-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_2295175-2390837

-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_27-snap.550-T1
Valid prediction for snap_scaffold_27-snap.537-T1
Valid prediction for snap_scaffold_27-snap.546-T1
Couldn't classify 29105, 29247
Couldn't classify 29294, 29324
Sorry, prediction CodingQuarry_transcript_41804-T1 fails validation.
(ATG)	 TC	19678-19920	GT	AAG
(CGC)	 AG	22759-22860	GT	AGG
(CTG)	 AG	22968-23046	GT	TGG
(CCT)	 AG	23177-23280	GT	AGG
(GTG)	 AG	23462-23593	GT	AGG
(GTG)	 AG	23816-23927	GT	CTG
(TCA)	 AG	24094-24176	GT	ATG
(TTC)	 AG	24302-24445	GT	AGG
(GTT)	 AG	24624-24716	GT	AGG
(GCT)	 AG	25024-25170	GT	AGG
(AGA)	 AG	25536-25699	GT	GTG
(ATT)	 AG	25944-26058	GT	AGG
(AAA)	 AG	26400-26501	GT	AGG
(GAG)	 AG	26642-26789	GT	CCG
(GCA)	 AG	27113-27171	GT	AGG
(GCG)	 AG	27751-27892	GT	AGG
(CCA)	 AG	28150-28357	GT	GGG
(ATA)	 AG	28525-28659	GT	AGG
(GTT)	 AG	28784-28850	GT	AGG
(GAC)	 AG	29105-29247	CC	AAC
(CCC)	 CC	29294-29324	CC	AGC
-recovered CodingQuarry_transcript_41804-T1, initial, 19678, 19920
-recovered CodingQuarry_transcript_41804-T1, internal, 22759, 22860
-recovered CodingQuarry_transcript_41804-T1, internal, 22968, 23046
-recovered CodingQuarry_transcript_41804-T1, internal, 23177, 23280
-recovered CodingQuarry_transcript_41804-T1, internal, 23462, 23593
-recovered CodingQuarry_transcript_41804-T1, internal, 23816, 23927
-recovered CodingQuarry_transcript_41804-T1, internal, 24094, 24176
-recovered CodingQuarry_transcript_41804-T1, internal, 24302, 24445
-recovered CodingQuarry_transcript_41804-T1, internal, 24624, 24716
-recovered CodingQuarry_transcript_41804-T1, internal, 25024, 25170
-recovered CodingQuarry_transcript_41804-T1, internal, 25536, 25699
-recovered CodingQuarry_transcript_41804-T1, internal, 25944, 26058
-recovered CodingQuarry_transcript_41804-T1, internal, 26400, 26501
-recovered CodingQuarry_transcript_41804-T1, internal, 26642, 26789
-recovered CodingQuarry_transcript_41804-T1, internal, 27113, 27171
-recovered CodingQuarry_transcript_41804-T1, internal, 27751, 27892
-recovered CodingQuarry_transcript_41804-T1, internal, 28150, 28357
-recovered CodingQuarry_transcript_41804-T1, internal, 28525, 28659
-recovered CodingQuarry_transcript_41804-T1, internal, 28784, 28850
Valid prediction for HiQ_model.g37647.t1
Valid prediction for pasa_asmbl_36077.p1
Valid prediction for Augustus_model.g37646.t1
Valid prediction for GlimmerHMM_glimmerT_56829-T1
Valid prediction for snap_scaffold_27-snap.555-T1
Valid prediction for snap_scaffold_27-snap.541-T1
Valid prediction for GlimmerHMM_glimmerT_56810-T1
Valid prediction for snap_scaffold_27-snap.549-T1
Valid prediction for snap_scaffold_27-snap.552-T1
Valid prediction for GlimmerHMM_glimmerT_56815-T1
Valid prediction for GlimmerHMM_glimmerT_56816-T1
Valid prediction for snap_scaffold_27-snap.538-T1
Valid prediction for GlimmerHMM_glimmerT_56813-T1
Valid prediction for GlimmerHMM_glimmerT_56825-T1
Valid prediction for HiQ_model.g37644.t1
Valid prediction for GlimmerHMM_glimmerT_56811-T1
Valid prediction for GlimmerHMM_glimmerT_56807-T1
Valid prediction for GlimmerHMM_glimmerT_56824-T1
Valid prediction for snap_scaffold_27-snap.557-T1
Valid prediction for GlimmerHMM_glimmerT_56812-T1
Valid prediction for snap_scaffold_27-snap.539-T1
Valid prediction for GlimmerHMM_glimmerT_56814-T1
Valid prediction for GlimmerHMM_glimmerT_56823-T1
Valid prediction for GlimmerHMM_glimmerT_56827-T1
Valid prediction for snap_scaffold_27-snap.540-T1
Valid prediction for GlimmerHMM_glimmerT_56821-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_56808-T1
Valid prediction for GlimmerHMM_glimmerT_56820-T1
Valid prediction for Augustus_model.g37645.t1
Valid prediction for snap_scaffold_27-snap.553-T1
Valid prediction for Augustus_model.g37648.t1
Valid prediction for snap_scaffold_27-snap.548-T1
Valid prediction for Augustus_model.g37643.t1
Valid prediction for GlimmerHMM_glimmerT_56826-T1
Valid prediction for GlimmerHMM_glimmerT_56818-T1
Valid prediction for GlimmerHMM_glimmerT_56809-T1
Valid prediction for snap_scaffold_27-snap.544-T1
Valid prediction for Augustus_model.g37642.t1
Valid prediction for GlimmerHMM_glimmerT_56819-T1
Valid prediction for snap_scaffold_27-snap.536-T1
Valid prediction for snap_scaffold_27-snap.551-T1
Valid prediction for snap_scaffold_27-snap.533-T1
Valid prediction for GlimmerHMM_glimmerT_56806-T1
Valid prediction for GlimmerHMM_glimmerT_56831-T1
Valid prediction for Augustus_model.g37650.t1
Valid prediction for snap_scaffold_27-snap.543-T1
Valid prediction for snap_scaffold_27-snap.542-T1
Valid prediction for snap_scaffold_27-snap.535-T1
Couldn't classify 82418, 82423
Couldn't classify 83410, 83551
Sorry, prediction pasa_asmbl_36821.p1 fails validation.
(CCA)	 GG	82418-82423	GT	TGG
(TCC)	 AG	82856-82954	GT	AGG
(TCC)	 AG	83072-83187	GT	CAG
(GGA)	 AG	83410-83551	GT	TGG
-recovered pasa_asmbl_36821.p1, internal, 82856, 82954
-recovered pasa_asmbl_36821.p1, internal, 83072, 83187
-recovered pasa_asmbl_36821.p1, internal, 83410, 83551
Valid prediction for snap_scaffold_27-snap.545-T1
Valid prediction for GlimmerHMM_glimmerT_56830-T1
Valid prediction for snap_scaffold_27-snap.534-T1
Valid prediction for Augustus_model.g37651.t1
Valid prediction for Augustus_model.g37652.t1
Valid prediction for Augustus_model.g37653.t1
Valid prediction for snap_scaffold_27-snap.547-T1
Valid prediction for GlimmerHMM_glimmerT_56822-T1
Valid prediction for GlimmerHMM_glimmerT_56817-T1
Valid prediction for snap_scaffold_27-snap.556-T1
Valid prediction for snap_scaffold_27-snap.554-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g37649.t1
Valid prediction for GlimmerHMM_glimmerT_56828-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17923, rend_intergenic: 14027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52697, rend_intergenic: 50796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61957, rend_intergenic: 55645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64445, rend_intergenic: 64227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74935, rend_intergenic: 70211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80872, rend_intergenic: 75922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95158, rend_intergenic: 88147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 95663
-exon list size: 264


building trellis

0.4    
0.8    
1.1    
1.5    
1.9    
2.3    
2.6    
3.0    
3.4    
3.8    
4.1    
4.5    
4.9    
5.3    
5.6    
6.0    
6.4    
6.8    
7.1    
7.5    
7.9    
8.3    
8.6    
9.0    
9.4    
9.8    
10.2    
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    
23.3    
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 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 17923, rend_intergenic: 14027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52697, rend_intergenic: 50796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61957, rend_intergenic: 55645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64445, rend_intergenic: 64227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74935, rend_intergenic: 70211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80872, rend_intergenic: 75922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95158, rend_intergenic: 88147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support