-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_11688041-11872605

-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_21-snap.2540-T1
Valid prediction for snap_scaffold_21-snap.2523-T1
Valid prediction for GlimmerHMM_glimmerT_48691-T1
Valid prediction for snap_scaffold_21-snap.2549-T1
Valid prediction for GlimmerHMM_glimmerT_48674-T1
Valid prediction for Augustus_model.g32523.t1
Valid prediction for Augustus_model.g32522.t1
Valid prediction for GlimmerHMM_glimmerT_48681-T1
Valid prediction for snap_scaffold_21-snap.2511-T1
Valid prediction for snap_scaffold_21-snap.2555-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_48677-T1
Valid prediction for GlimmerHMM_glimmerT_48676-T1
Valid prediction for snap_scaffold_21-snap.2535-T1
Valid prediction for Augustus_model.g32513.t1
Valid prediction for Augustus_model.g32518.t1
Valid prediction for GlimmerHMM_glimmerT_48685-T1
Couldn't classify 17504, 17569
Couldn't classify 26357, 26469
Sorry, prediction pasa_asmbl_29022.p1 fails validation.
(GTC)	 AG	17504-17569	GT	AGG
(GTT)	 AG	17683-17754	GT	CTG
(ACT)	 AG	18409-18474	GT	AGG
(GTG)	 AG	19830-19917	GT	GGG
(CTA)	 AG	20055-20161	GT	AGG
(GCG)	 AG	20259-20435	GT	AGG
(GTG)	 AG	20747-20957	GT	TGG
(CGG)	 AG	21076-21218	GT	AGG
(ACC)	 AG	22671-22771	GT	AGG
(GAC)	 AG	23051-23114	GT	AGG
(TCA)	 AG	23240-23384	GT	GGG
(GTG)	 AG	26357-26469	CT	CGC
-recovered pasa_asmbl_29022.p1, internal, 17504, 17569
-recovered pasa_asmbl_29022.p1, internal, 17683, 17754
-recovered pasa_asmbl_29022.p1, internal, 18409, 18474
-recovered pasa_asmbl_29022.p1, internal, 19830, 19917
-recovered pasa_asmbl_29022.p1, internal, 20055, 20161
-recovered pasa_asmbl_29022.p1, internal, 20259, 20435
-recovered pasa_asmbl_29022.p1, internal, 20747, 20957
-recovered pasa_asmbl_29022.p1, internal, 21076, 21218
-recovered pasa_asmbl_29022.p1, internal, 22671, 22771
-recovered pasa_asmbl_29022.p1, internal, 23051, 23114
-recovered pasa_asmbl_29022.p1, internal, 23240, 23384
Couldn't classify 16528, 16941
Sorry, prediction pasa_asmbl_28936.p2 fails validation.
(ATG)	 TC	16528-16941	AG	CCA
Valid prediction for snap_scaffold_21-snap.2553-T1
Valid prediction for GlimmerHMM_glimmerT_48670-T1
Valid prediction for GlimmerHMM_glimmerT_48686-T1
Valid prediction for GlimmerHMM_glimmerT_48682-T1
Valid prediction for GlimmerHMM_glimmerT_48695-T1
Valid prediction for snap_scaffold_21-snap.2527-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_48679-T1
Valid prediction for Augustus_model.g32520.t1
Couldn't classify 27134, 27225
Couldn't classify 32610, 32689
Sorry, prediction pasa_asmbl_28937.p1 fails validation.
(GGG)	 CA	27134-27225	GT	AGG
(GGC)	 AG	27944-28136	GT	AGG
(GAG)	 AG	29005-29091	GT	TGG
(GTG)	 AG	30750-30888	GT	AGG
(GTC)	 AG	31446-31605	GT	AAG
(GAA)	 AG	31731-31917	GT	TGG
(GAT)	 AG	32172-32394	GT	AGG
(GTT)	 AG	32610-32689	CG	GAC
-recovered pasa_asmbl_28937.p1, internal, 27944, 28136
-recovered pasa_asmbl_28937.p1, internal, 29005, 29091
-recovered pasa_asmbl_28937.p1, internal, 30750, 30888
-recovered pasa_asmbl_28937.p1, internal, 31446, 31605
-recovered pasa_asmbl_28937.p1, internal, 31731, 31917
-recovered pasa_asmbl_28937.p1, internal, 32172, 32394
Valid prediction for snap_scaffold_21-snap.2534-T1
Valid prediction for GlimmerHMM_glimmerT_48675-T1
Valid prediction for snap_scaffold_21-snap.2537-T1
Valid prediction for snap_scaffold_21-snap.2531-T1
Valid prediction for GlimmerHMM_glimmerT_48697-T1
Valid prediction for snap_scaffold_21-snap.2513-T1
Couldn't classify 54143, 54259
Couldn't classify 57905, 58090
Sorry, prediction pasa_asmbl_28969.p1 fails validation.
(CTG)	 AG	54143-54259	GT	AGG
(TCT)	 AG	55588-55671	GT	AGG
(CTG)	 AG	57351-57488	GT	AGG
(AGT)	 AG	57905-58090	GT	TGG
-recovered pasa_asmbl_28969.p1, internal, 54143, 54259
-recovered pasa_asmbl_28969.p1, internal, 55588, 55671
-recovered pasa_asmbl_28969.p1, internal, 57351, 57488
-recovered pasa_asmbl_28969.p1, internal, 57905, 58090
Valid prediction for Augustus_model.g32515.t1
Valid prediction for GlimmerHMM_glimmerT_48688-T1
Valid prediction for Augustus_model.g32511.t1
Valid prediction for HiQ_model.g32512.t1
Valid prediction for snap_scaffold_21-snap.2532-T1
Valid prediction for snap_scaffold_21-snap.2551-T1
Valid prediction for snap_scaffold_21-snap.2520-T1
Couldn't classify 61333, 61454
Sorry, prediction pasa_asmbl_28938.p1 fails validation.
(GGA)	 GC	61333-61454	GT	AGG
(ACA)	 AG	61785-63147	AG	AGA
-recovered pasa_asmbl_28938.p1, terminal, 61785, 63147
Valid prediction for GlimmerHMM_glimmerT_48690-T1
Valid prediction for snap_scaffold_21-snap.2514-T1
Valid prediction for snap_scaffold_21-snap.2544-T1
Valid prediction for GlimmerHMM_glimmerT_48672-T1
Valid prediction for Augustus_model.g32516.t1
Valid prediction for snap_scaffold_21-snap.2529-T1
Valid prediction for GlimmerHMM_glimmerT_48680-T1
Valid prediction for snap_scaffold_21-snap.2546-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 snap_scaffold_21-snap.2545-T1
Valid prediction for GlimmerHMM_glimmerT_48693-T1
Valid prediction for snap_scaffold_21-snap.2547-T1
Valid prediction for GlimmerHMM_glimmerT_48692-T1
Valid prediction for GlimmerHMM_glimmerT_48689-T1
Valid prediction for snap_scaffold_21-snap.2533-T1
Valid prediction for snap_scaffold_21-snap.2550-T1
Valid prediction for snap_scaffold_21-snap.2525-T1
Valid prediction for snap_scaffold_21-snap.2548-T1
Valid prediction for Augustus_model.g32519.t1
Valid prediction for snap_scaffold_21-snap.2512-T1
Valid prediction for snap_scaffold_21-snap.2541-T1
Valid prediction for snap_scaffold_21-snap.2542-T1
Valid prediction for Augustus_model.g32521.t1
Valid prediction for snap_scaffold_21-snap.2516-T1
Valid prediction for snap_scaffold_21-snap.2518-T1
Valid prediction for snap_scaffold_21-snap.2515-T1
Valid prediction for snap_scaffold_21-snap.2530-T1
Valid prediction for GlimmerHMM_glimmerT_48696-T1
Valid prediction for GlimmerHMM_glimmerT_48673-T1
Valid prediction for GlimmerHMM_glimmerT_48683-T1
Valid prediction for snap_scaffold_21-snap.2526-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.2521-T1
Valid prediction for GlimmerHMM_glimmerT_48671-T1
Valid prediction for snap_scaffold_21-snap.2519-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_48678-T1
Valid prediction for snap_scaffold_21-snap.2536-T1
Valid prediction for snap_scaffold_21-snap.2522-T1
Valid prediction for snap_scaffold_21-snap.2554-T1
Valid prediction for snap_scaffold_21-snap.2538-T1
Valid prediction for snap_scaffold_21-snap.2552-T1
Valid prediction for GlimmerHMM_glimmerT_48694-T1
Valid prediction for snap_scaffold_21-snap.2543-T1
Valid prediction for snap_scaffold_21-snap.2556-T1
Valid prediction for snap_scaffold_21-snap.2524-T1
Valid prediction for Augustus_model.g32517.t1
Valid prediction for GlimmerHMM_glimmerT_48687-T1
Valid prediction for Augustus_model.g32514.t1
Valid prediction for snap_scaffold_21-snap.2539-T1
Valid prediction for snap_scaffold_21-snap.2517-T1
Valid prediction for GlimmerHMM_glimmerT_48684-T1
Valid prediction for snap_scaffold_21-snap.2528-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 162102, rend_intergenic: 162099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7338, rend_intergenic: 5402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18646, rend_intergenic: 7529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33698, rend_intergenic: 19010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34195, rend_intergenic: 33755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43896, rend_intergenic: 42031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63147, rend_intergenic: 44115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69670, rend_intergenic: 63556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71545, rend_intergenic: 70044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77967, rend_intergenic: 71607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80791, rend_intergenic: 78000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82316, rend_intergenic: 80816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91301, rend_intergenic: 87627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96658, rend_intergenic: 91332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102298, rend_intergenic: 97072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108627, rend_intergenic: 104077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111386, rend_intergenic: 108872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113190, rend_intergenic: 112585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126355, rend_intergenic: 114697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132803, rend_intergenic: 127444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142334, rend_intergenic: 139015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148789, rend_intergenic: 142820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152771, rend_intergenic: 149421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153939, rend_intergenic: 153841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158843, rend_intergenic: 158223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161780, rend_intergenic: 159560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162943, rend_intergenic: 162099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171063, rend_intergenic: 167899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178736, rend_intergenic: 171264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184565
-exon list size: 400


building trellis

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24.4    
24.6    
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25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.2    
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63.9    
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70.4    
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75.4    
75.6    
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77.4    
77.6    
77.9    
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81.3    
81.6    
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88.6    
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89.6    
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90.5    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
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95.0    
95.3    
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96.0    
96.3    
96.5    
96.8    
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97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 28 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 162102, rend_intergenic: 162099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7338, rend_intergenic: 5402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18646, rend_intergenic: 7529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33698, rend_intergenic: 19010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34195, rend_intergenic: 33755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43896, rend_intergenic: 42031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63147, rend_intergenic: 44115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69670, rend_intergenic: 63556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71545, rend_intergenic: 70044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77967, rend_intergenic: 71607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80791, rend_intergenic: 78000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82316, rend_intergenic: 80816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91301, rend_intergenic: 87627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96658, rend_intergenic: 91332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102298, rend_intergenic: 97072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108627, rend_intergenic: 104077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111386, rend_intergenic: 108872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113190, rend_intergenic: 112585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126355, rend_intergenic: 114697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132803, rend_intergenic: 127444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142334, rend_intergenic: 139015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148789, rend_intergenic: 142820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152771, rend_intergenic: 149421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153939, rend_intergenic: 153841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158843, rend_intergenic: 158223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161780, rend_intergenic: 159560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162943, rend_intergenic: 162099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171063, rend_intergenic: 167899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178736, rend_intergenic: 171264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support