-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_7837958-8030306

-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_6-snap.1749-T1
Valid prediction for snap_scaffold_6-snap.1775-T1
Valid prediction for snap_scaffold_6-snap.1756-T1
Valid prediction for GlimmerHMM_glimmerT_15367-T1
Valid prediction for GeneMark_model.25934_t
Valid prediction for CodingQuarry_transcript_54965-T1
Valid prediction for snap_scaffold_6-snap.1766-T1
Valid prediction for GeneMark_model.25912_t
Valid prediction for CodingQuarry_transcript_54966-T1
Valid prediction for GeneMark_model.25930_t
Valid prediction for GeneMark_model.25922_t
Valid prediction for GeneMark_model.25928_t
Valid prediction for Augustus_model.g10237.t1
Valid prediction for GeneMark_model.25940_t
Valid prediction for snap_scaffold_6-snap.1743-T1
Valid prediction for Augustus_model.g10238.t1
Valid prediction for GeneMark_model.25946_t
Valid prediction for GeneMark_model.25914_t
Valid prediction for snap_scaffold_6-snap.1773-T1
Valid prediction for Augustus_model.g10246.t1
Valid prediction for pasa_asmbl_47021.p2
Valid prediction for GeneMark_model.25951_t
Valid prediction for snap_scaffold_6-snap.1774-T1
Valid prediction for GeneMark_model.25948_t
Valid prediction for GeneMark_model.25924_t
Valid prediction for GeneMark_model.25944_t
Valid prediction for snap_scaffold_6-snap.1768-T1
Valid prediction for GlimmerHMM_glimmerT_15385-T1
Valid prediction for GlimmerHMM_glimmerT_15357-T1
Valid prediction for GlimmerHMM_glimmerT_15374-T1
Valid prediction for snap_scaffold_6-snap.1744-T1
Valid prediction for pasa_asmbl_47024.p1
Valid prediction for HiQ_model.g10233.t1
Valid prediction for GlimmerHMM_glimmerT_15365-T1
Valid prediction for snap_scaffold_6-snap.1778-T1
Valid prediction for Augustus_model.g10250.t1
Valid prediction for GeneMark_model.25943_t
Valid prediction for snap_scaffold_6-snap.1752-T1
Valid prediction for HiQ_model.g10253.t1
Valid prediction for snap_scaffold_6-snap.1754-T1
Valid prediction for GeneMark_model.25950_t
Valid prediction for GlimmerHMM_glimmerT_15377-T1
Valid prediction for GeneMark_model.25909_t
Valid prediction for snap_scaffold_6-snap.1759-T1
Valid prediction for snap_scaffold_6-snap.1757-T1
Valid prediction for GeneMark_model.25925_t
Valid prediction for GlimmerHMM_glimmerT_15361-T1
Valid prediction for GeneMark_model.25955_t
Valid prediction for GlimmerHMM_glimmerT_15364-T1
Valid prediction for GeneMark_model.25911_t
Couldn't classify 173514, 173574
Couldn't classify 173759, 173817
Sorry, prediction pasa_asmbl_47025.p1 fails validation.
(ATG)	 AA	173514-173574	AT	GAA
(AGC)	 AC	173759-173817	GT	CGG
(GTT)	 AG	173940-174056	GT	TTG
(TTT)	 AG	174236-174351	GT	AGG
(GGA)	 AG	174478-174643	CC	GAC
-recovered pasa_asmbl_47025.p1, terminal, 174478, 174643
-recovered pasa_asmbl_47025.p1, internal, 173940, 174056
-recovered pasa_asmbl_47025.p1, internal, 174236, 174351
Valid prediction for GeneMark_model.25936_t
Valid prediction for HiQ_model.g10239.t1
Valid prediction for Augustus_model.g10247.t1
Valid prediction for GlimmerHMM_glimmerT_15381-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 HiQ_model.g10252.t1
Valid prediction for GeneMark_model.25929_t
Valid prediction for GeneMark_model.25921_t
Valid prediction for CodingQuarry_transcript_54968-T1
Valid prediction for GlimmerHMM_glimmerT_15372-T1
Valid prediction for GlimmerHMM_glimmerT_15379-T1
Valid prediction for GlimmerHMM_glimmerT_15358-T1
Valid prediction for Augustus_model.g10236.t1
Valid prediction for pasa_asmbl_48460.p1
Valid prediction for snap_scaffold_6-snap.1740-T1
Valid prediction for GlimmerHMM_glimmerT_15368-T1
Valid prediction for snap_scaffold_6-snap.1746-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g10245.t1
Valid prediction for snap_scaffold_6-snap.1762-T1
Valid prediction for Augustus_model.g10248.t1
Valid prediction for snap_scaffold_6-snap.1763-T1
Valid prediction for GeneMark_model.25956_t
Valid prediction for GlimmerHMM_glimmerT_15383-T1
Valid prediction for snap_scaffold_6-snap.1772-T1
Valid prediction for GlimmerHMM_glimmerT_15360-T1
Valid prediction for Augustus_model.g10232.t1
Couldn't classify 15196, 15229
Sorry, prediction pasa_asmbl_48463.p1 fails validation.
(AGC)	 CC	15196-15229	GT	AGG
(GTG)	 AG	15312-15380	GT	GGG
(ATG)	 AG	15473-15709	GT	AGG
(GAC)	 AG	15883-16178	GG	GAG
add_exon() Sorry, pasa_asmbl_48463.p1 15473-15709-initial-1 is invalid.
-recovered pasa_asmbl_48463.p1, initial, 15473, 15709
-recovered pasa_asmbl_48463.p1, terminal, 15883, 16178
-recovered pasa_asmbl_48463.p1, internal, 15312, 15380
-recovered pasa_asmbl_48463.p1, internal, 15473, 15709
Couldn't classify 22953, 22990
Couldn't classify 25411, 25477
Sorry, prediction pasa_asmbl_48458.p1 fails validation.
(GAC)	 GT	22953-22990	GT	AAG
(GTT)	 AG	23236-23368	GT	TGG
(GCA)	 AG	24155-24200	GT	CGG
(CCC)	 AG	24300-24432	GT	AGG
(ATA)	 AG	24542-24684	GT	CGG
(AGC)	 AG	24803-24863	GT	GGG
(AAT)	 AG	25120-25194	GT	AGG
(TTT)	 AG	25411-25477	CT	GCC
-recovered pasa_asmbl_48458.p1, internal, 23236, 23368
-recovered pasa_asmbl_48458.p1, internal, 24155, 24200
-recovered pasa_asmbl_48458.p1, internal, 24300, 24432
-recovered pasa_asmbl_48458.p1, internal, 24542, 24684
-recovered pasa_asmbl_48458.p1, internal, 24803, 24863
-recovered pasa_asmbl_48458.p1, internal, 25120, 25194
Valid prediction for pasa_asmbl_48448.p1
Valid prediction for GeneMark_model.25927_t
Valid prediction for GlimmerHMM_glimmerT_15366-T1
Couldn't classify 8363, 8899
Sorry, prediction pasa_asmbl_48464.p1 fails validation.
(CCC)	 GA	8363-8899	CG	GGC
Valid prediction for CodingQuarry_transcript_54972-T1
Valid prediction for snap_scaffold_6-snap.1767-T1
Couldn't classify 42160, 42207
Sorry, prediction pasa_asmbl_48457.p1 fails validation.
(TGT)	 CC	42160-42207	GT	GGG
(GTT)	 AG	42304-42425	GT	CGG
(GGT)	 AG	42571-42648	GT	GAG
(TCA)	 AG	42768-42857	GT	GTG
(GTT)	 AG	42972-43059	GT	TGG
(ATC)	 AG	43168-43277	GT	TGG
(GGA)	 AG	43388-43472	GT	AGG
(AGC)	 AG	43798-43812	AG	AGA
-recovered pasa_asmbl_48457.p1, terminal, 43798, 43812
-recovered pasa_asmbl_48457.p1, internal, 42304, 42425
-recovered pasa_asmbl_48457.p1, internal, 42571, 42648
-recovered pasa_asmbl_48457.p1, internal, 42768, 42857
-recovered pasa_asmbl_48457.p1, internal, 42972, 43059
-recovered pasa_asmbl_48457.p1, internal, 43168, 43277
-recovered pasa_asmbl_48457.p1, internal, 43388, 43472
Valid prediction for snap_scaffold_6-snap.1741-T1
Valid prediction for GeneMark_model.25913_t
Valid prediction for GeneMark_model.25952_t
Valid prediction for GeneMark_model.25932_t
Valid prediction for GlimmerHMM_glimmerT_15382-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.25945_t
Valid prediction for snap_scaffold_6-snap.1779-T1
Valid prediction for snap_scaffold_6-snap.1755-T1
Valid prediction for GlimmerHMM_glimmerT_15376-T1
Valid prediction for GeneMark_model.25938_t
Valid prediction for GeneMark_model.25954_t
Valid prediction for GlimmerHMM_glimmerT_15378-T1
Valid prediction for GeneMark_model.25937_t
Valid prediction for snap_scaffold_6-snap.1745-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g10235.t1
Valid prediction for snap_scaffold_6-snap.1751-T1
Couldn't classify 22211, 22272
Sorry, prediction pasa_asmbl_48459.p1 fails validation.
(ATG)	 CC	21766-21952	GT	GGG
(TCA)	 AG	22083-22133	GT	GGG
(AAT)	 AG	22211-22272	CA	CCC
-recovered pasa_asmbl_48459.p1, initial, 21766, 21952
-recovered pasa_asmbl_48459.p1, internal, 22083, 22133
Valid prediction for GlimmerHMM_glimmerT_15380-T1
Valid prediction for GeneMark_model.25949_t
Valid prediction for GlimmerHMM_glimmerT_15370-T1
Valid prediction for snap_scaffold_6-snap.1753-T1
Valid prediction for Augustus_model.g10244.t1
Valid prediction for Augustus_model.g10254.t1
Valid prediction for GlimmerHMM_glimmerT_15362-T1
Valid prediction for GeneMark_model.25910_t
Valid prediction for GeneMark_model.25926_t
Valid prediction for snap_scaffold_6-snap.1776-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.1750-T1
Valid prediction for GeneMark_model.25931_t
Valid prediction for snap_scaffold_6-snap.1742-T1
Valid prediction for GlimmerHMM_glimmerT_15373-T1
Valid prediction for GeneMark_model.25920_t
Valid prediction for snap_scaffold_6-snap.1764-T1
Valid prediction for GlimmerHMM_glimmerT_15356-T1
Valid prediction for snap_scaffold_6-snap.1777-T1
Valid prediction for snap_scaffold_6-snap.1771-T1
Valid prediction for GlimmerHMM_glimmerT_15363-T1
Valid prediction for GlimmerHMM_glimmerT_15384-T1
Couldn't classify 35417, 35514
Sorry, prediction pasa_asmbl_48456.p1 fails validation.
(CTG)	 CA	35417-35514	GT	AGG
(GCC)	 AG	35696-35756	GT	AGG
(CTG)	 AG	35985-36007	GT	AGG
(GGG)	 AG	36108-36139	GT	AGG
(TCT)	 AG	36253-36315	GT	CGG
(CTG)	 AG	36553-36629	GT	AGG
(GAG)	 AG	36749-36830	GT	GGG
(AGG)	 AG	36966-37084	GT	GGG
(ATC)	 AG	37224-37315	GT	CAG
(GGT)	 AG	37554-37694	GT	TGG
(GGT)	 AG	38352-38435	GT	CTG
(CGT)	 AG	38605-38763	GT	CTG
(GGA)	 AG	39906-40044	GT	CGG
(GTT)	 AG	42304-42425	GT	CGG
(GGT)	 AG	42571-42648	GT	GAG
(TCA)	 AG	42768-42857	GT	GTG
(GTT)	 AG	42972-43059	GT	TGG
(ATC)	 AG	43168-43277	GT	TGG
(GGA)	 AG	43388-43472	GT	AGG
(AGC)	 AG	43798-43812	AG	AGA
add_exon() Sorry, pasa_asmbl_48456.p1 35985-36007-terminal-2 is invalid.
-recovered pasa_asmbl_48456.p1, terminal, 35985, 36007
-recovered pasa_asmbl_48456.p1, terminal, 43798, 43812
-recovered pasa_asmbl_48456.p1, internal, 35696, 35756
-recovered pasa_asmbl_48456.p1, internal, 35985, 36007
-recovered pasa_asmbl_48456.p1, internal, 36108, 36139
-recovered pasa_asmbl_48456.p1, internal, 36253, 36315
-recovered pasa_asmbl_48456.p1, internal, 36553, 36629
-recovered pasa_asmbl_48456.p1, internal, 36749, 36830
-recovered pasa_asmbl_48456.p1, internal, 36966, 37084
-recovered pasa_asmbl_48456.p1, internal, 37224, 37315
-recovered pasa_asmbl_48456.p1, internal, 37554, 37694
-recovered pasa_asmbl_48456.p1, internal, 38352, 38435
-recovered pasa_asmbl_48456.p1, internal, 38605, 38763
-recovered pasa_asmbl_48456.p1, internal, 39906, 40044
-recovered pasa_asmbl_48456.p1, internal, 42304, 42425
-recovered pasa_asmbl_48456.p1, internal, 42571, 42648
-recovered pasa_asmbl_48456.p1, internal, 42768, 42857
-recovered pasa_asmbl_48456.p1, internal, 42972, 43059
-recovered pasa_asmbl_48456.p1, internal, 43168, 43277
-recovered pasa_asmbl_48456.p1, internal, 43388, 43472
Valid prediction for GlimmerHMM_glimmerT_15369-T1
Valid prediction for Augustus_model.g10243.t1
Valid prediction for GeneMark_model.25941_t
Valid prediction for snap_scaffold_6-snap.1758-T1
Valid prediction for GlimmerHMM_glimmerT_15375-T1
Couldn't classify 77457, 77460
Sorry, prediction pasa_asmbl_48454.p1 fails validation.
(TTT)	 AC	77457-77460	GT	TGG
(TGG)	 AG	77617-77930	GC	GAG
-recovered pasa_asmbl_48454.p1, terminal, 77617, 77930
-recovered pasa_asmbl_48454.p1, internal, 77617, 77930
Valid prediction for GeneMark_model.25947_t
Valid prediction for snap_scaffold_6-snap.1748-T1
Valid prediction for Augustus_model.g10242.t1
Valid prediction for snap_scaffold_6-snap.1760-T1
Valid prediction for Augustus_model.g10234.t1
Valid prediction for GeneMark_model.25935_t
Valid prediction for GeneMark_model.25933_t
Valid prediction for snap_scaffold_6-snap.1747-T1
Valid prediction for CodingQuarry_transcript_54970-T1
Valid prediction for GeneMark_model.25918_t
Valid prediction for snap_scaffold_6-snap.1770-T1
Valid prediction for GeneMark_model.25919_t
Valid prediction for Augustus_model.g10251.t1
Valid prediction for snap_scaffold_6-snap.1769-T1
Couldn't classify 73679, 74003
Sorry, prediction pasa_asmbl_48455.p1 fails validation.
(ATG)	 AC	71691-71788	GT	AGG
(TGG)	 AG	73679-74003	AT	AGA
-recovered pasa_asmbl_48455.p1, initial, 71691, 71788
Valid prediction for GeneMark_model.25953_t
Valid prediction for Augustus_model.g10249.t1
Valid prediction for GeneMark_model.25916_t
Valid prediction for Augustus_model.g10240.t1
Valid prediction for GlimmerHMM_glimmerT_15371-T1
Valid prediction for HiQ_model.g10241.t1
Valid prediction for GeneMark_model.25923_t
Valid prediction for GlimmerHMM_glimmerT_15359-T1
Valid prediction for GeneMark_model.25942_t
Valid prediction for GeneMark_model.25939_t
Valid prediction for GeneMark_model.25917_t
Valid prediction for snap_scaffold_6-snap.1761-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.1780-T1
Valid prediction for snap_scaffold_6-snap.1765-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37110, rend_intergenic: 36085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61625, rend_intergenic: 58946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88814, rend_intergenic: 87414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124008, rend_intergenic: 123426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129111, rend_intergenic: 127066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139085, rend_intergenic: 129238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162417, rend_intergenic: 152068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192349
-exon list size: 640


building trellis

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62.5    
62.6    
62.8    
62.9    
63.1    
63.2    
63.4    
63.6    
63.7    
63.9    
64.0    
64.2    
64.3    
64.5    
64.6    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.9    
66.0    
66.2    
66.4    
66.5    
66.7    
66.8    
67.0    
67.1    
67.3    
67.4    
67.6    
67.8    
67.9    
68.1    
68.2    
68.4    
68.5    
68.7    
68.8    
69.0    
69.2    
69.3    
69.5    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.6    
70.7    
70.9    
71.0    
71.2    
71.3    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.4    
72.6    
72.7    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.5    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.5    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 37110, rend_intergenic: 36085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61625, rend_intergenic: 58946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88814, rend_intergenic: 87414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124008, rend_intergenic: 123426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129111, rend_intergenic: 127066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139085, rend_intergenic: 129238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162417, rend_intergenic: 152068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support