-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_5474563-5652293

-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.g2616.t1
Valid prediction for snap_scaffold_2-snap.1255-T1
Valid prediction for Augustus_model.g2622.t1
Valid prediction for snap_scaffold_2-snap.1256-T1
Valid prediction for GeneMark_model.6432_t
Valid prediction for GeneMark_model.6426_t
Valid prediction for snap_scaffold_2-snap.1261-T1
Valid prediction for GeneMark_model.6448_t
Valid prediction for snap_scaffold_2-snap.1264-T1
Valid prediction for GeneMark_model.6449_t
Valid prediction for GeneMark_model.6441_t
Valid prediction for GeneMark_model.6452_t
Valid prediction for snap_scaffold_2-snap.1262-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.6430_t
Valid prediction for GeneMark_model.6454_t
Valid prediction for GlimmerHMM_glimmerT_3929-T1
Valid prediction for snap_scaffold_2-snap.1260-T1
Valid prediction for snap_scaffold_2-snap.1252-T1
Valid prediction for GlimmerHMM_glimmerT_3931-T1
Valid prediction for snap_scaffold_2-snap.1271-T1
Couldn't classify 28455, 28605
Couldn't classify 30265, 30305
Sorry, prediction pasa_asmbl_24451.p1 fails validation.
(GAC)	 TG	28455-28605	GT	CAG
(AGT)	 AG	29172-29294	GT	CAG
(ACT)	 AG	29511-29681	GT	CCG
(TGG)	 AG	30265-30305	AC	GCA
-recovered pasa_asmbl_24451.p1, internal, 29172, 29294
-recovered pasa_asmbl_24451.p1, internal, 29511, 29681
Valid prediction for GeneMark_model.6422_t
Valid prediction for snap_scaffold_2-snap.1249-T1
Valid prediction for GlimmerHMM_glimmerT_3926-T1
Valid prediction for Augustus_model.g2620.t1
Valid prediction for GeneMark_model.6437_t
Valid prediction for snap_scaffold_2-snap.1250-T1
Valid prediction for snap_scaffold_2-snap.1247-T1
Valid prediction for GeneMark_model.6433_t
Valid prediction for GeneMark_model.6439_t
Valid prediction for GlimmerHMM_glimmerT_3922-T1
Valid prediction for Augustus_model.g2618.t1
Valid prediction for snap_scaffold_2-snap.1265-T1
Valid prediction for GeneMark_model.6447_t
Valid prediction for snap_scaffold_2-snap.1268-T1
Valid prediction for GlimmerHMM_glimmerT_3921-T1
Valid prediction for GeneMark_model.6442_t
Couldn't classify 35994, 36032
Couldn't classify 37527, 37648
Sorry, prediction pasa_asmbl_24452.p1 fails validation.
(CAT)	 GT	35994-36032	GT	AGG
(CCA)	 AG	36327-36552	GT	CCG
(TGC)	 AG	36831-36946	GT	AGG
(TTG)	 AG	37154-37358	GT	AGG
(TTC)	 AG	37527-37648	GG	CAG
-recovered pasa_asmbl_24452.p1, internal, 36327, 36552
-recovered pasa_asmbl_24452.p1, internal, 36831, 36946
-recovered pasa_asmbl_24452.p1, internal, 37154, 37358
Valid prediction for GlimmerHMM_glimmerT_3925-T1
Valid prediction for GeneMark_model.6436_t
Valid prediction for GlimmerHMM_glimmerT_3932-T1
Valid prediction for snap_scaffold_2-snap.1253-T1
Valid prediction for GeneMark_model.6446_t
Valid prediction for snap_scaffold_2-snap.1270-T1
Valid prediction for GeneMark_model.6445_t
Valid prediction for snap_scaffold_2-snap.1246-T1
Valid prediction for Augustus_model.g2619.t1
Valid prediction for GeneMark_model.6424_t
Valid prediction for snap_scaffold_2-snap.1257-T1
Valid prediction for GeneMark_model.6427_t
Valid prediction for snap_scaffold_2-snap.1245-T1
Valid prediction for Augustus_model.g2617.t1
Valid prediction for GeneMark_model.6458_t
Valid prediction for GeneMark_model.6429_t
Couldn't classify 41258, 41288
Couldn't classify 44994, 45060
Sorry, prediction pasa_asmbl_24453.p1 fails validation.
(CAC)	 AC	41258-41288	GT	AGG
(CTA)	 AG	42098-42229	GT	AGG
(TGA)	 AG	42377-42455	GT	AGG
(TGA)	 AG	44994-45060	GA	GCG
-recovered pasa_asmbl_24453.p1, internal, 42098, 42229
-recovered pasa_asmbl_24453.p1, internal, 42377, 42455
Valid prediction for snap_scaffold_2-snap.1263-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 GeneMark_model.6453_t
Valid prediction for GeneMark_model.6443_t
Valid prediction for GlimmerHMM_glimmerT_3933-T1
Valid prediction for Augustus_model.g2614.t1
Valid prediction for GlimmerHMM_glimmerT_3919-T1
Valid prediction for GeneMark_model.6431_t
Valid prediction for GeneMark_model.6450_t
Valid prediction for Augustus_model.g2621.t1
Valid prediction for GeneMark_model.6425_t
Valid prediction for GlimmerHMM_glimmerT_3930-T1
Valid prediction for Augustus_model.g2615.t1
Valid prediction for Augustus_model.g2623.t1
Valid prediction for GeneMark_model.6444_t
Valid prediction for snap_scaffold_2-snap.1258-T1
Valid prediction for GlimmerHMM_glimmerT_3935-T1
Valid prediction for GlimmerHMM_glimmerT_3934-T1
Valid prediction for GlimmerHMM_glimmerT_3927-T1
Valid prediction for GlimmerHMM_glimmerT_3920-T1
Valid prediction for snap_scaffold_2-snap.1267-T1
Valid prediction for snap_scaffold_2-snap.1251-T1
Valid prediction for snap_scaffold_2-snap.1269-T1
Valid prediction for GeneMark_model.6451_t
Valid prediction for snap_scaffold_2-snap.1254-T1
Valid prediction for GeneMark_model.6435_t
Valid prediction for snap_scaffold_2-snap.1248-T1
Valid prediction for GeneMark_model.6423_t
Valid prediction for GeneMark_model.6438_t
Valid prediction for GeneMark_model.6428_t
Valid prediction for GlimmerHMM_glimmerT_3923-T1
Valid prediction for snap_scaffold_2-snap.1259-T1
Valid prediction for snap_scaffold_2-snap.1266-T1
Valid prediction for GeneMark_model.6456_t
Valid prediction for snap_scaffold_2-snap.1272-T1
Valid prediction for GlimmerHMM_glimmerT_3924-T1
Valid prediction for GeneMark_model.6457_t
Valid prediction for snap_scaffold_2-snap.1273-T1
Valid prediction for GeneMark_model.6455_t
Valid prediction for GeneMark_model.6440_t
Valid prediction for GlimmerHMM_glimmerT_3928-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42657, rend_intergenic: 28052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67279, rend_intergenic: 65242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100418, rend_intergenic: 80331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161746, rend_intergenic: 160743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173000, rend_intergenic: 166079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177731
-exon list size: 433


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.4    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.1    
5.3    
5.5    
5.7    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.4    
7.6    
7.8    
8.0    
8.3    
8.5    
8.7    
9.0    
9.2    
9.4    
9.7    
9.9    
10.1    
10.3    
10.6    
10.8    
11.0    
11.3    
11.5    
11.7    
12.0    
12.2    
12.4    
12.6    
12.9    
13.1    
13.3    
13.6    
13.8    
14.0    
14.3    
14.5    
14.7    
14.9    
15.2    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.0    
17.2    
17.5    
17.7    
17.9    
18.2    
18.4    
18.6    
18.9    
19.1    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
20.9    
21.1    
21.4    
21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
23.0    
23.2    
23.4    
23.7    
23.9    
24.1    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.4    
27.6    
27.8    
28.0    
28.3    
28.5    
28.7    
29.0    
29.2    
29.4    
29.7    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.3    
31.5    
31.7    
32.0    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
34.9    
35.2    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.5    
37.7    
37.9    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
40.9    
41.1    
41.4    
41.6    
41.8    
42.1    
42.3    
42.5    
42.8    
43.0    
43.2    
43.4    
43.7    
43.9    
44.1    
44.4    
44.6    
44.8    
45.1    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.7    
54.9    
55.2    
55.4    
55.6    
55.9    
56.1    
56.3    
56.6    
56.8    
57.0    
57.2    
57.5    
57.7    
57.9    
58.2    
58.4    
58.6    
58.9    
59.1    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.1    
62.3    
62.5    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.4    
64.6    
64.8    
65.1    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.0    
68.3    
68.5    
68.7    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.3    
70.6    
70.8    
71.0    
71.3    
71.5    
71.7    
72.0    
72.2    
72.4    
72.6    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.2    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.4    
87.6    
87.8    
88.0    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 42657, rend_intergenic: 28052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67279, rend_intergenic: 65242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100418, rend_intergenic: 80331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161746, rend_intergenic: 160743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173000, rend_intergenic: 166079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11788
-exon list size: 22


building trellis

4.2    
8.3    
12.5    
16.7    
20.8    
25.0    
29.2    
33.3    
37.5    
41.7    
45.8    
50.0    
54.2    
58.3    
62.5    
66.7    
70.8    
75.0    
79.2    
83.3    
87.5    
91.7    
95.8    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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