-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_13363620-13548495

-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 HiQ_model.g5105.t1
Valid prediction for snap_scaffold_3-snap.2606-T1
Valid prediction for Augustus_model.g5108.t1
Valid prediction for snap_scaffold_3-snap.2605-T1
Valid prediction for snap_scaffold_3-snap.2608-T1
Couldn't classify 94735, 94830
Couldn't classify 101184, 101297
Sorry, prediction pasa_asmbl_40399.p1 fails validation.
(GCT)	 AT	94735-94830	GT	AGG
(GTC)	 AG	95130-95243	GT	AGG
(GTG)	 AG	95324-95418	GT	ATG
(AGC)	 AG	95707-95818	GT	AGG
(TGG)	 AG	95935-96033	GT	AGG
(GAT)	 AG	96123-96179	GT	CTG
(GAA)	 AG	96291-96391	GT	AGG
(ACG)	 AG	96681-96717	GT	AGG
(GCA)	 AG	98045-98143	GT	AGG
(CTG)	 AG	98246-98296	GT	CGG
(GGG)	 AG	98379-98465	GT	GGG
(CAA)	 AG	98994-99110	GT	AAG
(TTG)	 AG	99233-99295	GT	AGG
(GCT)	 AG	99421-99494	GT	AGG
(ACT)	 AG	99593-99674	GT	GAG
(GAG)	 AG	99813-99887	GT	AGG
(GAG)	 AG	100002-100073	GT	TGG
(GCA)	 AG	100168-100276	GT	AGG
(TTT)	 AG	100402-100484	GT	AGG
(GTG)	 AG	100568-100605	GT	CAG
(GGC)	 AG	100720-100804	GT	AGG
(ATG)	 AG	101184-101297	GT	AGG
-recovered pasa_asmbl_40399.p1, initial, 101184, 101297
add_exon() Sorry, pasa_asmbl_40399.p1 99421-99494-terminal-2 is invalid.
-recovered pasa_asmbl_40399.p1, terminal, 99421, 99494
-recovered pasa_asmbl_40399.p1, internal, 95130, 95243
-recovered pasa_asmbl_40399.p1, internal, 95324, 95418
-recovered pasa_asmbl_40399.p1, internal, 95707, 95818
-recovered pasa_asmbl_40399.p1, internal, 95935, 96033
-recovered pasa_asmbl_40399.p1, internal, 96123, 96179
-recovered pasa_asmbl_40399.p1, internal, 96291, 96391
-recovered pasa_asmbl_40399.p1, internal, 96681, 96717
-recovered pasa_asmbl_40399.p1, internal, 98045, 98143
-recovered pasa_asmbl_40399.p1, internal, 98246, 98296
-recovered pasa_asmbl_40399.p1, internal, 98379, 98465
-recovered pasa_asmbl_40399.p1, internal, 98994, 99110
-recovered pasa_asmbl_40399.p1, internal, 99233, 99295
-recovered pasa_asmbl_40399.p1, internal, 99421, 99494
-recovered pasa_asmbl_40399.p1, internal, 99593, 99674
-recovered pasa_asmbl_40399.p1, internal, 99813, 99887
-recovered pasa_asmbl_40399.p1, internal, 100002, 100073
-recovered pasa_asmbl_40399.p1, internal, 100168, 100276
-recovered pasa_asmbl_40399.p1, internal, 100402, 100484
-recovered pasa_asmbl_40399.p1, internal, 100568, 100605
-recovered pasa_asmbl_40399.p1, internal, 100720, 100804
-recovered pasa_asmbl_40399.p1, internal, 101184, 101297
Valid prediction for GeneMark_model.12751_t
Valid prediction for GlimmerHMM_glimmerT_7753-T1
Valid prediction for GeneMark_model.12764_t
Valid prediction for GeneMark_model.12754_t
Valid prediction for Augustus_model.g5113.t1
Valid prediction for Augustus_model.g5099.t1
Valid prediction for GeneMark_model.12758_t
Valid prediction for snap_scaffold_3-snap.2597-T1
Valid prediction for GlimmerHMM_glimmerT_7754-T1
Valid prediction for snap_scaffold_3-snap.2593-T1
Valid prediction for GlimmerHMM_glimmerT_7750-T1
Valid prediction for Augustus_model.g5101.t1
Valid prediction for snap_scaffold_3-snap.2598-T1
Valid prediction for Augustus_model.g5104.t1
Valid prediction for Augustus_model.g5100.t1
Valid prediction for snap_scaffold_3-snap.2584-T1
Valid prediction for GeneMark_model.12749_t
Valid prediction for Augustus_model.g5102.t1
Valid prediction for GeneMark_model.12766_t
Valid prediction for GeneMark_model.12757_t
Valid prediction for GeneMark_model.12765_t
Valid prediction for snap_scaffold_3-snap.2587-T1
Valid prediction for snap_scaffold_3-snap.2592-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g5109.t1
Valid prediction for GlimmerHMM_glimmerT_7746-T1
Valid prediction for GlimmerHMM_glimmerT_7755-T1
Valid prediction for GlimmerHMM_glimmerT_7749-T1
Valid prediction for GeneMark_model.12755_t
Valid prediction for Augustus_model.g5103.t1
Valid prediction for GlimmerHMM_glimmerT_7760-T1
Valid prediction for GeneMark_model.12759_t
Valid prediction for GlimmerHMM_glimmerT_7747-T1
Valid prediction for GlimmerHMM_glimmerT_7756-T1
Valid prediction for GlimmerHMM_glimmerT_7761-T1
Valid prediction for GlimmerHMM_glimmerT_7751-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.g5097.t1
Valid prediction for snap_scaffold_3-snap.2607-T1
Valid prediction for GeneMark_model.12771_t
Valid prediction for HiQ_model.g5117.t1
Valid prediction for snap_scaffold_3-snap.2594-T1
Valid prediction for snap_scaffold_3-snap.2590-T1
Valid prediction for CodingQuarry_transcript_46222-T1
Valid prediction for snap_scaffold_3-snap.2603-T1
Valid prediction for GlimmerHMM_glimmerT_7757-T1
Valid prediction for GlimmerHMM_glimmerT_7759-T1
Valid prediction for snap_scaffold_3-snap.2600-T1
Valid prediction for snap_scaffold_3-snap.2588-T1
Valid prediction for Augustus_model.g5115.t1
Couldn't classify 162271, 162275
Couldn't classify 165628, 165754
Sorry, prediction pasa_asmbl_39209.p1 fails validation.
(TCC)	 AG	162271-162275	GT	AAG
(AGT)	 AG	162570-162704	GT	ACG
(GAC)	 AG	165064-165186	GT	TCG
(TTT)	 AG	165628-165754	GC	CTG
-recovered pasa_asmbl_39209.p1, internal, 162271, 162275
-recovered pasa_asmbl_39209.p1, internal, 162570, 162704
-recovered pasa_asmbl_39209.p1, internal, 165064, 165186
-recovered pasa_asmbl_39209.p1, internal, 165628, 165754
Valid prediction for CodingQuarry_transcript_46216-T1
Valid prediction for GeneMark_model.12763_t
Valid prediction for snap_scaffold_3-snap.2604-T1
Valid prediction for snap_scaffold_3-snap.2602-T1
Valid prediction for CodingQuarry_transcript_46223-T1
Valid prediction for GlimmerHMM_glimmerT_7758-T1
Valid prediction for GeneMark_model.12748_t
Valid prediction for Augustus_model.g5098.t1
Valid prediction for snap_scaffold_3-snap.2589-T1
Valid prediction for Augustus_model.g5112.t1
Valid prediction for Augustus_model.g5107.t1
Valid prediction for snap_scaffold_3-snap.2595-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.12752_t
Valid prediction for Augustus_model.g5106.t1
Valid prediction for CodingQuarry_transcript_46220-T1
Valid prediction for Augustus_model.g5095.t1
Valid prediction for GlimmerHMM_glimmerT_7762-T1
Valid prediction for GeneMark_model.12769_t
Valid prediction for pasa_asmbl_39213.p1
Valid prediction for snap_scaffold_3-snap.2596-T1
Valid prediction for CodingQuarry_transcript_46221-T1
Valid prediction for GeneMark_model.12762_t
Couldn't classify 26262, 26381
Sorry, prediction pasa_asmbl_39223.p1 fails validation.
(TAC)	 CA	26262-26381	GT	ATG
(CCA)	 AG	27055-27126	GT	AGG
(GAC)	 AG	27333-27447	GT	AGG
(GTC)	 AG	27528-27610	GC	GAG
-recovered pasa_asmbl_39223.p1, terminal, 27528, 27610
-recovered pasa_asmbl_39223.p1, internal, 27055, 27126
-recovered pasa_asmbl_39223.p1, internal, 27333, 27447
-recovered pasa_asmbl_39223.p1, internal, 27528, 27610
Valid prediction for Augustus_model.g5114.t1
Valid prediction for GeneMark_model.12767_t
Valid prediction for GeneMark_model.12761_t
Valid prediction for snap_scaffold_3-snap.2585-T1
Valid prediction for Augustus_model.g5111.t1
Valid prediction for GlimmerHMM_glimmerT_7744-T1
Couldn't classify 169464, 169574
Couldn't classify 170383, 170496
Sorry, prediction pasa_asmbl_39208.p1 fails validation.
(GAA)	 TT	169464-169574	GT	AGG
(ATT)	 AG	169968-170042	GT	AGG
(GCC)	 AG	170162-170293	GT	CGG
(GTG)	 AG	170383-170496	GT	AGG
-recovered pasa_asmbl_39208.p1, internal, 169968, 170042
-recovered pasa_asmbl_39208.p1, internal, 170162, 170293
-recovered pasa_asmbl_39208.p1, internal, 170383, 170496
Valid prediction for GlimmerHMM_glimmerT_7745-T1
Couldn't classify 59954, 60013
Couldn't classify 61495, 61938
Sorry, prediction pasa_asmbl_39221.p1 fails validation.
(GAG)	 AG	59954-60013	GT	AGG
(ATC)	 AG	60226-60357	GT	AGG
(CTG)	 AG	60469-60681	GT	TGG
(ATA)	 AG	60838-60921	GT	AGG
(AAT)	 AG	61082-61223	GT	TGG
(TTT)	 AG	61314-61408	GT	AGG
(ACT)	 AG	61495-61938	GA	GGG
-recovered pasa_asmbl_39221.p1, internal, 59954, 60013
-recovered pasa_asmbl_39221.p1, internal, 60226, 60357
-recovered pasa_asmbl_39221.p1, internal, 60469, 60681
-recovered pasa_asmbl_39221.p1, internal, 60838, 60921
-recovered pasa_asmbl_39221.p1, internal, 61082, 61223
-recovered pasa_asmbl_39221.p1, internal, 61314, 61408
Valid prediction for GeneMark_model.12747_t
Valid prediction for GlimmerHMM_glimmerT_7752-T1
Couldn't classify 62221, 62805
Sorry, prediction pasa_asmbl_39220.p1 fails validation.
(GAG)	 AG	62221-62805	TG	ACT
Valid prediction for GlimmerHMM_glimmerT_7748-T1
Valid prediction for GlimmerHMM_glimmerT_7763-T1
Valid prediction for snap_scaffold_3-snap.2599-T1
Valid prediction for Augustus_model.g5096.t1
Valid prediction for GlimmerHMM_glimmerT_7765-T1
Valid prediction for CodingQuarry_transcript_46219-T1
Valid prediction for snap_scaffold_3-snap.2601-T1
Valid prediction for Augustus_model.g5094.t1
Valid prediction for Augustus_model.g5110.t1
Valid prediction for GeneMark_model.12750_t
Valid prediction for GlimmerHMM_glimmerT_7764-T1
Valid prediction for GeneMark_model.12760_t
Valid prediction for snap_scaffold_3-snap.2591-T1
Valid prediction for GeneMark_model.12753_t
Valid prediction for snap_scaffold_3-snap.2610-T1
Couldn't classify 95099, 95431
Sorry, prediction pasa_asmbl_39218.p1 fails validation.
(CCA)	 AC	95099-95431	CA	AGC
Valid prediction for snap_scaffold_3-snap.2586-T1
Valid prediction for snap_scaffold_3-snap.2609-T1
Valid prediction for GlimmerHMM_glimmerT_7742-T1
Valid prediction for GlimmerHMM_glimmerT_7743-T1
Valid prediction for GeneMark_model.12756_t
Valid prediction for Augustus_model.g5116.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28967, rend_intergenic: 27214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184876
-exon list size: 416


building trellis

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1.0    
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21.5    
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22.0    
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22.5    
22.7    
23.0    
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23.9    
24.2    
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24.6    
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25.1    
25.4    
25.6    
25.8    
26.1    
26.3    
26.6    
26.8    
27.0    
27.3    
27.5    
27.8    
28.0    
28.2    
28.5    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.3    
31.6    
31.8    
32.1    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.5    
54.8    
55.0    
55.3    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.4    
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62.9    
63.2    
63.4    
63.6    
63.9    
64.1    
64.4    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
67.9    
68.2    
68.4    
68.7    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.5    
71.8    
72.0    
72.2    
72.5    
72.7    
73.0    
73.2    
73.4    
73.7    
73.9    
74.2    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.0    
77.3    
77.5    
77.8    
78.0    
78.2    
78.5    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
84.7    
84.9    
85.2    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.1    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 28967, rend_intergenic: 27214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14380
-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
GOT 5prime partial gene.

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