-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_4933192-5110987

-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 Augustus_model.g467.t1
Valid prediction for GlimmerHMM_glimmerT_611-T1
Valid prediction for Augustus_model.g463.t1
Couldn't classify 66549, 66579
Sorry, prediction GeneMark_model.748_t fails validation.
(ATG)	 CC	64191-64330	GT	GGG
(GCT)	 AG	64418-64450	GT	AGG
(GGT)	 AG	64749-65125	GT	GGG
(GGC)	 AG	65207-65217	GT	AGG
(CGG)	 AG	66209-66222	GT	CTG
(GAA)	 AG	66406-66426	GT	AGG
(TGG)	 AG	66459-66470	GT	GGG
(CGG)	 AG	66494-66523	GT	ATG
(GGA)	 AG	66549-66579	GT	AAG
-recovered GeneMark_model.748_t, initial, 64191, 64330
-recovered GeneMark_model.748_t, internal, 64418, 64450
-recovered GeneMark_model.748_t, internal, 64749, 65125
-recovered GeneMark_model.748_t, internal, 65207, 65217
-recovered GeneMark_model.748_t, internal, 66209, 66222
-recovered GeneMark_model.748_t, internal, 66406, 66426
-recovered GeneMark_model.748_t, internal, 66459, 66470
-recovered GeneMark_model.748_t, internal, 66494, 66523
-recovered GeneMark_model.748_t, internal, 66549, 66579
Valid prediction for GeneMark_model.754_t
Valid prediction for GeneMark_model.770_t
Valid prediction for GeneMark_model.745_t
Valid prediction for GeneMark_model.772_t
Valid prediction for snap_scaffold_1-snap.765-T1
Valid prediction for snap_scaffold_1-snap.755-T1
Valid prediction for Augustus_model.g460.t1
Valid prediction for GlimmerHMM_glimmerT_613-T1
Valid prediction for snap_scaffold_1-snap.764-T1
Valid prediction for snap_scaffold_1-snap.772-T1
Valid prediction for snap_scaffold_1-snap.779-T1
Valid prediction for GlimmerHMM_glimmerT_607-T1
Valid prediction for snap_scaffold_1-snap.758-T1
Valid prediction for GeneMark_model.766_t
Valid prediction for Augustus_model.g459.t1
Valid prediction for GeneMark_model.761_t
Valid prediction for snap_scaffold_1-snap.754-T1
Valid prediction for snap_scaffold_1-snap.770-T1
Valid prediction for snap_scaffold_1-snap.759-T1
Valid prediction for GeneMark_model.764_t
Valid prediction for snap_scaffold_1-snap.767-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.746_t
Valid prediction for GlimmerHMM_glimmerT_616-T1
Valid prediction for GlimmerHMM_glimmerT_594-T1
Valid prediction for GeneMark_model.752_t
Valid prediction for GeneMark_model.768_t
Valid prediction for GeneMark_model.769_t
Valid prediction for GlimmerHMM_glimmerT_610-T1
Valid prediction for GeneMark_model.736_t
Valid prediction for Augustus_model.g461.t1
Valid prediction for GeneMark_model.739_t
Valid prediction for snap_scaffold_1-snap.763-T1
Valid prediction for GlimmerHMM_glimmerT_606-T1
Couldn't classify 66844, 67038
Sorry, prediction GeneMark_model.749_t fails validation.
(GTG)	 AG	66844-67038	GT	GAG
(CGG)	 AG	67469-67481	GT	CTG
(GAG)	 AG	67707-67816	GT	AAG
(GTG)	 AG	68138-68323	GT	GGG
(GCC)	 AG	68369-68451	GT	AAG
(ATT)	 AG	69619-69903	AG	AGA
-recovered GeneMark_model.749_t, terminal, 69619, 69903
-recovered GeneMark_model.749_t, internal, 66844, 67038
-recovered GeneMark_model.749_t, internal, 67469, 67481
-recovered GeneMark_model.749_t, internal, 67707, 67816
-recovered GeneMark_model.749_t, internal, 68138, 68323
-recovered GeneMark_model.749_t, internal, 68369, 68451
Valid prediction for Augustus_model.g457.t1
Valid prediction for GlimmerHMM_glimmerT_618-T1
Valid prediction for snap_scaffold_1-snap.766-T1
Valid prediction for snap_scaffold_1-snap.760-T1
Valid prediction for GeneMark_model.732_t
Valid prediction for GlimmerHMM_glimmerT_603-T1
Valid prediction for GlimmerHMM_glimmerT_615-T1
Valid prediction for GeneMark_model.759_t
Valid prediction for GeneMark_model.776_t
Valid prediction for GlimmerHMM_glimmerT_602-T1
Valid prediction for snap_scaffold_1-snap.762-T1
Valid prediction for GeneMark_model.758_t
Valid prediction for Augustus_model.g455.t1
Valid prediction for snap_scaffold_1-snap.751-T1
Valid prediction for snap_scaffold_1-snap.781-T1
Couldn't classify 80271, 80404
Sorry, prediction pasa_asmbl_1692.p1 fails validation.
(CAG)	 CC	80271-80404	GT	AGG
(GCT)	 AG	80928-81124	GT	AGG
(CCT)	 AG	81866-82053	GT	TTG
(CAA)	 AG	82329-82421	TG	GAT
-recovered pasa_asmbl_1692.p1, terminal, 82329, 82421
-recovered pasa_asmbl_1692.p1, internal, 80928, 81124
-recovered pasa_asmbl_1692.p1, internal, 81866, 82053
Valid prediction for GeneMark_model.743_t
Valid prediction for GlimmerHMM_glimmerT_601-T1
Valid prediction for GlimmerHMM_glimmerT_596-T1
Valid prediction for GlimmerHMM_glimmerT_595-T1
Valid prediction for GlimmerHMM_glimmerT_599-T1
Valid prediction for Augustus_model.g464.t1
Valid prediction for snap_scaffold_1-snap.768-T1
Valid prediction for GeneMark_model.777_t
Valid prediction for GeneMark_model.750_t
Valid prediction for GeneMark_model.767_t
Valid prediction for GeneMark_model.733_t
Valid prediction for GeneMark_model.756_t
Valid prediction for snap_scaffold_1-snap.753-T1
Valid prediction for snap_scaffold_1-snap.785-T1
Valid prediction for GlimmerHMM_glimmerT_605-T1
Valid prediction for snap_scaffold_1-snap.782-T1
Valid prediction for snap_scaffold_1-snap.776-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 GlimmerHMM_glimmerT_614-T1
Valid prediction for Augustus_model.g468.t1
Valid prediction for GlimmerHMM_glimmerT_597-T1
Valid prediction for GeneMark_model.755_t
Valid prediction for GeneMark_model.731_t
Valid prediction for GeneMark_model.753_t
Valid prediction for GlimmerHMM_glimmerT_600-T1
Valid prediction for GeneMark_model.738_t
Valid prediction for GeneMark_model.763_t
Valid prediction for snap_scaffold_1-snap.780-T1
Valid prediction for GeneMark_model.740_t
Valid prediction for GeneMark_model.730_t
Valid prediction for GeneMark_model.734_t
Valid prediction for GeneMark_model.762_t
Valid prediction for snap_scaffold_1-snap.774-T1
Valid prediction for GlimmerHMM_glimmerT_598-T1
Valid prediction for GeneMark_model.773_t
Valid prediction for GeneMark_model.744_t
Valid prediction for GeneMark_model.741_t
Valid prediction for snap_scaffold_1-snap.771-T1
Valid prediction for GeneMark_model.765_t
Valid prediction for GeneMark_model.751_t
Valid prediction for GeneMark_model.742_t
Valid prediction for Augustus_model.g469.t1
Valid prediction for GlimmerHMM_glimmerT_617-T1
Valid prediction for snap_scaffold_1-snap.783-T1
Valid prediction for Augustus_model.g465.t1
Valid prediction for snap_scaffold_1-snap.752-T1
Valid prediction for GeneMark_model.737_t
Couldn't classify 176421, 176562
Sorry, prediction pasa_asmbl_234.p1 fails validation.
(ATG)	 CC	174771-174795	GT	TGG
(TCC)	 AG	175011-175152	GT	GTG
(AAT)	 AG	175377-175501	GT	ATG
(TGT)	 AG	175991-176122	GT	CGG
(CTG)	 AG	176246-176294	GT	AGG
(GTC)	 AG	176421-176562	CC	GGC
-recovered pasa_asmbl_234.p1, initial, 174771, 174795
-recovered pasa_asmbl_234.p1, internal, 175011, 175152
-recovered pasa_asmbl_234.p1, internal, 175377, 175501
-recovered pasa_asmbl_234.p1, internal, 175991, 176122
-recovered pasa_asmbl_234.p1, internal, 176246, 176294
Valid prediction for snap_scaffold_1-snap.757-T1
Couldn't classify 142914, 143027
Couldn't classify 146002, 146074
Sorry, prediction pasa_asmbl_236.p1 fails validation.
(GGC)	 GC	142914-143027	GT	TGG
(AAT)	 AG	143266-143355	GT	AGG
(GCA)	 AG	145601-145782	GT	AGG
(AGG)	 AG	146002-146074	AG	TCA
-recovered pasa_asmbl_236.p1, internal, 143266, 143355
-recovered pasa_asmbl_236.p1, internal, 145601, 145782
Valid prediction for snap_scaffold_1-snap.756-T1
Valid prediction for GeneMark_model.760_t
Valid prediction for Augustus_model.g470.t1
Valid prediction for snap_scaffold_1-snap.784-T1
Valid prediction for GeneMark_model.735_t
Valid prediction for GlimmerHMM_glimmerT_608-T1
Valid prediction for GlimmerHMM_glimmerT_604-T1
Valid prediction for GeneMark_model.729_t
Valid prediction for GeneMark_model.774_t
Valid prediction for GeneMark_model.757_t
Valid prediction for Augustus_model.g456.t1
Valid prediction for Augustus_model.g458.t1
Valid prediction for snap_scaffold_1-snap.778-T1
Valid prediction for snap_scaffold_1-snap.761-T1
Valid prediction for snap_scaffold_1-snap.769-T1
Valid prediction for GeneMark_model.747_t
Valid prediction for GeneMark_model.771_t
Valid prediction for snap_scaffold_1-snap.773-T1
Valid prediction for GlimmerHMM_glimmerT_609-T1
Valid prediction for snap_scaffold_1-snap.777-T1
Couldn't classify 146138, 146252
Sorry, prediction pasa_asmbl_235.p2 fails validation.
(CCC)	 CG	146138-146252	GT	AGG
(GCA)	 AG	148043-148128	GT	ATG
(GTG)	 AG	148442-148625	GT	CGG
(ACT)	 AG	149579-149647	GT	AGG
(AAG)	 AG	149850-150040	GT	AGG
(TGT)	 AG	150187-150507	GA	AGG
-recovered pasa_asmbl_235.p2, terminal, 150187, 150507
-recovered pasa_asmbl_235.p2, internal, 148043, 148128
-recovered pasa_asmbl_235.p2, internal, 148442, 148625
-recovered pasa_asmbl_235.p2, internal, 149579, 149647
-recovered pasa_asmbl_235.p2, internal, 149850, 150040
Valid prediction for GeneMark_model.775_t
Valid prediction for Augustus_model.g462.t1
Valid prediction for snap_scaffold_1-snap.775-T1
Valid prediction for GeneMark_model.778_t
Valid prediction for GlimmerHMM_glimmerT_612-T1
Valid prediction for Augustus_model.g466.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 45225, rend_intergenic: 29963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83111, rend_intergenic: 80012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98830, rend_intergenic: 91629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131914, rend_intergenic: 130016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177796
-exon list size: 616


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 45225, rend_intergenic: 29963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83111, rend_intergenic: 80012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98830, rend_intergenic: 91629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131914, rend_intergenic: 130016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 149768 - 177796
-exon list size: 27


building trellis

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58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 149768 - 166407
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 155526 - 166407
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 166414 - 177796
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 166652 - 177796
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support