-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_10113744-10303887

-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.16738_t
Valid prediction for GeneMark_model.16733_t
Valid prediction for Augustus_model.g6728.t1
Valid prediction for GlimmerHMM_glimmerT_10268-T1
Valid prediction for GeneMark_model.16730_t
Valid prediction for GlimmerHMM_glimmerT_10263-T1
Valid prediction for GeneMark_model.16670_t
Valid prediction for snap_scaffold_4-snap.2165-T1
Valid prediction for HiQ_model.g6722.t1
Valid prediction for HiQ_model.g6725.t1
Valid prediction for GlimmerHMM_glimmerT_10267-T1
Valid prediction for snap_scaffold_4-snap.2181-T1
Valid prediction for GeneMark_model.16673_t
Valid prediction for snap_scaffold_4-snap.2162-T1
Valid prediction for CodingQuarry_transcript_49002-T1
Valid prediction for GeneMark_model.16694_t
Valid prediction for GeneMark_model.16718_t
Valid prediction for Augustus_model.g6727.t1
Valid prediction for snap_scaffold_4-snap.2189-T1
Valid prediction for GeneMark_model.16720_t
Valid prediction for snap_scaffold_4-snap.2168-T1
Valid prediction for GeneMark_model.16743_t
Valid prediction for snap_scaffold_4-snap.2157-T1
Valid prediction for GeneMark_model.16726_t
Valid prediction for GeneMark_model.16701_t
Valid prediction for GeneMark_model.16724_t
Valid prediction for pasa_asmbl_42987.p1
Valid prediction for GeneMark_model.16705_t
Valid prediction for GeneMark_model.16662_t
Valid prediction for GlimmerHMM_glimmerT_10260-T1
Valid prediction for snap_scaffold_4-snap.2178-T1
Valid prediction for HiQ_model.g6721.t1
Valid prediction for GeneMark_model.16739_t
Valid prediction for GeneMark_model.16699_t
Valid prediction for GeneMark_model.16741_t
Valid prediction for GeneMark_model.16685_t
Valid prediction for GeneMark_model.16666_t
Valid prediction for GeneMark_model.16683_t
Valid prediction for GeneMark_model.16708_t
Valid prediction for snap_scaffold_4-snap.2160-T1
Valid prediction for GlimmerHMM_glimmerT_10261-T1
Valid prediction for GlimmerHMM_glimmerT_10258-T1
Valid prediction for snap_scaffold_4-snap.2190-T1
Valid prediction for GlimmerHMM_glimmerT_10270-T1
Valid prediction for GlimmerHMM_glimmerT_10264-T1
Valid prediction for GeneMark_model.16681_t
Valid prediction for GeneMark_model.16663_t
Valid prediction for snap_scaffold_4-snap.2180-T1
Valid prediction for GeneMark_model.16736_t
Valid prediction for snap_scaffold_4-snap.2179-T1
Valid prediction for GeneMark_model.16692_t
Valid prediction for GeneMark_model.16716_t
Valid prediction for GeneMark_model.16734_t
Valid prediction for snap_scaffold_4-snap.2172-T1
Valid prediction for GeneMark_model.16719_t
Valid prediction for GlimmerHMM_glimmerT_10277-T1
Valid prediction for GeneMark_model.16674_t
Valid prediction for GeneMark_model.16712_t
Valid prediction for GlimmerHMM_glimmerT_10262-T1
Valid prediction for GeneMark_model.16680_t
Valid prediction for GlimmerHMM_glimmerT_10275-T1
Valid prediction for GeneMark_model.16687_t
Valid prediction for GeneMark_model.16728_t
Valid prediction for GlimmerHMM_glimmerT_10250-T1
Valid prediction for GeneMark_model.16676_t
Valid prediction for snap_scaffold_4-snap.2164-T1
Valid prediction for snap_scaffold_4-snap.2185-T1
Valid prediction for CodingQuarry_transcript_48999-T1
Valid prediction for GlimmerHMM_glimmerT_10273-T1
Valid prediction for snap_scaffold_4-snap.2174-T1
Valid prediction for GeneMark_model.16703_t
Valid prediction for GeneMark_model.16688_t
Valid prediction for Augustus_model.g6730.t1
Valid prediction for pasa_asmbl_42986.p1
Valid prediction for GeneMark_model.16706_t
Valid prediction for snap_scaffold_4-snap.2153-T1
Valid prediction for Augustus_model.g6720.t1
Valid prediction for GlimmerHMM_glimmerT_10252-T1
Valid prediction for snap_scaffold_4-snap.2177-T1
Valid prediction for GeneMark_model.16722_t
Valid prediction for pasa_asmbl_42988.p1
Valid prediction for GlimmerHMM_glimmerT_10266-T1
Valid prediction for GeneMark_model.16668_t
Couldn't classify 2963, 3406
Sorry, prediction pasa_asmbl_42985.p1 fails validation.
(CAG)	 TT	2963-3406	AT	GAA
Valid prediction for GeneMark_model.16704_t
Valid prediction for snap_scaffold_4-snap.2167-T1
Valid prediction for GlimmerHMM_glimmerT_10255-T1
Valid prediction for snap_scaffold_4-snap.2183-T1
Valid prediction for GeneMark_model.16678_t
Valid prediction for GeneMark_model.16732_t
Valid prediction for GeneMark_model.16690_t
Valid prediction for snap_scaffold_4-snap.2188-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.2154-T1
Valid prediction for CodingQuarry_transcript_49000-T1
Valid prediction for GlimmerHMM_glimmerT_10251-T1
Valid prediction for GeneMark_model.16710_t
Valid prediction for GeneMark_model.16714_t

-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.16700_t
Valid prediction for GeneMark_model.16727_t
Valid prediction for GlimmerHMM_glimmerT_10253-T1
Valid prediction for snap_scaffold_4-snap.2163-T1
Valid prediction for GeneMark_model.16721_t
Valid prediction for HiQ_model.g6724.t1
Valid prediction for GlimmerHMM_glimmerT_10254-T1
Valid prediction for Augustus_model.g6726.t1
Valid prediction for snap_scaffold_4-snap.2152-T1
Valid prediction for snap_scaffold_4-snap.2170-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.16664_t
Valid prediction for GeneMark_model.16737_t
Valid prediction for snap_scaffold_4-snap.2176-T1
Valid prediction for snap_scaffold_4-snap.2175-T1
Valid prediction for GeneMark_model.16740_t
Valid prediction for snap_scaffold_4-snap.2155-T1
Valid prediction for GlimmerHMM_glimmerT_10272-T1
Valid prediction for GlimmerHMM_glimmerT_10278-T1
Valid prediction for GlimmerHMM_glimmerT_10274-T1
Valid prediction for Augustus_model.g6731.t1
Valid prediction for GeneMark_model.16731_t
Valid prediction for GeneMark_model.16707_t
Valid prediction for GeneMark_model.16725_t
Valid prediction for GeneMark_model.16689_t
Valid prediction for GeneMark_model.16723_t
Valid prediction for snap_scaffold_4-snap.2156-T1
Valid prediction for GeneMark_model.16696_t
Valid prediction for GlimmerHMM_glimmerT_10256-T1
Valid prediction for GlimmerHMM_glimmerT_10265-T1
Valid prediction for GeneMark_model.16742_t
Valid prediction for GeneMark_model.16679_t
Valid prediction for GeneMark_model.16665_t
Valid prediction for snap_scaffold_4-snap.2166-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.2171-T1
Valid prediction for GeneMark_model.16672_t
Valid prediction for GeneMark_model.16675_t
Valid prediction for GeneMark_model.16695_t
Valid prediction for snap_scaffold_4-snap.2158-T1
Valid prediction for GlimmerHMM_glimmerT_10271-T1
Valid prediction for snap_scaffold_4-snap.2161-T1
Valid prediction for GeneMark_model.16682_t
Valid prediction for GeneMark_model.16711_t
Valid prediction for GlimmerHMM_glimmerT_10269-T1
Valid prediction for GeneMark_model.16693_t
Valid prediction for GeneMark_model.16715_t
Valid prediction for GeneMark_model.16677_t
Valid prediction for GlimmerHMM_glimmerT_10257-T1
Valid prediction for GeneMark_model.16698_t
Couldn't classify 171364, 171999
Sorry, prediction pasa_asmbl_41579.p1 fails validation.
(ATG)	 AC	171364-171999	CG	AGC
Valid prediction for GeneMark_model.16702_t
Valid prediction for GeneMark_model.16697_t
Valid prediction for Augustus_model.g6723.t1
Couldn't classify 25959, 27254
Sorry, prediction pasa_asmbl_41580.p1 fails validation.
(AAT)	 GG	25959-27254	GA	AAG
Valid prediction for GeneMark_model.16669_t
Valid prediction for Augustus_model.g6729.t1
Valid prediction for GeneMark_model.16729_t
Valid prediction for snap_scaffold_4-snap.2159-T1
Valid prediction for GeneMark_model.16735_t
Valid prediction for snap_scaffold_4-snap.2187-T1
Valid prediction for GeneMark_model.16717_t
Valid prediction for GeneMark_model.16691_t
Valid prediction for GlimmerHMM_glimmerT_10259-T1
Valid prediction for GeneMark_model.16713_t
Couldn't classify 24387, 25724
Sorry, prediction pasa_asmbl_41581.p1 fails validation.
(AAT)	 CC	24387-25724	CA	CAC
Valid prediction for GeneMark_model.16667_t
Couldn't classify 172238, 172274
Sorry, prediction pasa_asmbl_41576.p1 fails validation.
(ACT)	 GA	172238-172274	GT	CGG
(TAG)	 AG	172362-172424	GT	AGG
(GTA)	 AG	172834-172953	GT	AGG
(ACC)	 AG	173073-173164	GT	AGG
(AAA)	 AG	173364-173532	GT	GGG
(GTG)	 AG	174187-174375	GT	AGG
(ACG)	 AG	174516-174681	GT	AGG
(AGC)	 AG	174822-174985	GT	AGG
(GCC)	 AG	175182-175408	GT	AGG
(ACC)	 AG	175512-175559	AG	GAA
-recovered pasa_asmbl_41576.p1, terminal, 175512, 175559
-recovered pasa_asmbl_41576.p1, internal, 172362, 172424
-recovered pasa_asmbl_41576.p1, internal, 172834, 172953
-recovered pasa_asmbl_41576.p1, internal, 173073, 173164
-recovered pasa_asmbl_41576.p1, internal, 173364, 173532
-recovered pasa_asmbl_41576.p1, internal, 174187, 174375
-recovered pasa_asmbl_41576.p1, internal, 174516, 174681
-recovered pasa_asmbl_41576.p1, internal, 174822, 174985
-recovered pasa_asmbl_41576.p1, internal, 175182, 175408
Valid prediction for snap_scaffold_4-snap.2182-T1
Valid prediction for GeneMark_model.16671_t
Valid prediction for snap_scaffold_4-snap.2173-T1
Valid prediction for snap_scaffold_4-snap.2184-T1
Valid prediction for GlimmerHMM_glimmerT_10276-T1
Valid prediction for snap_scaffold_4-snap.2186-T1
Valid prediction for snap_scaffold_4-snap.2169-T1
Valid prediction for GeneMark_model.16684_t
Valid prediction for GeneMark_model.16686_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6593, rend_intergenic: 5029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18018, rend_intergenic: 14710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24763, rend_intergenic: 19952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29781, rend_intergenic: 26437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33034, rend_intergenic: 30629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46557, rend_intergenic: 34009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66841, rend_intergenic: 49404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76985, rend_intergenic: 67740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82009, rend_intergenic: 78241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83206, rend_intergenic: 82942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90386, rend_intergenic: 83509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98476, rend_intergenic: 90614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126345, rend_intergenic: 98796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130507, rend_intergenic: 126863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137010, rend_intergenic: 130696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150215, rend_intergenic: 137021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153433, rend_intergenic: 151034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160583, rend_intergenic: 154381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187270, rend_intergenic: 166625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190144
-exon list size: 920


building trellis

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61.9    
62.0    
62.1    
62.3    
62.4    
62.5    
62.6    
62.7    
62.8    
62.9    
63.0    
63.1    
63.2    
63.3    
63.4    
63.6    
63.7    
63.8    
63.9    
64.0    
64.1    
64.2    
64.3    
64.4    
64.5    
64.6    
64.8    
64.9    
65.0    
65.1    
65.2    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
65.9    
66.1    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.8    
66.9    
67.0    
67.1    
67.2    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.4    
69.5    
69.6    
69.7    
69.8    
70.0    
70.1    
70.2    
70.3    
70.4    
70.5    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.3    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.3    
73.4    
73.5    
73.6    
73.8    
73.9    
74.0    
74.1    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
84.9    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.7    
85.8    
85.9    
86.0    
86.1    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.1    
92.2    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 56 predictions from path traversal
Error with prediction: snap lend_intergenic: 6593, rend_intergenic: 5029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18018, rend_intergenic: 14710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24763, rend_intergenic: 19952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29781, rend_intergenic: 26437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33034, rend_intergenic: 30629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46557, rend_intergenic: 34009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66841, rend_intergenic: 49404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76985, rend_intergenic: 67740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82009, rend_intergenic: 78241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83206, rend_intergenic: 82942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90386, rend_intergenic: 83509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98476, rend_intergenic: 90614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126345, rend_intergenic: 98796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130507, rend_intergenic: 126863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137010, rend_intergenic: 130696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150215, rend_intergenic: 137021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153433, rend_intergenic: 151034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160583, rend_intergenic: 154381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187270, rend_intergenic: 166625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support