-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_8744212-9039527

-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_5-snap.1671-T1
Valid prediction for GlimmerHMM_glimmerT_12338-T1
Couldn't classify 264254, 264649
Sorry, prediction pasa_asmbl_45587.p1 fails validation.
(GTC)	 TA	264254-264649	CA	CAC
Valid prediction for CodingQuarry_transcript_52159-T1
Valid prediction for CodingQuarry_transcript_52166-T1
Valid prediction for GlimmerHMM_glimmerT_12352-T1
Valid prediction for snap_scaffold_5-snap.1688-T1
Couldn't classify 278458, 278536
Couldn't classify 279335, 279502
Sorry, prediction pasa_asmbl_45591.p1 fails validation.
(CGC)	 CT	278458-278536	GT	TGG
(AGC)	 AG	278645-278793	GT	AGG
(GCT)	 AG	279126-279260	GT	AGG
(GAG)	 AG	279335-279502	GT	AGG
-recovered pasa_asmbl_45591.p1, internal, 278645, 278793
-recovered pasa_asmbl_45591.p1, internal, 279126, 279260
-recovered pasa_asmbl_45591.p1, internal, 279335, 279502
Valid prediction for Augustus_model.g8139.t1
Valid prediction for snap_scaffold_5-snap.1695-T1
Valid prediction for GlimmerHMM_glimmerT_12339-T1
Valid prediction for pasa_asmbl_45574.p1
Valid prediction for snap_scaffold_5-snap.1664-T1
Valid prediction for snap_scaffold_5-snap.1660-T1
Valid prediction for snap_scaffold_5-snap.1686-T1
Valid prediction for Augustus_model.g8137.t1
Valid prediction for snap_scaffold_5-snap.1681-T1
Valid prediction for snap_scaffold_5-snap.1687-T1
Valid prediction for GlimmerHMM_glimmerT_12368-T1
Valid prediction for snap_scaffold_5-snap.1670-T1
Valid prediction for GlimmerHMM_glimmerT_12350-T1
Valid prediction for pasa_asmbl_45582.p1
Valid prediction for Augustus_model.g8141.t1
Valid prediction for pasa_asmbl_45565.p1
Valid prediction for HiQ_model.g8114.t1
Couldn't classify 273988, 274115
Couldn't classify 274242, 274410
Sorry, prediction pasa_asmbl_45589.p1 fails validation.
(GGC)	 AA	273988-274115	GT	AGG
(GTT)	 AG	274242-274410	AC	GCA
Valid prediction for GlimmerHMM_glimmerT_12331-T1
Valid prediction for GlimmerHMM_glimmerT_12343-T1
Valid prediction for snap_scaffold_5-snap.1682-T1
Valid prediction for CodingQuarry_transcript_52158-T1
Valid prediction for GlimmerHMM_glimmerT_12356-T1
Valid prediction for snap_scaffold_5-snap.1683-T1
Valid prediction for GlimmerHMM_glimmerT_12366-T1
Valid prediction for CodingQuarry_transcript_52164-T1
Valid prediction for CodingQuarry_transcript_52157-T1
Valid prediction for HiQ_model.g8115.t1
Valid prediction for HiQ_model.g8130.t1
Valid prediction for GlimmerHMM_glimmerT_12357-T1
Couldn't classify 156826, 157923
Sorry, prediction pasa_asmbl_45584.p1 fails validation.
(GGG)	 TG	156826-157923	GA	GAG
Valid prediction for snap_scaffold_5-snap.1680-T1
Valid prediction for GlimmerHMM_glimmerT_12361-T1
Valid prediction for snap_scaffold_5-snap.1692-T1
Valid prediction for GlimmerHMM_glimmerT_12364-T1
Valid prediction for snap_scaffold_5-snap.1689-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for pasa_asmbl_45570.p1
Valid prediction for Augustus_model.g8129.t1
Valid prediction for snap_scaffold_5-snap.1679-T1
Valid prediction for HiQ_model.g8121.t1
Valid prediction for snap_scaffold_5-snap.1693-T1
Valid prediction for snap_scaffold_5-snap.1694-T1
Valid prediction for GlimmerHMM_glimmerT_12365-T1
Couldn't classify 268418, 268489
Couldn't classify 268918, 269062
Sorry, prediction pasa_asmbl_46446.p1 fails validation.
(CTG)	 TC	268418-268489	GT	ACG
(ACG)	 AG	268670-268785	GT	AGG
(GTT)	 AG	268918-269062	CA	AGC
-recovered pasa_asmbl_46446.p1, internal, 268670, 268785
Valid prediction for Augustus_model.g8140.t1
Valid prediction for GlimmerHMM_glimmerT_12360-T1
Valid prediction for GlimmerHMM_glimmerT_12367-T1
Valid prediction for GlimmerHMM_glimmerT_12345-T1
Valid prediction for snap_scaffold_5-snap.1674-T1
Valid prediction for GlimmerHMM_glimmerT_12370-T1
Valid prediction for Augustus_model.g8122.t1
Valid prediction for snap_scaffold_5-snap.1672-T1
Valid prediction for Augustus_model.g8142.t1
Valid prediction for Augustus_model.g8125.t1
Valid prediction for pasa_asmbl_45592.p1
Couldn't classify 274730, 274790
Couldn't classify 277884, 277997
Sorry, prediction pasa_asmbl_45590.p1 fails validation.
(CGA)	 TG	274730-274790	GT	CGG
(GCT)	 AG	274928-275054	GT	ATG
(GTG)	 AG	275248-275390	GT	CGG
(GCA)	 AG	275526-275656	GT	AGG
(GGC)	 AG	275743-275918	GT	AGG
(GGA)	 AG	276036-276159	GT	AGG
(GTG)	 AG	276246-276481	GT	CAG
(AGC)	 AG	276585-276687	GT	AGG
(GAG)	 AG	276812-276969	GT	AGG
(CTT)	 AG	277078-277186	GT	AGG
(GCT)	 AG	277353-277535	GT	AGG
(ATC)	 AG	277696-277800	GT	AGG
(GTG)	 AG	277884-277997	AA	CCA
add_exon() Sorry, pasa_asmbl_45590.p1 276812-276969-terminal-2 is invalid.
-recovered pasa_asmbl_45590.p1, terminal, 276812, 276969
-recovered pasa_asmbl_45590.p1, internal, 274928, 275054
-recovered pasa_asmbl_45590.p1, internal, 275248, 275390
-recovered pasa_asmbl_45590.p1, internal, 275526, 275656
-recovered pasa_asmbl_45590.p1, internal, 275743, 275918
-recovered pasa_asmbl_45590.p1, internal, 276036, 276159
-recovered pasa_asmbl_45590.p1, internal, 276246, 276481
-recovered pasa_asmbl_45590.p1, internal, 276585, 276687
-recovered pasa_asmbl_45590.p1, internal, 276812, 276969
-recovered pasa_asmbl_45590.p1, internal, 277078, 277186
-recovered pasa_asmbl_45590.p1, internal, 277353, 277535
-recovered pasa_asmbl_45590.p1, internal, 277696, 277800
Valid prediction for snap_scaffold_5-snap.1691-T1
Valid prediction for snap_scaffold_5-snap.1654-T1
Valid prediction for Augustus_model.g8132.t1
Valid prediction for snap_scaffold_5-snap.1669-T1
Valid prediction for snap_scaffold_5-snap.1661-T1
Valid prediction for GlimmerHMM_glimmerT_12340-T1
Valid prediction for Augustus_model.g8143.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 CodingQuarry_transcript_52160-T1
Valid prediction for HiQ_model.g8135.t1
Valid prediction for snap_scaffold_5-snap.1663-T1
Valid prediction for HiQ_model.g8116.t1
Valid prediction for HiQ_model.g8126.t1
Couldn't classify 178346, 178524
Couldn't classify 179431, 179550
Sorry, prediction pasa_asmbl_44251.p1 fails validation.
(GCA)	 CT	178346-178524	GT	GGG
(GGA)	 AG	178710-178753	GT	AGG
(GCT)	 AG	178909-179090	GT	TGG
(AGT)	 AG	179431-179550	CC	GAC
-recovered pasa_asmbl_44251.p1, internal, 178710, 178753
-recovered pasa_asmbl_44251.p1, internal, 178909, 179090
Valid prediction for GlimmerHMM_glimmerT_12336-T1
Valid prediction for Augustus_model.g8124.t1
Valid prediction for pasa_asmbl_44241.p1
Valid prediction for GlimmerHMM_glimmerT_12337-T1
Couldn't classify 4135, 4371
Sorry, prediction pasa_asmbl_44259.p1 fails validation.
(ATG)	 AA	1918-2112	GT	AGG
(GTG)	 AG	3346-3489	GT	AGG
(GTG)	 AG	3866-3985	GT	GGG
(ACT)	 AG	4135-4371	CG	TAC
-recovered pasa_asmbl_44259.p1, initial, 1918, 2112
-recovered pasa_asmbl_44259.p1, internal, 3346, 3489
-recovered pasa_asmbl_44259.p1, internal, 3866, 3985
Valid prediction for snap_scaffold_5-snap.1659-T1
Valid prediction for snap_scaffold_5-snap.1675-T1
Valid prediction for GlimmerHMM_glimmerT_12332-T1
Valid prediction for snap_scaffold_5-snap.1656-T1
Valid prediction for Augustus_model.g8144.t1
Valid prediction for snap_scaffold_5-snap.1678-T1
Valid prediction for snap_scaffold_5-snap.1667-T1
Valid prediction for HiQ_model.g8117.t1
Valid prediction for snap_scaffold_5-snap.1690-T1
Valid prediction for Augustus_model.g8118.t1
Valid prediction for Augustus_model.g8127.t1
Valid prediction for pasa_asmbl_44232.p1
Valid prediction for CodingQuarry_transcript_52165-T1
Valid prediction for snap_scaffold_5-snap.1662-T1
Valid prediction for snap_scaffold_5-snap.1684-T1
Valid prediction for GlimmerHMM_glimmerT_12371-T1
Valid prediction for CodingQuarry_transcript_52163-T1
Valid prediction for GlimmerHMM_glimmerT_12363-T1
Valid prediction for GlimmerHMM_glimmerT_12344-T1
Valid prediction for snap_scaffold_5-snap.1697-T1
Valid prediction for Augustus_model.g8119.t1
Valid prediction for Augustus_model.g8133.t1
Couldn't classify 152257, 153420
Sorry, prediction pasa_asmbl_44253.p1 fails validation.
(ATG)	 CT	152257-153420	AA	AGA
Valid prediction for GlimmerHMM_glimmerT_12355-T1
Valid prediction for GlimmerHMM_glimmerT_12362-T1
Valid prediction for pasa_asmbl_44254.p1
Valid prediction for CodingQuarry_transcript_52162-T1
Valid prediction for pasa_asmbl_44233.p1
Valid prediction for Augustus_model.g8131.t1
Valid prediction for pasa_asmbl_44240.p1
Valid prediction for GlimmerHMM_glimmerT_12348-T1
Valid prediction for GlimmerHMM_glimmerT_12354-T1
Valid prediction for snap_scaffold_5-snap.1665-T1
Valid prediction for GlimmerHMM_glimmerT_12351-T1
Valid prediction for Augustus_model.g8138.t1
Valid prediction for Augustus_model.g8123.t1
Valid prediction for Augustus_model.g8134.t1
Valid prediction for pasa_asmbl_44256.p1
Valid prediction for snap_scaffold_5-snap.1696-T1
Valid prediction for snap_scaffold_5-snap.1657-T1
Valid prediction for snap_scaffold_5-snap.1658-T1
Valid prediction for GlimmerHMM_glimmerT_12359-T1
Valid prediction for GlimmerHMM_glimmerT_12333-T1
Valid prediction for GlimmerHMM_glimmerT_12335-T1
Valid prediction for GlimmerHMM_glimmerT_12346-T1
Valid prediction for snap_scaffold_5-snap.1655-T1
Valid prediction for GlimmerHMM_glimmerT_12349-T1
Valid prediction for snap_scaffold_5-snap.1677-T1
Valid prediction for GlimmerHMM_glimmerT_12369-T1
Valid prediction for snap_scaffold_5-snap.1685-T1
Valid prediction for GlimmerHMM_glimmerT_12341-T1
Valid prediction for GlimmerHMM_glimmerT_12342-T1
Valid prediction for GlimmerHMM_glimmerT_12347-T1
Valid prediction for GlimmerHMM_glimmerT_12353-T1
Couldn't classify 186779, 186979
Couldn't classify 188194, 188219
Sorry, prediction pasa_asmbl_44247.p1 fails validation.
(CAA)	 GC	186779-186979	GT	AGG
(ATA)	 AG	187292-187438	GT	GTG
(TGC)	 AG	187612-187741	GT	AAG
(TCG)	 AG	188194-188219	AG	CCA
-recovered pasa_asmbl_44247.p1, internal, 187292, 187438
-recovered pasa_asmbl_44247.p1, internal, 187612, 187741
Couldn't classify 186320, 186580
Sorry, prediction pasa_asmbl_44248.p1 fails validation.
(ATG)	 AC	184961-184979	GT	AGG
(TTT)	 AG	185729-185874	GT	AGG
(GAT)	 AG	186320-186580	CG	GCC
-recovered pasa_asmbl_44248.p1, initial, 184961, 184979
-recovered pasa_asmbl_44248.p1, internal, 185729, 185874
Couldn't classify 276928, 278304
Sorry, prediction pasa_asmbl_44234.p1 fails validation.
(TTG)	 CC	276928-278304	CT	GAC
Couldn't classify 233865, 233961
Sorry, prediction pasa_asmbl_44245.p1 fails validation.
(AGG)	 AA	233865-233961	GT	GAG
(GGG)	 AG	234115-234184	GT	GGG
(GTC)	 AG	234280-234424	GT	CGG
(TGT)	 AG	234609-234831	GT	AGG
(ATC)	 AG	235004-235092	GT	GGG
(GTC)	 AG	235179-235220	GT	GGG
(CAA)	 AG	235340-235497	GT	AGG
(GCG)	 AG	235600-235667	GT	AGG
(TTG)	 AG	235791-235918	GT	TGG
(CTG)	 AG	236066-236479	AT	AAA
-recovered pasa_asmbl_44245.p1, terminal, 236066, 236479
-recovered pasa_asmbl_44245.p1, internal, 234115, 234184
-recovered pasa_asmbl_44245.p1, internal, 234280, 234424
-recovered pasa_asmbl_44245.p1, internal, 234609, 234831
-recovered pasa_asmbl_44245.p1, internal, 235004, 235092
-recovered pasa_asmbl_44245.p1, internal, 235179, 235220
-recovered pasa_asmbl_44245.p1, internal, 235340, 235497
-recovered pasa_asmbl_44245.p1, internal, 235600, 235667
-recovered pasa_asmbl_44245.p1, internal, 235791, 235918
Valid prediction for pasa_asmbl_44252.p1
Valid prediction for GlimmerHMM_glimmerT_12358-T1
Valid prediction for Augustus_model.g8136.t1
Valid prediction for snap_scaffold_5-snap.1676-T1
Valid prediction for HiQ_model.g8128.t1
Valid prediction for snap_scaffold_5-snap.1668-T1
Valid prediction for HiQ_model.g8120.t1
Valid prediction for snap_scaffold_5-snap.1673-T1
Couldn't classify 274820, 274978
Couldn't classify 276179, 276454
Sorry, prediction pasa_asmbl_44235.p1 fails validation.
(GCT)	 AG	274820-274978	GT	AGG
(GTT)	 AG	276179-276454	GT	AGG
-recovered pasa_asmbl_44235.p1, internal, 274820, 274978
-recovered pasa_asmbl_44235.p1, internal, 276179, 276454
Couldn't classify 179825, 179925
Sorry, prediction pasa_asmbl_44250.p1 fails validation.
(GTA)	 CA	179825-179925	GT	TGG
(GGA)	 AG	180045-180145	GT	ATG
(ATG)	 AG	180225-180301	GT	ATG
(GGC)	 AG	180413-180476	GT	CGG
(TTT)	 AG	180583-180668	GT	AGG
(GAG)	 AG	180798-180908	GT	AGG
(GGT)	 AG	181003-181104	TT	GAT
add_exon() Sorry, pasa_asmbl_44250.p1 180225-180301-initial-1 is invalid.
-recovered pasa_asmbl_44250.p1, initial, 180225, 180301
-recovered pasa_asmbl_44250.p1, terminal, 181003, 181104
-recovered pasa_asmbl_44250.p1, internal, 180045, 180145
-recovered pasa_asmbl_44250.p1, internal, 180225, 180301
-recovered pasa_asmbl_44250.p1, internal, 180413, 180476
-recovered pasa_asmbl_44250.p1, internal, 180583, 180668
-recovered pasa_asmbl_44250.p1, internal, 180798, 180908
Valid prediction for GlimmerHMM_glimmerT_12334-T1
Valid prediction for snap_scaffold_5-snap.1666-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 287157, rend_intergenic: 282455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 295316
-exon list size: 569


building trellis

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69.7    
69.9    
70.1    
70.2    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.6    
73.7    
73.9    
74.1    
74.3    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.8    
77.9    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.6    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 287157, rend_intergenic: 282455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support