-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_7916490-8178572

-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 GlimmerHMM_glimmerT_12241-T1
Valid prediction for GlimmerHMM_glimmerT_12265-T1
Couldn't classify 221545, 221738
Sorry, prediction pasa_asmbl_45537.p1 fails validation.
(GGG)	 CT	221545-221738	GT	AGG
(GAC)	 AG	221870-222032	GT	AAG
(ACA)	 AG	223938-224062	GT	AGG
(CCC)	 AG	224327-224435	GT	CGG
(GAG)	 AG	224615-224722	GT	AGG
(GTG)	 AG	225201-225354	GT	AGG
(GTG)	 AG	225453-225520	GT	AGG
(GAG)	 AG	225663-225784	GT	AGG
(GAT)	 AG	226094-226325	GT	ACG
(GAG)	 AG	227275-227377	GT	TGG
(AGG)	 AG	227468-227688	GT	AGG
(GTG)	 AG	227821-227976	GT	TGG
(ATC)	 AG	228082-228278	GT	CAG
(GGA)	 AG	228748-228882	GT	AGG
(GAA)	 AG	229103-229172	AT	AGA
-recovered pasa_asmbl_45537.p1, terminal, 229103, 229172
-recovered pasa_asmbl_45537.p1, internal, 221870, 222032
-recovered pasa_asmbl_45537.p1, internal, 223938, 224062
-recovered pasa_asmbl_45537.p1, internal, 224327, 224435
-recovered pasa_asmbl_45537.p1, internal, 224615, 224722
-recovered pasa_asmbl_45537.p1, internal, 225201, 225354
-recovered pasa_asmbl_45537.p1, internal, 225453, 225520
-recovered pasa_asmbl_45537.p1, internal, 225663, 225784
-recovered pasa_asmbl_45537.p1, internal, 226094, 226325
-recovered pasa_asmbl_45537.p1, internal, 227275, 227377
-recovered pasa_asmbl_45537.p1, internal, 227468, 227688
-recovered pasa_asmbl_45537.p1, internal, 227821, 227976
-recovered pasa_asmbl_45537.p1, internal, 228082, 228278
-recovered pasa_asmbl_45537.p1, internal, 228748, 228882
Valid prediction for GlimmerHMM_glimmerT_12258-T1
Valid prediction for CodingQuarry_transcript_52138-T1
Valid prediction for snap_scaffold_5-snap.1557-T1
Valid prediction for GlimmerHMM_glimmerT_12253-T1
Valid prediction for snap_scaffold_5-snap.1526-T1
Valid prediction for snap_scaffold_5-snap.1560-T1
Valid prediction for snap_scaffold_5-snap.1531-T1
Valid prediction for HiQ_model.g8059.t1
Valid prediction for CodingQuarry_transcript_52136-T1
Valid prediction for snap_scaffold_5-snap.1545-T1
Valid prediction for GlimmerHMM_glimmerT_12239-T1
Valid prediction for snap_scaffold_5-snap.1523-T1
Valid prediction for snap_scaffold_5-snap.1537-T1
Valid prediction for pasa_asmbl_45523.p1
Valid prediction for GlimmerHMM_glimmerT_12252-T1
Valid prediction for snap_scaffold_5-snap.1549-T1
Valid prediction for snap_scaffold_5-snap.1551-T1
Valid prediction for Augustus_model.g8055.t1
Valid prediction for GlimmerHMM_glimmerT_12245-T1
Valid prediction for snap_scaffold_5-snap.1561-T1
Valid prediction for GlimmerHMM_glimmerT_12256-T1
Valid prediction for snap_scaffold_5-snap.1543-T1
Valid prediction for snap_scaffold_5-snap.1534-T1
Valid prediction for GlimmerHMM_glimmerT_12240-T1
Valid prediction for CodingQuarry_transcript_52134-T1
Valid prediction for snap_scaffold_5-snap.1548-T1
Valid prediction for GlimmerHMM_glimmerT_12260-T1
Valid prediction for snap_scaffold_5-snap.1547-T1
Valid prediction for GlimmerHMM_glimmerT_12238-T1
Valid prediction for CodingQuarry_transcript_52132-T1
Valid prediction for GlimmerHMM_glimmerT_12259-T1
Valid prediction for Augustus_model.g8052.t1
Valid prediction for GlimmerHMM_glimmerT_12264-T1
Valid prediction for GlimmerHMM_glimmerT_12255-T1
Valid prediction for snap_scaffold_5-snap.1529-T1
Valid prediction for snap_scaffold_5-snap.1555-T1
Couldn't classify 175687, 175752
Couldn't classify 176488, 176550
Sorry, prediction pasa_asmbl_45527.p1 fails validation.
(GGG)	 CG	175687-175752	GT	AGG
(TGT)	 AG	175850-176016	GT	AGG
(GGT)	 AG	176213-176342	GT	TGG
(GTG)	 AG	176488-176550	AA	ACA
-recovered pasa_asmbl_45527.p1, internal, 175850, 176016
-recovered pasa_asmbl_45527.p1, internal, 176213, 176342
Valid prediction for GlimmerHMM_glimmerT_12250-T1
Valid prediction for snap_scaffold_5-snap.1556-T1
Valid prediction for GlimmerHMM_glimmerT_12249-T1
Valid prediction for Augustus_model.g8044.t1
Valid prediction for HiQ_model.g8060.t1
Valid prediction for Augustus_model.g8053.t1
Valid prediction for GlimmerHMM_glimmerT_12246-T1
Valid prediction for snap_scaffold_5-snap.1559-T1
Valid prediction for pasa_asmbl_45529.p1
Valid prediction for CodingQuarry_transcript_52133-T1
Valid prediction for snap_scaffold_5-snap.1538-T1
Valid prediction for CodingQuarry_transcript_52137-T1
Valid prediction for GlimmerHMM_glimmerT_12244-T1
Couldn't classify 165127, 165277
Sorry, prediction pasa_asmbl_45525.p1 fails validation.
(CCC)	 AT	165127-165277	GT	AGG
(TGT)	 AG	165466-165610	GT	AGG
(ATT)	 AG	165783-165996	GT	AGG
(GTC)	 AG	166220-166335	GT	AGG
(GGA)	 AG	166447-166567	GT	TAG
(TAT)	 AG	166682-166792	GT	AGG
(GTG)	 AG	167001-167051	CA	AAC
add_exon() Sorry, pasa_asmbl_45525.p1 165466-165610-terminal-3 is invalid.
-recovered pasa_asmbl_45525.p1, terminal, 165466, 165610
-recovered pasa_asmbl_45525.p1, terminal, 167001, 167051
-recovered pasa_asmbl_45525.p1, internal, 165466, 165610
-recovered pasa_asmbl_45525.p1, internal, 165783, 165996
-recovered pasa_asmbl_45525.p1, internal, 166220, 166335
-recovered pasa_asmbl_45525.p1, internal, 166447, 166567
-recovered pasa_asmbl_45525.p1, internal, 166682, 166792

-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.g8057.t1
Valid prediction for GlimmerHMM_glimmerT_12243-T1
Valid prediction for snap_scaffold_5-snap.1528-T1
Valid prediction for GlimmerHMM_glimmerT_12254-T1
Valid prediction for snap_scaffold_5-snap.1540-T1
Valid prediction for Augustus_model.g8049.t1
Valid prediction for snap_scaffold_5-snap.1554-T1
Valid prediction for GlimmerHMM_glimmerT_12269-T1
Valid prediction for GlimmerHMM_glimmerT_12251-T1
Valid prediction for Augustus_model.g8051.t1
Valid prediction for snap_scaffold_5-snap.1550-T1
Valid prediction for snap_scaffold_5-snap.1542-T1
Valid prediction for GlimmerHMM_glimmerT_12268-T1
Valid prediction for snap_scaffold_5-snap.1527-T1
Valid prediction for snap_scaffold_5-snap.1522-T1
Valid prediction for snap_scaffold_5-snap.1541-T1
Couldn't classify 55528, 56101
Sorry, prediction pasa_asmbl_44198.p1 fails validation.
(CAT)	 TT	55528-56101	GT	AGG
(GGG)	 AG	56329-57188	AC	AAA
-recovered pasa_asmbl_44198.p1, terminal, 56329, 57188
Valid prediction for GlimmerHMM_glimmerT_12266-T1
Valid prediction for GlimmerHMM_glimmerT_12262-T1
Valid prediction for snap_scaffold_5-snap.1533-T1
Valid prediction for GlimmerHMM_glimmerT_12263-T1
Valid prediction for Augustus_model.g8045.t1
Valid prediction for Augustus_model.g8056.t1
Valid prediction for Augustus_model.g8048.t1
Valid prediction for snap_scaffold_5-snap.1535-T1
Valid prediction for Augustus_model.g8050.t1
Valid prediction for GlimmerHMM_glimmerT_12270-T1
Valid prediction for snap_scaffold_5-snap.1553-T1
Valid prediction for snap_scaffold_5-snap.1539-T1
Valid prediction for snap_scaffold_5-snap.1544-T1
Valid prediction for GlimmerHMM_glimmerT_12237-T1
Valid prediction for HiQ_model.g8058.t1
Valid prediction for snap_scaffold_5-snap.1536-T1
Valid prediction for GlimmerHMM_glimmerT_12247-T1
Valid prediction for Augustus_model.g8046.t1
Valid prediction for snap_scaffold_5-snap.1530-T1
Valid prediction for snap_scaffold_5-snap.1552-T1
Valid prediction for GlimmerHMM_glimmerT_12271-T1
Valid prediction for GlimmerHMM_glimmerT_12267-T1
Valid prediction for pasa_asmbl_44195.p1
Valid prediction for HiQ_model.g8054.t1
Valid prediction for CodingQuarry_transcript_52131-T1
Valid prediction for snap_scaffold_5-snap.1524-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.1532-T1
Valid prediction for Augustus_model.g8061.t1
Valid prediction for CodingQuarry_transcript_52135-T1
Valid prediction for GlimmerHMM_glimmerT_12257-T1
Valid prediction for Augustus_model.g8047.t1
Valid prediction for GlimmerHMM_glimmerT_12242-T1
Valid prediction for pasa_asmbl_44193.p1
Valid prediction for snap_scaffold_5-snap.1525-T1
Valid prediction for GlimmerHMM_glimmerT_12261-T1
Valid prediction for GlimmerHMM_glimmerT_12248-T1
Valid prediction for snap_scaffold_5-snap.1558-T1
Valid prediction for snap_scaffold_5-snap.1546-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12689, rend_intergenic: 9614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16649, rend_intergenic: 13024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22546, rend_intergenic: 20385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55371, rend_intergenic: 48688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81810, rend_intergenic: 74546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100506, rend_intergenic: 90814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119567, rend_intergenic: 116296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141732, rend_intergenic: 132855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 262083
-exon list size: 409


building trellis

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11.9    
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13.4    
13.6    
13.9    
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14.4    
14.6    
14.8    
15.1    
15.3    
15.6    
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16.8    
17.0    
17.3    
17.5    
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18.7    
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19.2    
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26.3    
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27.3    
27.5    
27.7    
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28.2    
28.5    
28.7    
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29.4    
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30.4    
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31.6    
31.9    
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32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.8    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
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53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.2    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.0    
62.3    
62.5    
62.8    
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64.0    
64.2    
64.5    
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65.0    
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65.5    
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65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
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67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.8    
71.0    
71.3    
71.5    
71.8    
72.0    
72.3    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.4    
76.6    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 12689, rend_intergenic: 9614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16649, rend_intergenic: 13024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22546, rend_intergenic: 20385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55371, rend_intergenic: 48688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81810, rend_intergenic: 74546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100506, rend_intergenic: 90814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119567, rend_intergenic: 116296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141732, rend_intergenic: 132855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11955
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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