-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_2334997-2580215

-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_41908-T1
Valid prediction for pasa_asmbl_20410.p1
Valid prediction for GlimmerHMM_glimmerT_41913-T1
Couldn't classify 199818, 200138
Sorry, prediction pasa_asmbl_20409.p1 fails validation.
(ATG)	 AA	199818-200138	AA	AGA
Valid prediction for snap_scaffold_18-snap.494-T1
Valid prediction for snap_scaffold_18-snap.497-T1
Valid prediction for GlimmerHMM_glimmerT_41917-T1
Valid prediction for Augustus_model.g27903.t1
Valid prediction for GlimmerHMM_glimmerT_41919-T1
Valid prediction for CodingQuarry_transcript_23696-T1
Valid prediction for GlimmerHMM_glimmerT_41904-T1
Valid prediction for snap_scaffold_18-snap.519-T1
Valid prediction for snap_scaffold_18-snap.493-T1
Valid prediction for snap_scaffold_18-snap.515-T1
Valid prediction for snap_scaffold_18-snap.518-T1
Valid prediction for Augustus_model.g27904.t1
Valid prediction for GlimmerHMM_glimmerT_41906-T1
Valid prediction for GlimmerHMM_glimmerT_41916-T1
Valid prediction for snap_scaffold_18-snap.526-T1
Valid prediction for CodingQuarry_transcript_23697-T1
Valid prediction for Augustus_model.g27909.t1
Valid prediction for Augustus_model.g27921.t1
Valid prediction for HiQ_model.g27917.t1
Valid prediction for GlimmerHMM_glimmerT_41929-T1
Valid prediction for GlimmerHMM_glimmerT_41920-T1
Valid prediction for Augustus_model.g27916.t1
Valid prediction for snap_scaffold_18-snap.520-T1
Valid prediction for snap_scaffold_18-snap.491-T1
Valid prediction for snap_scaffold_18-snap.522-T1
Valid prediction for snap_scaffold_18-snap.521-T1
Valid prediction for snap_scaffold_18-snap.513-T1
Valid prediction for GlimmerHMM_glimmerT_41911-T1
Valid prediction for GlimmerHMM_glimmerT_41910-T1
Valid prediction for snap_scaffold_18-snap.495-T1
Valid prediction for GlimmerHMM_glimmerT_41928-T1
Valid prediction for snap_scaffold_18-snap.524-T1
Valid prediction for GlimmerHMM_glimmerT_41925-T1
Valid prediction for GlimmerHMM_glimmerT_41926-T1
Valid prediction for Augustus_model.g27912.t1
Valid prediction for Augustus_model.g27915.t1
Valid prediction for snap_scaffold_18-snap.529-T1
Valid prediction for snap_scaffold_18-snap.506-T1
Valid prediction for Augustus_model.g27918.t1
Valid prediction for GlimmerHMM_glimmerT_41923-T1
Valid prediction for pasa_asmbl_20412.p1
Valid prediction for GlimmerHMM_glimmerT_41924-T1
Valid prediction for GlimmerHMM_glimmerT_41907-T1
Valid prediction for Augustus_model.g27911.t1
Valid prediction for GlimmerHMM_glimmerT_41915-T1
Valid prediction for snap_scaffold_18-snap.502-T1
Valid prediction for snap_scaffold_18-snap.511-T1
Valid prediction for snap_scaffold_18-snap.507-T1
Valid prediction for Augustus_model.g27914.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_18-snap.500-T1
Valid prediction for Augustus_model.g27922.t1
Valid prediction for snap_scaffold_18-snap.514-T1
Valid prediction for snap_scaffold_18-snap.508-T1
Valid prediction for snap_scaffold_18-snap.509-T1
Valid prediction for snap_scaffold_18-snap.527-T1
Valid prediction for snap_scaffold_18-snap.499-T1
Valid prediction for GlimmerHMM_glimmerT_41912-T1
Valid prediction for Augustus_model.g27913.t1
Valid prediction for snap_scaffold_18-snap.503-T1
Valid prediction for snap_scaffold_18-snap.530-T1
Valid prediction for GlimmerHMM_glimmerT_41930-T1
Valid prediction for GlimmerHMM_glimmerT_41921-T1
Valid prediction for GlimmerHMM_glimmerT_41922-T1
Valid prediction for snap_scaffold_18-snap.501-T1
Valid prediction for CodingQuarry_transcript_23694-T1
Valid prediction for GlimmerHMM_glimmerT_41905-T1
Valid prediction for Augustus_model.g27902.t1
Couldn't classify 33127, 33189
Sorry, prediction pasa_asmbl_20204.p1 fails validation.
(GGC)	 AG	33127-33189	GT	GGG
(CTG)	 AG	33338-33450	GC	AGG
(GTC)	 AG	33644-33761	GT	ATG
(GAA)	 AG	33851-33949	GT	GCG
(GAT)	 AG	34099-34270	GT	TCG
(CGG)	 AG	34387-34520	CC	GAC
-recovered pasa_asmbl_20204.p1, terminal, 34387, 34520
-recovered pasa_asmbl_20204.p1, internal, 33127, 33189
-recovered pasa_asmbl_20204.p1, internal, 33338, 33450
-recovered pasa_asmbl_20204.p1, internal, 33644, 33761
-recovered pasa_asmbl_20204.p1, internal, 33851, 33949
-recovered pasa_asmbl_20204.p1, internal, 34099, 34270
Valid prediction for snap_scaffold_18-snap.505-T1
Valid prediction for GlimmerHMM_glimmerT_41909-T1
Valid prediction for Augustus_model.g27920.t1
Valid prediction for GlimmerHMM_glimmerT_41918-T1
Valid prediction for GlimmerHMM_glimmerT_41914-T1
Valid prediction for GlimmerHMM_glimmerT_41931-T1
Valid prediction for snap_scaffold_18-snap.525-T1
Valid prediction for snap_scaffold_18-snap.492-T1
Valid prediction for snap_scaffold_18-snap.512-T1
Couldn't classify 75935, 76095
Sorry, prediction pasa_asmbl_20219.p1 fails validation.
(ATG)	 GG	73884-73980	GT	AGG
(GTA)	 AG	74322-74495	GT	AGG
(GAG)	 AG	75935-76095	GG	AAG
-recovered pasa_asmbl_20219.p1, initial, 73884, 73980
-recovered pasa_asmbl_20219.p1, internal, 74322, 74495
Valid prediction for snap_scaffold_18-snap.496-T1
Valid prediction for snap_scaffold_18-snap.510-T1
Valid prediction for snap_scaffold_18-snap.517-T1
Couldn't classify 185712, 185817
Sorry, prediction pasa_asmbl_19725.p1 fails validation.
(GGA)	 TC	185712-185817	GT	AGG
(GGA)	 AG	186002-186111	GT	AGG
(GCA)	 AG	188526-188639	GT	ACG
(GCT)	 AG	189695-189778	GT	AGG
(TAG)	 AG	190524-190526	AC	AGA
-recovered pasa_asmbl_19725.p1, terminal, 190524, 190526
-recovered pasa_asmbl_19725.p1, internal, 186002, 186111
-recovered pasa_asmbl_19725.p1, internal, 188526, 188639
-recovered pasa_asmbl_19725.p1, internal, 189695, 189778
Valid prediction for GlimmerHMM_glimmerT_41927-T1
Valid prediction for snap_scaffold_18-snap.498-T1
Valid prediction for Augustus_model.g27910.t1
Valid prediction for Augustus_model.g27908.t1
Valid prediction for Augustus_model.g27905.t1
Valid prediction for snap_scaffold_18-snap.489-T1
Valid prediction for Augustus_model.g27906.t1
Valid prediction for pasa_asmbl_19728.p1
Valid prediction for HiQ_model.g27907.t1
Valid prediction for snap_scaffold_18-snap.488-T1
Valid prediction for snap_scaffold_18-snap.516-T1
Valid prediction for snap_scaffold_18-snap.523-T1
Valid prediction for snap_scaffold_18-snap.504-T1
Valid prediction for snap_scaffold_18-snap.490-T1
Valid prediction for Augustus_model.g27919.t1
Valid prediction for snap_scaffold_18-snap.528-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13331, rend_intergenic: 11774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16189, rend_intergenic: 14120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37690, rend_intergenic: 31782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92833, rend_intergenic: 86903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172876, rend_intergenic: 168914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186084, rend_intergenic: 180376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218790, rend_intergenic: 214638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223234, rend_intergenic: 219458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226299, rend_intergenic: 224496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 245219
-exon list size: 319


building trellis

0.3    
0.6    
0.9    
1.2    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.5    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.8    
99.1    
99.4    
99.7    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 13331, rend_intergenic: 11774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16189, rend_intergenic: 14120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37690, rend_intergenic: 31782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92833, rend_intergenic: 86903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172876, rend_intergenic: 168914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186084, rend_intergenic: 180376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218790, rend_intergenic: 214638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223234, rend_intergenic: 219458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226299, rend_intergenic: 224496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support