-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_7892927-8137237

-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_26-snap.1872-T1
Valid prediction for GlimmerHMM_glimmerT_56185-T1
Valid prediction for snap_scaffold_26-snap.1863-T1
Valid prediction for CodingQuarry_transcript_40406-T1
Valid prediction for GlimmerHMM_glimmerT_56188-T1
Valid prediction for snap_scaffold_26-snap.1875-T1
Valid prediction for Augustus_model.g37224.t1
Valid prediction for snap_scaffold_26-snap.1865-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g37227.t1
Valid prediction for GlimmerHMM_glimmerT_56174-T1
Valid prediction for Augustus_model.g37217.t1
Valid prediction for GlimmerHMM_glimmerT_56183-T1
Valid prediction for snap_scaffold_26-snap.1876-T1
Valid prediction for GlimmerHMM_glimmerT_56187-T1
Valid prediction for snap_scaffold_26-snap.1852-T1
Valid prediction for GlimmerHMM_glimmerT_56166-T1
Valid prediction for Augustus_model.g37220.t1
Valid prediction for snap_scaffold_26-snap.1867-T1
Couldn't classify 211845, 211979
Couldn't classify 213351, 213535
Sorry, prediction pasa_asmbl_35158.p1 fails validation.
(CGG)	 TG	211845-211979	GT	TGG
(ATT)	 AG	213083-213227	GT	AGG
(GTT)	 AG	213351-213535	GT	AGG
-recovered pasa_asmbl_35158.p1, internal, 213083, 213227
-recovered pasa_asmbl_35158.p1, internal, 213351, 213535
Valid prediction for snap_scaffold_26-snap.1851-T1
Valid prediction for Augustus_model.g37223.t1
Valid prediction for snap_scaffold_26-snap.1870-T1
Valid prediction for snap_scaffold_26-snap.1873-T1
Valid prediction for GlimmerHMM_glimmerT_56165-T1
Valid prediction for GlimmerHMM_glimmerT_56178-T1
Valid prediction for GlimmerHMM_glimmerT_56181-T1
Couldn't classify 9448, 9517
Sorry, prediction pasa_asmbl_35154.p1 fails validation.
(ATG)	 TC	7512-7628	GT	AGG
(CCG)	 AG	7721-7843	GT	TGG
(GGC)	 AG	7944-8017	GT	ATG
(GCT)	 AG	8103-8316	GT	AGG
(ACG)	 AG	8498-8661	GT	AGG
(CTA)	 AG	9448-9517	CG	GAC
-recovered pasa_asmbl_35154.p1, initial, 7512, 7628
-recovered pasa_asmbl_35154.p1, internal, 7721, 7843
-recovered pasa_asmbl_35154.p1, internal, 7944, 8017
-recovered pasa_asmbl_35154.p1, internal, 8103, 8316
-recovered pasa_asmbl_35154.p1, internal, 8498, 8661
Valid prediction for snap_scaffold_26-snap.1871-T1
Valid prediction for GlimmerHMM_glimmerT_56177-T1
Valid prediction for GlimmerHMM_glimmerT_56179-T1
Valid prediction for snap_scaffold_26-snap.1855-T1
Valid prediction for snap_scaffold_26-snap.1866-T1
Valid prediction for HiQ_model.g37216.t1
Valid prediction for Augustus_model.g37226.t1
Valid prediction for Augustus_model.g37225.t1
Valid prediction for snap_scaffold_26-snap.1850-T1
Valid prediction for GlimmerHMM_glimmerT_56169-T1
Valid prediction for GlimmerHMM_glimmerT_56182-T1
Valid prediction for snap_scaffold_26-snap.1861-T1
Valid prediction for snap_scaffold_26-snap.1859-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_56180-T1
Valid prediction for snap_scaffold_26-snap.1864-T1
Valid prediction for snap_scaffold_26-snap.1849-T1
Valid prediction for GlimmerHMM_glimmerT_56189-T1
Valid prediction for snap_scaffold_26-snap.1868-T1
Couldn't classify 211028, 211558
Sorry, prediction pasa_asmbl_35724.p1 fails validation.
(ATG)	 AA	211028-211558	TA	AGT
Valid prediction for Augustus_model.g37222.t1
Valid prediction for snap_scaffold_26-snap.1857-T1
Valid prediction for snap_scaffold_26-snap.1874-T1
Valid prediction for HiQ_model.g37219.t1
Valid prediction for GlimmerHMM_glimmerT_56173-T1
Valid prediction for GlimmerHMM_glimmerT_56171-T1
Valid prediction for GlimmerHMM_glimmerT_56184-T1
Valid prediction for Augustus_model.g37221.t1
Valid prediction for Augustus_model.g37218.t1
Valid prediction for GlimmerHMM_glimmerT_56176-T1
Valid prediction for snap_scaffold_26-snap.1862-T1
Couldn't classify 223496, 223647
Couldn't classify 230049, 230156
Sorry, prediction pasa_asmbl_35865.p1 fails validation.
(TGG)	 GG	223496-223647	GT	AGG
(GAT)	 AG	225311-225446	GT	AGG
(CCC)	 AG	225808-225878	GT	AGG
(CTT)	 AG	226415-226532	GT	TGG
(GGC)	 AG	226913-226944	GT	ATG
(CTG)	 AG	227128-227180	GT	AGG
(TCG)	 AG	227325-227475	GT	CGG
(CGT)	 AG	227596-227674	GT	AGG
(CAC)	 AG	227768-227891	GT	AGG
(GCA)	 AG	228024-228180	GT	AGG
(GCC)	 AG	228273-228360	GT	AGG
(GAC)	 AG	228549-228629	GT	AGG
(GTG)	 AG	228722-228879	GT	GAG
(CGA)	 AG	228967-229043	GT	CCG
(TGT)	 AG	229194-229366	GT	AGG
(CTG)	 AG	229469-229628	GT	GGG
(ACG)	 AG	229744-229886	GC	AGG
(CTG)	 AG	230049-230156	AC	TCA
add_exon() Sorry, pasa_asmbl_35865.p1 228722-228879-terminal-2 is invalid.
-recovered pasa_asmbl_35865.p1, terminal, 228722, 228879
-recovered pasa_asmbl_35865.p1, internal, 225311, 225446
-recovered pasa_asmbl_35865.p1, internal, 225808, 225878
-recovered pasa_asmbl_35865.p1, internal, 226415, 226532
-recovered pasa_asmbl_35865.p1, internal, 226913, 226944
-recovered pasa_asmbl_35865.p1, internal, 227128, 227180
-recovered pasa_asmbl_35865.p1, internal, 227325, 227475
-recovered pasa_asmbl_35865.p1, internal, 227596, 227674
-recovered pasa_asmbl_35865.p1, internal, 227768, 227891
-recovered pasa_asmbl_35865.p1, internal, 228024, 228180
-recovered pasa_asmbl_35865.p1, internal, 228273, 228360
-recovered pasa_asmbl_35865.p1, internal, 228549, 228629
-recovered pasa_asmbl_35865.p1, internal, 228722, 228879
-recovered pasa_asmbl_35865.p1, internal, 228967, 229043
-recovered pasa_asmbl_35865.p1, internal, 229194, 229366
-recovered pasa_asmbl_35865.p1, internal, 229469, 229628
-recovered pasa_asmbl_35865.p1, internal, 229744, 229886
Valid prediction for snap_scaffold_26-snap.1858-T1
Valid prediction for Augustus_model.g37215.t1
Valid prediction for snap_scaffold_26-snap.1869-T1
Valid prediction for GlimmerHMM_glimmerT_56167-T1
Valid prediction for snap_scaffold_26-snap.1854-T1
Couldn't classify 230273, 230358
Sorry, prediction pasa_asmbl_35723.p1 fails validation.
(ACT)	 GG	230273-230358	GT	AGG
(CGG)	 AG	230449-230516	GT	CGG
(ACC)	 AG	230614-230702	GT	AGG
(GAG)	 AG	230800-230877	GT	GGG
(AAC)	 AG	230974-231108	GT	AGG
(CAC)	 AG	231537-231620	TA	AGT
-recovered pasa_asmbl_35723.p1, terminal, 231537, 231620
-recovered pasa_asmbl_35723.p1, internal, 230449, 230516
-recovered pasa_asmbl_35723.p1, internal, 230614, 230702
-recovered pasa_asmbl_35723.p1, internal, 230800, 230877
-recovered pasa_asmbl_35723.p1, internal, 230974, 231108
Valid prediction for snap_scaffold_26-snap.1860-T1
Valid prediction for GlimmerHMM_glimmerT_56168-T1
Valid prediction for GlimmerHMM_glimmerT_56164-T1
Valid prediction for snap_scaffold_26-snap.1853-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_56172-T1
Valid prediction for GlimmerHMM_glimmerT_56186-T1
Valid prediction for GlimmerHMM_glimmerT_56175-T1
Valid prediction for CodingQuarry_transcript_40407-T1
Valid prediction for snap_scaffold_26-snap.1856-T1
Valid prediction for GlimmerHMM_glimmerT_56170-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21189, rend_intergenic: 20225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24535, rend_intergenic: 21484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 244311
-exon list size: 264


building trellis

0.4    
0.8    
1.1    
1.5    
1.9    
2.3    
2.6    
3.0    
3.4    
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4.9    
5.3    
5.6    
6.0    
6.4    
6.8    
7.1    
7.5    
7.9    
8.3    
8.6    
9.0    
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10.5    
10.9    
11.3    
11.7    
12.0    
12.4    
12.8    
13.2    
13.5    
13.9    
14.3    
14.7    
15.0    
15.4    
15.8    
16.2    
16.5    
16.9    
17.3    
17.7    
18.0    
18.4    
18.8    
19.2    
19.5    
19.9    
20.3    
20.7    
21.1    
21.4    
21.8    
22.2    
22.6    
22.9    
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23.7    
24.1    
24.4    
24.8    
25.2    
25.6    
25.9    
26.3    
26.7    
27.1    
27.4    
27.8    
28.2    
28.6    
28.9    
29.3    
29.7    
30.1    
30.5    
30.8    
31.2    
31.6    
32.0    
32.3    
32.7    
33.1    
33.5    
33.8    
34.2    
34.6    
35.0    
35.3    
35.7    
36.1    
36.5    
36.8    
37.2    
37.6    
38.0    
38.3    
38.7    
39.1    
39.5    
39.8    
40.2    
40.6    
41.0    
41.4    
41.7    
42.1    
42.5    
42.9    
43.2    
43.6    
44.0    
44.4    
44.7    
45.1    
45.5    
45.9    
46.2    
46.6    
47.0    
47.4    
47.7    
48.1    
48.5    
48.9    
49.2    
49.6    
50.0    
50.4    
50.8    
51.1    
51.5    
51.9    
52.3    
52.6    
53.0    
53.4    
53.8    
54.1    
54.5    
54.9    
55.3    
55.6    
56.0    
56.4    
56.8    
57.1    
57.5    
57.9    
58.3    
58.6    
59.0    
59.4    
59.8    
60.2    
60.5    
60.9    
61.3    
61.7    
62.0    
62.4    
62.8    
63.2    
63.5    
63.9    
64.3    
64.7    
65.0    
65.4    
65.8    
66.2    
66.5    
66.9    
67.3    
67.7    
68.0    
68.4    
68.8    
69.2    
69.5    
69.9    
70.3    
70.7    
71.1    
71.4    
71.8    
72.2    
72.6    
72.9    
73.3    
73.7    
74.1    
74.4    
74.8    
75.2    
75.6    
75.9    
76.3    
76.7    
77.1    
77.4    
77.8    
78.2    
78.6    
78.9    
79.3    
79.7    
80.1    
80.5    
80.8    
81.2    
81.6    
82.0    
82.3    
82.7    
83.1    
83.5    
83.8    
84.2    
84.6    
85.0    
85.3    
85.7    
86.1    
86.5    
86.8    
87.2    
87.6    
88.0    
88.3    
88.7    
89.1    
89.5    
89.8    
90.2    
90.6    
91.0    
91.4    
91.7    
92.1    
92.5    
92.9    
93.2    
93.6    
94.0    
94.4    
94.7    
95.1    
95.5    
95.9    
96.2    
96.6    
97.0    
97.4    
97.7    
98.1    
98.5    
98.9    
99.2    
99.6    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 21189, rend_intergenic: 20225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24535, rend_intergenic: 21484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 226876 - 244311
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 226876 - 241644
-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