-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_17536003-17727886

-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: +)Couldn't classify 153667, 154029
Sorry, prediction pasa_asmbl_3793.p1 fails validation.
(CAG)	 AC	153667-154029	GC	AAG
Valid prediction for snap_scaffold_10-snap.3563-T1
Valid prediction for snap_scaffold_10-snap.3558-T1
Valid prediction for snap_scaffold_10-snap.3589-T1
Valid prediction for snap_scaffold_10-snap.3560-T1
Valid prediction for GlimmerHMM_glimmerT_26276-T1
Valid prediction for snap_scaffold_10-snap.3587-T1
Valid prediction for GlimmerHMM_glimmerT_26274-T1
Couldn't classify 89585, 89646
Sorry, prediction pasa_asmbl_3838.p1 fails validation.
(CAA)	 TC	89585-89646	GT	CTG
(CTT)	 AG	89712-89780	GT	GGG
(GTA)	 AG	89890-90023	GT	CTG
(GTT)	 AG	90598-90749	GC	GAG
-recovered pasa_asmbl_3838.p1, terminal, 90598, 90749
-recovered pasa_asmbl_3838.p1, internal, 89712, 89780
-recovered pasa_asmbl_3838.p1, internal, 89890, 90023
-recovered pasa_asmbl_3838.p1, internal, 90598, 90749
Valid prediction for GlimmerHMM_glimmerT_26270-T1
Valid prediction for snap_scaffold_10-snap.3575-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.3574-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.3564-T1
Valid prediction for snap_scaffold_10-snap.3566-T1
Valid prediction for snap_scaffold_10-snap.3572-T1
Valid prediction for snap_scaffold_10-snap.3580-T1
Valid prediction for CodingQuarry_transcript_5698-T1
Valid prediction for snap_scaffold_10-snap.3586-T1
Valid prediction for GlimmerHMM_glimmerT_26282-T1
Valid prediction for snap_scaffold_10-snap.3579-T1
Couldn't classify 164726, 165466
Sorry, prediction pasa_asmbl_5135.p1 fails validation.
(ATG)	 CC	164726-165466	AT	GTA
Valid prediction for snap_scaffold_10-snap.3554-T1
Valid prediction for GlimmerHMM_glimmerT_26284-T1
Valid prediction for GlimmerHMM_glimmerT_26267-T1
Valid prediction for snap_scaffold_10-snap.3584-T1
Valid prediction for snap_scaffold_10-snap.3583-T1
Valid prediction for snap_scaffold_10-snap.3581-T1
Valid prediction for snap_scaffold_10-snap.3570-T1
Valid prediction for snap_scaffold_10-snap.3561-T1
Couldn't classify 44357, 44599
Sorry, prediction pasa_asmbl_3782.p1 fails validation.
(ATG)	 GC	44190-44225	GT	AGG
(GCA)	 AG	44357-44599	GA	GTG
-recovered pasa_asmbl_3782.p1, initial, 44190, 44225
Valid prediction for GlimmerHMM_glimmerT_26285-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_26269-T1
Valid prediction for snap_scaffold_10-snap.3562-T1
Couldn't classify 96544, 96691
Couldn't classify 99548, 99572
Sorry, prediction pasa_asmbl_5116.p1 fails validation.
(GCG)	 TG	96544-96691	GT	AGG
(GCA)	 AG	96877-96978	GT	AGG
(ACA)	 AG	97552-97732	GT	GGG
(CTT)	 AG	99548-99572	GG	TAG
-recovered pasa_asmbl_5116.p1, internal, 96877, 96978
-recovered pasa_asmbl_5116.p1, internal, 97552, 97732
Valid prediction for GlimmerHMM_glimmerT_26271-T1
Valid prediction for snap_scaffold_10-snap.3567-T1
Valid prediction for snap_scaffold_10-snap.3559-T1
Valid prediction for snap_scaffold_10-snap.3555-T1
Valid prediction for GlimmerHMM_glimmerT_26277-T1
Valid prediction for snap_scaffold_10-snap.3585-T1
Couldn't classify 71258, 71346
Couldn't classify 71391, 71500
Sorry, prediction CodingQuarry_transcript_5695-T1 fails validation.
(ATG)	 GG	71258-71346	GA	AGG
(AGA)	 GG	71391-71500	AG	AGA
(GTC)	 AG	71545-71639	TC	AAT
-recovered CodingQuarry_transcript_5695-T1, terminal, 71545, 71639
Valid prediction for GlimmerHMM_glimmerT_26265-T1
Couldn't classify 46645, 46762
Couldn't classify 49489, 49736
Sorry, prediction pasa_asmbl_5211.p1 fails validation.
(GGC)	 CA	46645-46762	GT	AGG
(GCA)	 AG	49489-49736	CA	ACC
Valid prediction for snap_scaffold_10-snap.3573-T1
Valid prediction for snap_scaffold_10-snap.3569-T1
Valid prediction for snap_scaffold_10-snap.3571-T1
Valid prediction for snap_scaffold_10-snap.3556-T1
Valid prediction for snap_scaffold_10-snap.3568-T1
Valid prediction for snap_scaffold_10-snap.3582-T1
Valid prediction for GlimmerHMM_glimmerT_26273-T1
Couldn't classify 71160, 71346
Couldn't classify 71490, 71617
Sorry, prediction CodingQuarry_transcript_5696-T1 fails validation.
(ATG)	 AA	71160-71346	GA	AGG
(AGA)	 GG	71490-71617	CA	GAC
Valid prediction for snap_scaffold_10-snap.3578-T1
Valid prediction for GlimmerHMM_glimmerT_26279-T1
Couldn't classify 86682, 86748
Sorry, prediction pasa_asmbl_5064.p1 fails validation.
(GGT)	 CA	86682-86748	GT	AGG
(AGG)	 AG	87771-87851	GT	TGG
(GTC)	 AG	88178-88246	GT	AGG
(TGA)	 AG	89128-89228	GT	AGG
(AGC)	 AG	89489-90355	CG	AGC
-recovered pasa_asmbl_5064.p1, terminal, 89489, 90355
-recovered pasa_asmbl_5064.p1, internal, 87771, 87851
-recovered pasa_asmbl_5064.p1, internal, 88178, 88246
-recovered pasa_asmbl_5064.p1, internal, 89128, 89228
Valid prediction for GlimmerHMM_glimmerT_26286-T1
Valid prediction for GlimmerHMM_glimmerT_26266-T1
Valid prediction for snap_scaffold_10-snap.3565-T1
Valid prediction for GlimmerHMM_glimmerT_26275-T1
Valid prediction for GlimmerHMM_glimmerT_26281-T1
Valid prediction for snap_scaffold_10-snap.3577-T1
Valid prediction for GlimmerHMM_glimmerT_26278-T1
Valid prediction for GlimmerHMM_glimmerT_26272-T1
Valid prediction for snap_scaffold_10-snap.3557-T1
Valid prediction for snap_scaffold_10-snap.3553-T1
Valid prediction for GlimmerHMM_glimmerT_26280-T1
Valid prediction for GlimmerHMM_glimmerT_26283-T1
Valid prediction for GlimmerHMM_glimmerT_26268-T1
Valid prediction for snap_scaffold_10-snap.3588-T1
Valid prediction for snap_scaffold_10-snap.3576-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15318, rend_intergenic: 14908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28106, rend_intergenic: 21280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43856, rend_intergenic: 28990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45640, rend_intergenic: 44428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52030, rend_intergenic: 45692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66921, rend_intergenic: 57236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69872, rend_intergenic: 68729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73849, rend_intergenic: 70086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75768, rend_intergenic: 75015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100205, rend_intergenic: 92260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123665, rend_intergenic: 101591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145570, rend_intergenic: 136602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155299, rend_intergenic: 149228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166794, rend_intergenic: 164769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175779, rend_intergenic: 168230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186881, rend_intergenic: 179380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191884
-exon list size: 321


building trellis

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27.6    
27.9    
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30.3    
30.7    
31.0    
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31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.1    
34.4    
34.7    
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35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.2    
37.5    
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38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
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53.6    
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54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.7    
57.0    
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57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.8    
60.1    
60.4    
60.7    
61.0    
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61.6    
61.9    
62.2    
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63.8    
64.1    
64.4    
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65.0    
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65.6    
65.9    
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66.6    
66.9    
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67.8    
68.1    
68.4    
68.7    
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69.3    
69.7    
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70.6    
70.9    
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74.6    
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76.8    
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78.6    
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79.6    
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80.8    
81.1    
81.4    
81.7    
82.0    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 15318, rend_intergenic: 14908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28106, rend_intergenic: 21280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43856, rend_intergenic: 28990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45640, rend_intergenic: 44428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52030, rend_intergenic: 45692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66921, rend_intergenic: 57236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69872, rend_intergenic: 68729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73849, rend_intergenic: 70086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75768, rend_intergenic: 75015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100205, rend_intergenic: 92260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123665, rend_intergenic: 101591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145570, rend_intergenic: 136602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155299, rend_intergenic: 149228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166794, rend_intergenic: 164769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175779, rend_intergenic: 168230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186881, rend_intergenic: 179380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10901
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 1 - 10392
-exon list size: 1


building trellis

33.3    
66.7    
-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