-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_3570709-3688398

-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 Augustus_model.g37813.t1
Valid prediction for GlimmerHMM_glimmerT_57064-T1
Valid prediction for snap_scaffold_27-snap.854-T1
Valid prediction for snap_scaffold_27-snap.867-T1
Valid prediction for GlimmerHMM_glimmerT_57062-T1
Valid prediction for snap_scaffold_27-snap.868-T1
Valid prediction for snap_scaffold_27-snap.845-T1
Valid prediction for snap_scaffold_27-snap.856-T1
Valid prediction for snap_scaffold_27-snap.871-T1
Valid prediction for snap_scaffold_27-snap.849-T1
Valid prediction for snap_scaffold_27-snap.859-T1
Valid prediction for snap_scaffold_27-snap.858-T1
Valid prediction for snap_scaffold_27-snap.857-T1
Valid prediction for snap_scaffold_27-snap.851-T1
Valid prediction for Augustus_model.g37818.t1
Valid prediction for Augustus_model.g37816.t1
Valid prediction for CodingQuarry_transcript_41855-T1
Valid prediction for HiQ_model.g37815.t1
Valid prediction for snap_scaffold_27-snap.866-T1
Valid prediction for snap_scaffold_27-snap.855-T1
Valid prediction for Augustus_model.g37809.t1
Valid prediction for pasa_asmbl_36212.p1
Valid prediction for snap_scaffold_27-snap.848-T1
Valid prediction for snap_scaffold_27-snap.850-T1
Valid prediction for Augustus_model.g37814.t1
Valid prediction for snap_scaffold_27-snap.864-T1
Valid prediction for Augustus_model.g37817.t1
Valid prediction for GlimmerHMM_glimmerT_57058-T1
Valid prediction for GlimmerHMM_glimmerT_57067-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_57071-T1
Valid prediction for snap_scaffold_27-snap.870-T1
Couldn't classify 39064, 39109
Sorry, prediction pasa_asmbl_36914.p1 fails validation.
(GAC)	 AG	39064-39109	GT	GAG
(GGA)	 AG	40629-40679	GT	AAG
(TAA)	 AG	40794-40895	GT	ACG
(ATA)	 AG	42374-42546	GT	GGG
(GGT)	 AG	42751-42860	GT	ATG
(GGA)	 AG	43595-43686	GT	AGG
(CCC)	 AG	43796-43902	GA	AAG
add_exon() Sorry, pasa_asmbl_36914.p1 39064-39109-terminal-3 is invalid.
-recovered pasa_asmbl_36914.p1, terminal, 39064, 39109
-recovered pasa_asmbl_36914.p1, terminal, 43796, 43902
-recovered pasa_asmbl_36914.p1, internal, 39064, 39109
-recovered pasa_asmbl_36914.p1, internal, 40629, 40679
-recovered pasa_asmbl_36914.p1, internal, 40794, 40895
-recovered pasa_asmbl_36914.p1, internal, 42374, 42546
-recovered pasa_asmbl_36914.p1, internal, 42751, 42860
-recovered pasa_asmbl_36914.p1, internal, 43595, 43686
Valid prediction for GlimmerHMM_glimmerT_57066-T1
Valid prediction for snap_scaffold_27-snap.844-T1
Valid prediction for GlimmerHMM_glimmerT_57070-T1
Valid prediction for snap_scaffold_27-snap.860-T1
Valid prediction for GlimmerHMM_glimmerT_57065-T1
Valid prediction for Augustus_model.g37812.t1
Valid prediction for Augustus_model.g37810.t1
Couldn't classify 94591, 94596
Couldn't classify 99267, 99355
Sorry, prediction pasa_asmbl_36913.p1 fails validation.
(GAG)	 GA	94591-94596	GT	CGG
(GTC)	 AG	94837-94873	GT	CTG
(CCC)	 AG	95597-95659	GT	AGG
(GTA)	 AG	95992-96066	GT	GGG
(ATC)	 AG	96575-96659	GT	AGG
(GGT)	 AG	97095-97153	GT	CAG
(AGC)	 AG	99267-99355	AC	TGA
-recovered pasa_asmbl_36913.p1, internal, 94837, 94873
-recovered pasa_asmbl_36913.p1, internal, 95597, 95659
-recovered pasa_asmbl_36913.p1, internal, 95992, 96066
-recovered pasa_asmbl_36913.p1, internal, 96575, 96659
-recovered pasa_asmbl_36913.p1, internal, 97095, 97153
Valid prediction for snap_scaffold_27-snap.862-T1
Valid prediction for snap_scaffold_27-snap.853-T1
Valid prediction for snap_scaffold_27-snap.843-T1
Valid prediction for GlimmerHMM_glimmerT_57068-T1
Valid prediction for snap_scaffold_27-snap.865-T1
Valid prediction for snap_scaffold_27-snap.861-T1
Valid prediction for Augustus_model.g37821.t1
Valid prediction for snap_scaffold_27-snap.852-T1
Valid prediction for GlimmerHMM_glimmerT_57063-T1
Valid prediction for GlimmerHMM_glimmerT_57061-T1
Couldn't classify 23526, 23564
Couldn't classify 26656, 26818
Sorry, prediction pasa_asmbl_36917.p1 fails validation.
(ATT)	 CA	23526-23564	GT	ACG
(ATC)	 AG	23731-23781	GT	GTG
(GGG)	 AG	24184-24308	GT	CGG
(AGT)	 AG	26656-26818	CC	GAC
-recovered pasa_asmbl_36917.p1, internal, 23731, 23781
-recovered pasa_asmbl_36917.p1, internal, 24184, 24308
Valid prediction for GlimmerHMM_glimmerT_57074-T1
Valid prediction for GlimmerHMM_glimmerT_57059-T1
Valid prediction for Augustus_model.g37822.t1
Valid prediction for GlimmerHMM_glimmerT_57060-T1
Valid prediction for snap_scaffold_27-snap.872-T1
Valid prediction for snap_scaffold_27-snap.863-T1
Valid prediction for Augustus_model.g37820.t1
Valid prediction for HiQ_model.g37819.t1
Valid prediction for Augustus_model.g37811.t1
Valid prediction for GlimmerHMM_glimmerT_57069-T1
Valid prediction for GlimmerHMM_glimmerT_57073-T1
Valid prediction for CodingQuarry_transcript_41856-T1
Valid prediction for snap_scaffold_27-snap.846-T1
Valid prediction for snap_scaffold_27-snap.869-T1
Valid prediction for snap_scaffold_27-snap.847-T1
Valid prediction for GlimmerHMM_glimmerT_57072-T1
Valid prediction for GlimmerHMM_glimmerT_57075-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15612, rend_intergenic: 13533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38450, rend_intergenic: 19380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42149, rend_intergenic: 39349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49944, rend_intergenic: 44774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95899, rend_intergenic: 89543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 117690
-exon list size: 260


building trellis

0.4    
0.8    
1.1    
1.5    
1.9    
2.3    
2.7    
3.1    
3.4    
3.8    
4.2    
4.6    
5.0    
5.3    
5.7    
6.1    
6.5    
6.9    
7.3    
7.6    
8.0    
8.4    
8.8    
9.2    
9.5    
9.9    
10.3    
10.7    
11.1    
11.5    
11.8    
12.2    
12.6    
13.0    
13.4    
13.7    
14.1    
14.5    
14.9    
15.3    
15.6    
16.0    
16.4    
16.8    
17.2    
17.6    
17.9    
18.3    
18.7    
19.1    
19.5    
19.8    
20.2    
20.6    
21.0    
21.4    
21.8    
22.1    
22.5    
22.9    
23.3    
23.7    
24.0    
24.4    
24.8    
25.2    
25.6    
26.0    
26.3    
26.7    
27.1    
27.5    
27.9    
28.2    
28.6    
29.0    
29.4    
29.8    
30.2    
30.5    
30.9    
31.3    
31.7    
32.1    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.7    
35.1    
35.5    
35.9    
36.3    
36.6    
37.0    
37.4    
37.8    
38.2    
38.5    
38.9    
39.3    
39.7    
40.1    
40.5    
40.8    
41.2    
41.6    
42.0    
42.4    
42.7    
43.1    
43.5    
43.9    
44.3    
44.7    
45.0    
45.4    
45.8    
46.2    
46.6    
46.9    
47.3    
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    
52.7    
53.1    
53.4    
53.8    
54.2    
54.6    
55.0    
55.3    
55.7    
56.1    
56.5    
56.9    
57.3    
57.6    
58.0    
58.4    
58.8    
59.2    
59.5    
59.9    
60.3    
60.7    
61.1    
61.5    
61.8    
62.2    
62.6    
63.0    
63.4    
63.7    
64.1    
64.5    
64.9    
65.3    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
67.9    
68.3    
68.7    
69.1    
69.5    
69.8    
70.2    
70.6    
71.0    
71.4    
71.8    
72.1    
72.5    
72.9    
73.3    
73.7    
74.0    
74.4    
74.8    
75.2    
75.6    
76.0    
76.3    
76.7    
77.1    
77.5    
77.9    
78.2    
78.6    
79.0    
79.4    
79.8    
80.2    
80.5    
80.9    
81.3    
81.7    
82.1    
82.4    
82.8    
83.2    
83.6    
84.0    
84.4    
84.7    
85.1    
85.5    
85.9    
86.3    
86.6    
87.0    
87.4    
87.8    
88.2    
88.5    
88.9    
89.3    
89.7    
90.1    
90.5    
90.8    
91.2    
91.6    
92.0    
92.4    
92.7    
93.1    
93.5    
93.9    
94.3    
94.7    
95.0    
95.4    
95.8    
96.2    
96.6    
96.9    
97.3    
97.7    
98.1    
98.5    
98.9    
99.2    
99.6    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 15612, rend_intergenic: 13533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38450, rend_intergenic: 19380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42149, rend_intergenic: 39349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49944, rend_intergenic: 44774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95899, rend_intergenic: 89543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support