-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_3763729-4020753

-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_7-snap.911-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_17232-T1
Valid prediction for CodingQuarry_transcript_57479-T1
Valid prediction for GlimmerHMM_glimmerT_17248-T1
Valid prediction for GlimmerHMM_glimmerT_17229-T1
Valid prediction for snap_scaffold_7-snap.928-T1
Valid prediction for CodingQuarry_transcript_57473-T1
Valid prediction for snap_scaffold_7-snap.918-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g11515.t1
Valid prediction for snap_scaffold_7-snap.933-T1
Couldn't classify 52430, 52498
Sorry, prediction pasa_asmbl_49703.p1 fails validation.
(TTC)	 GC	52430-52498	GT	GGG
(ATC)	 AG	53013-53115	GT	GGG
(AGG)	 AG	54192-54318	GT	AGG
(GAC)	 AG	54595-54658	CA	GAC
-recovered pasa_asmbl_49703.p1, terminal, 54595, 54658
-recovered pasa_asmbl_49703.p1, internal, 53013, 53115
-recovered pasa_asmbl_49703.p1, internal, 54192, 54318
Valid prediction for snap_scaffold_7-snap.900-T1
Valid prediction for Augustus_model.g11513.t1
Valid prediction for GlimmerHMM_glimmerT_17245-T1
Valid prediction for snap_scaffold_7-snap.920-T1
Valid prediction for snap_scaffold_7-snap.931-T1
Valid prediction for snap_scaffold_7-snap.898-T1
Valid prediction for HiQ_model.g11508.t1
Valid prediction for snap_scaffold_7-snap.926-T1
Valid prediction for Augustus_model.g11512.t1
Valid prediction for GlimmerHMM_glimmerT_17226-T1
Valid prediction for snap_scaffold_7-snap.927-T1
Valid prediction for GlimmerHMM_glimmerT_17227-T1
Valid prediction for snap_scaffold_7-snap.923-T1
Valid prediction for snap_scaffold_7-snap.913-T1
Valid prediction for snap_scaffold_7-snap.932-T1
Valid prediction for GlimmerHMM_glimmerT_17236-T1
Valid prediction for snap_scaffold_7-snap.921-T1
Couldn't classify 48701, 48773
Couldn't classify 51970, 52041
Sorry, prediction pasa_asmbl_49701.p1 fails validation.
(CCA)	 CA	48701-48773	GT	AGG
(AAC)	 AG	51347-51504	GT	AGG
(ATC)	 AG	51622-51780	GT	AGG
(GCG)	 AG	51970-52041	TC	GGT
-recovered pasa_asmbl_49701.p1, internal, 51347, 51504
-recovered pasa_asmbl_49701.p1, internal, 51622, 51780
Valid prediction for Augustus_model.g11496.t1
Valid prediction for GlimmerHMM_glimmerT_17241-T1
Valid prediction for snap_scaffold_7-snap.895-T1
Valid prediction for GlimmerHMM_glimmerT_17247-T1
Valid prediction for GlimmerHMM_glimmerT_17225-T1
Valid prediction for Augustus_model.g11498.t1
Valid prediction for snap_scaffold_7-snap.917-T1
Valid prediction for GlimmerHMM_glimmerT_17246-T1
Valid prediction for pasa_asmbl_49707.p1
Valid prediction for snap_scaffold_7-snap.902-T1
Valid prediction for CodingQuarry_transcript_57469-T1
Valid prediction for pasa_asmbl_49705.p1
Valid prediction for Augustus_model.g11494.t1
Valid prediction for snap_scaffold_7-snap.937-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_7-snap.916-T1
Valid prediction for HiQ_model.g11510.t1
Valid prediction for GlimmerHMM_glimmerT_17238-T1
Valid prediction for snap_scaffold_7-snap.924-T1
Valid prediction for snap_scaffold_7-snap.919-T1
Valid prediction for GlimmerHMM_glimmerT_17234-T1
Valid prediction for Augustus_model.g11505.t1
Valid prediction for HiQ_model.g11509.t1
Valid prediction for snap_scaffold_7-snap.908-T1
Valid prediction for Augustus_model.g11501.t1
Valid prediction for snap_scaffold_7-snap.934-T1
Valid prediction for CodingQuarry_transcript_57477-T1
Valid prediction for CodingQuarry_transcript_57475-T1
Valid prediction for GlimmerHMM_glimmerT_17237-T1
Valid prediction for snap_scaffold_7-snap.925-T1
Valid prediction for Augustus_model.g11502.t1
Valid prediction for GlimmerHMM_glimmerT_17230-T1
Valid prediction for GlimmerHMM_glimmerT_17228-T1
Valid prediction for GlimmerHMM_glimmerT_17231-T1
Valid prediction for snap_scaffold_7-snap.914-T1
Valid prediction for snap_scaffold_7-snap.905-T1
Valid prediction for GlimmerHMM_glimmerT_17244-T1
Couldn't classify 158737, 158832
Couldn't classify 159455, 159550
Sorry, prediction pasa_asmbl_50820.p1 fails validation.
(GAG)	 TG	158737-158832	GT	AGG
(GAC)	 AG	159217-159336	GT	AGG
(GCT)	 AG	159455-159550	TG	GGT
-recovered pasa_asmbl_50820.p1, internal, 159217, 159336
Couldn't classify 146468, 146501
Couldn't classify 149266, 149323
Sorry, prediction pasa_asmbl_50821.p1 fails validation.
(GCT)	 AG	146468-146501	GT	AGG
(AGC)	 AG	146748-147474	GT	AGG
(GAA)	 AG	148634-148765	GT	AAG
(GTA)	 AG	149266-149323	AT	GGA
-recovered pasa_asmbl_50821.p1, internal, 146468, 146501
-recovered pasa_asmbl_50821.p1, internal, 146748, 147474
-recovered pasa_asmbl_50821.p1, internal, 148634, 148765
Valid prediction for Augustus_model.g11495.t1
Valid prediction for Augustus_model.g11507.t1
Valid prediction for snap_scaffold_7-snap.929-T1
Valid prediction for snap_scaffold_7-snap.896-T1
Valid prediction for snap_scaffold_7-snap.897-T1
Valid prediction for Augustus_model.g11506.t1
Valid prediction for snap_scaffold_7-snap.909-T1
Couldn't classify 198141, 198288
Sorry, prediction pasa_asmbl_50816.p1 fails validation.
(GGT)	 CT	198141-198288	GT	AGG
(CAC)	 AG	198494-198561	GT	CAG
(CCT)	 AG	199369-199566	AG	AGA
-recovered pasa_asmbl_50816.p1, terminal, 199369, 199566
-recovered pasa_asmbl_50816.p1, internal, 198494, 198561
Valid prediction for CodingQuarry_transcript_57478-T1
Valid prediction for GlimmerHMM_glimmerT_17240-T1
Valid prediction for Augustus_model.g11514.t1
Valid prediction for snap_scaffold_7-snap.907-T1
Valid prediction for CodingQuarry_transcript_57472-T1
Valid prediction for GlimmerHMM_glimmerT_17235-T1
Valid prediction for snap_scaffold_7-snap.906-T1
Valid prediction for CodingQuarry_transcript_57474-T1
Valid prediction for Augustus_model.g11497.t1
Valid prediction for HiQ_model.g11511.t1
Valid prediction for snap_scaffold_7-snap.930-T1
Couldn't classify 160379, 160847
Couldn't classify 162204, 162261
Sorry, prediction pasa_asmbl_50819.p1 fails validation.
(GAA)	 CT	160379-160847	GT	TGG
(GCA)	 AG	161261-161429	GT	AGG
(GAA)	 AG	162204-162261	CC	CTC
-recovered pasa_asmbl_50819.p1, internal, 161261, 161429
Valid prediction for snap_scaffold_7-snap.903-T1
Valid prediction for pasa_asmbl_50829.p1
Valid prediction for pasa_asmbl_50840.p1
Valid prediction for snap_scaffold_7-snap.936-T1
Valid prediction for GlimmerHMM_glimmerT_17233-T1
Valid prediction for Augustus_model.g11503.t1
Valid prediction for GlimmerHMM_glimmerT_17242-T1
Valid prediction for snap_scaffold_7-snap.922-T1
Valid prediction for Augustus_model.g11499.t1
Valid prediction for pasa_asmbl_50828.p1
Valid prediction for GlimmerHMM_glimmerT_17243-T1
Valid prediction for snap_scaffold_7-snap.912-T1
Valid prediction for snap_scaffold_7-snap.899-T1
Valid prediction for snap_scaffold_7-snap.935-T1
Valid prediction for snap_scaffold_7-snap.910-T1
Valid prediction for HiQ_model.g11504.t1
Valid prediction for snap_scaffold_7-snap.904-T1
Valid prediction for CodingQuarry_transcript_57476-T1
Valid prediction for snap_scaffold_7-snap.901-T1
Couldn't classify 14743, 14769
Sorry, prediction pasa_asmbl_50843.p1 fails validation.
(CGC)	 CA	14743-14769	GT	AGG
(GTT)	 AG	15807-15928	GT	TGG
(CTT)	 AG	16067-16305	GT	AGG
(TGA)	 AG	16741-16868	GT	AGG
(GCT)	 AG	17371-17472	GT	TGG
(GGT)	 AG	17605-17771	GT	AGG
(GAT)	 AG	18632-18762	GT	AGG
(GTT)	 AG	19583-19743	GA	GAG
-recovered pasa_asmbl_50843.p1, terminal, 19583, 19743
-recovered pasa_asmbl_50843.p1, internal, 15807, 15928
-recovered pasa_asmbl_50843.p1, internal, 16067, 16305
-recovered pasa_asmbl_50843.p1, internal, 16741, 16868
-recovered pasa_asmbl_50843.p1, internal, 17371, 17472
-recovered pasa_asmbl_50843.p1, internal, 17605, 17771
-recovered pasa_asmbl_50843.p1, internal, 18632, 18762
Valid prediction for GlimmerHMM_glimmerT_17239-T1
Valid prediction for Augustus_model.g11500.t1
Valid prediction for snap_scaffold_7-snap.915-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12960, rend_intergenic: 1648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23166, rend_intergenic: 14610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28731, rend_intergenic: 25329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56877, rend_intergenic: 30259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75565, rend_intergenic: 68949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76997, rend_intergenic: 76564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78682, rend_intergenic: 78087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84414, rend_intergenic: 78696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104725, rend_intergenic: 95847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110802, rend_intergenic: 105505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141453, rend_intergenic: 138937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153057, rend_intergenic: 150497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190740, rend_intergenic: 188922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 43190, rend_intergenic: 43187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 257025
-exon list size: 408


building trellis

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17.6    
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18.0    
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18.5    
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19.3    
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22.9    
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23.9    
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24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.0    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
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    
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52.9    
53.2    
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53.7    
53.9    
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54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.3    
56.6    
56.8    
57.1    
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57.6    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
61.0    
61.2    
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70.5    
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72.0    
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73.2    
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74.6    
74.9    
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75.9    
76.1    
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76.8    
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77.3    
77.6    
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78.0    
78.3    
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79.0    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.4    
82.7    
82.9    
83.2    
83.4    
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83.9    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
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86.1    
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86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 12960, rend_intergenic: 1648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23166, rend_intergenic: 14610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28731, rend_intergenic: 25329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56877, rend_intergenic: 30259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75565, rend_intergenic: 68949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76997, rend_intergenic: 76564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78682, rend_intergenic: 78087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84414, rend_intergenic: 78696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104725, rend_intergenic: 95847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110802, rend_intergenic: 105505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141453, rend_intergenic: 138937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153057, rend_intergenic: 150497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190740, rend_intergenic: 188922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 43190, rend_intergenic: 43187  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 242413 - 257025
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support