25-snap.1900-T1
Valid prediction for GeneMark_model.97609_t
Valid prediction for snap_scaffold_25-snap.1888-T1
Valid prediction for snap_scaffold_25-snap.1894-T1
Valid prediction for CodingQuarry_transcript_38724-T1
Valid prediction for snap_scaffold_25-snap.1919-T1
Valid prediction for snap_scaffold_25-snap.1917-T1
Valid prediction for Augustus_model.g37350.t1
Valid prediction for GlimmerHMM_glimmerT_56007-T1
Valid prediction for GlimmerHMM_glimmerT_56003-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23628, rend_intergenic: 21256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35791, rend_intergenic: 29608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73856, rend_intergenic: 72341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80854, rend_intergenic: 78591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92029, rend_intergenic: 86049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152094, rend_intergenic: 150826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 216955
-exon list size: 599


building trellis

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61.7    
61.9    
62.1    
62.2    
62.4    
62.6    
62.7    
62.9    
63.1    
63.2    
63.4    
63.6    
63.7    
63.9    
64.1    
64.2    
64.4    
64.6    
64.7    
64.9    
65.1    
65.2    
65.4    
65.6    
65.7    
65.9    
66.1    
66.2    
66.4    
66.6    
66.7    
66.9    
67.1    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 23628, rend_intergenic: 21256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35791, rend_intergenic: 29608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73856, rend_intergenic: 72341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80854, rend_intergenic: 78591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92029, rend_intergenic: 86049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152094, rend_intergenic: 150826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support