-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_6105366-6279317

-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_14765-T1
Valid prediction for snap_scaffold_6-snap.1387-T1
Valid prediction for snap_scaffold_6-snap.1390-T1
Couldn't classify 25708, 25830
Couldn't classify 26341, 26508
Sorry, prediction pasa_asmbl_47925.p1 fails validation.
(CAC)	 GC	25708-25830	GT	AGG
(TTA)	 AG	26055-26219	GT	AGG
(GTC)	 AG	26341-26508	GA	TGG
-recovered pasa_asmbl_47925.p1, internal, 26055, 26219
Couldn't classify 41333, 41569
Sorry, prediction pasa_asmbl_47002.p1 fails validation.
(CCA)	 CC	41333-41569	GT	ACG
(GGC)	 AG	41702-41779	GT	AGG
(GAA)	 AG	41895-42092	GT	AGG
(ACC)	 AG	42272-42361	GT	GGG
(GAC)	 AG	42588-42766	GT	AGG
(TCT)	 AG	43066-43219	GT	AGG
-recovered pasa_asmbl_47002.p1, terminal, 43066, 43219
-recovered pasa_asmbl_47002.p1, internal, 41702, 41779
-recovered pasa_asmbl_47002.p1, internal, 41895, 42092
-recovered pasa_asmbl_47002.p1, internal, 42272, 42361
-recovered pasa_asmbl_47002.p1, internal, 42588, 42766
-recovered pasa_asmbl_47002.p1, internal, 43066, 43219
Valid prediction for snap_scaffold_6-snap.1405-T1
Valid prediction for GlimmerHMM_glimmerT_14762-T1
Valid prediction for Augustus_model.g9775.t1
Valid prediction for GlimmerHMM_glimmerT_14747-T1
Valid prediction for snap_scaffold_6-snap.1380-T1
Valid prediction for snap_scaffold_6-snap.1404-T1
Valid prediction for GlimmerHMM_glimmerT_14748-T1
Valid prediction for GlimmerHMM_glimmerT_14759-T1
Valid prediction for GlimmerHMM_glimmerT_14745-T1
Valid prediction for snap_scaffold_6-snap.1389-T1
Valid prediction for snap_scaffold_6-snap.1394-T1
Valid prediction for Augustus_model.g9779.t1
Valid prediction for snap_scaffold_6-snap.1376-T1
Valid prediction for snap_scaffold_6-snap.1398-T1
Valid prediction for GlimmerHMM_glimmerT_14751-T1
Valid prediction for GlimmerHMM_glimmerT_14757-T1
Valid prediction for snap_scaffold_6-snap.1408-T1
Couldn't classify 28801, 29271
Sorry, prediction pasa_asmbl_46998.p1 fails validation.
(GAC)	 AC	28801-29271	GA	CAG
Valid prediction for Augustus_model.g9776.t1
Valid prediction for snap_scaffold_6-snap.1379-T1
Valid prediction for snap_scaffold_6-snap.1396-T1
Valid prediction for snap_scaffold_6-snap.1377-T1
Valid prediction for snap_scaffold_6-snap.1392-T1
Valid prediction for snap_scaffold_6-snap.1410-T1
Valid prediction for GlimmerHMM_glimmerT_14756-T1
Valid prediction for snap_scaffold_6-snap.1384-T1
Valid prediction for snap_scaffold_6-snap.1381-T1
Valid prediction for Augustus_model.g9769.t1
Valid prediction for snap_scaffold_6-snap.1411-T1
Valid prediction for snap_scaffold_6-snap.1400-T1
Valid prediction for Augustus_model.g9773.t1
Valid prediction for GlimmerHMM_glimmerT_14749-T1
Valid prediction for Augustus_model.g9780.t1
Valid prediction for snap_scaffold_6-snap.1374-T1
Valid prediction for snap_scaffold_6-snap.1378-T1
Couldn't classify 36034, 36178
Sorry, prediction pasa_asmbl_46999.p1 fails validation.
(ATG)	 GG	32459-32495	GT	AGG
(GTC)	 AG	32577-32699	GT	ACG
(CTA)	 AG	32825-32889	GT	CTG
(GGC)	 AG	32980-33133	GT	AGG
(GCG)	 AG	33229-33370	GT	AGG
(ACA)	 AG	33545-33736	GT	AAG
(TGC)	 AG	33878-34008	GT	AGG
(GTC)	 AG	34133-34290	GT	AGG
(CTT)	 AG	34394-34606	GT	TGG
(GTC)	 AG	34783-34970	GT	CAG
(GAT)	 AG	35261-35381	GT	AAG
(GTA)	 AG	35500-35600	GT	AGG
(GTT)	 AG	35721-35903	GT	CGG
(TCA)	 AG	36034-36178	AA	TGA
-recovered pasa_asmbl_46999.p1, initial, 32459, 32495
add_exon() Sorry, pasa_asmbl_46999.p1 33545-33736-terminal-1 is invalid.
-recovered pasa_asmbl_46999.p1, terminal, 33545, 33736
-recovered pasa_asmbl_46999.p1, internal, 32577, 32699
-recovered pasa_asmbl_46999.p1, internal, 32825, 32889
-recovered pasa_asmbl_46999.p1, internal, 32980, 33133
-recovered pasa_asmbl_46999.p1, internal, 33229, 33370
-recovered pasa_asmbl_46999.p1, internal, 33545, 33736
-recovered pasa_asmbl_46999.p1, internal, 33878, 34008
-recovered pasa_asmbl_46999.p1, internal, 34133, 34290
-recovered pasa_asmbl_46999.p1, internal, 34394, 34606
-recovered pasa_asmbl_46999.p1, internal, 34783, 34970
-recovered pasa_asmbl_46999.p1, internal, 35261, 35381
-recovered pasa_asmbl_46999.p1, internal, 35500, 35600
-recovered pasa_asmbl_46999.p1, internal, 35721, 35903
Valid prediction for GlimmerHMM_glimmerT_14754-T1
Valid prediction for Augustus_model.g9772.t1
Couldn't classify 36462, 36578
Couldn't classify 37197, 37396
Sorry, prediction pasa_asmbl_47000.p1 fails validation.
(AGC)	 CA	36462-36578	GT	AGG
(GAC)	 AG	36809-37019	GT	AGG
(ATG)	 AG	37197-37396	GT	AGG
add_exon() Sorry, pasa_asmbl_47000.p1 37197-37396-initial-1 is invalid.
-recovered pasa_asmbl_47000.p1, initial, 37197, 37396
-recovered pasa_asmbl_47000.p1, internal, 36809, 37019
-recovered pasa_asmbl_47000.p1, internal, 37197, 37396
Valid prediction for GlimmerHMM_glimmerT_14769-T1
Valid prediction for GlimmerHMM_glimmerT_14770-T1
Valid prediction for snap_scaffold_6-snap.1382-T1
Valid prediction for GlimmerHMM_glimmerT_14744-T1
Valid prediction for Augustus_model.g9771.t1
Valid prediction for GlimmerHMM_glimmerT_14752-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_14753-T1
Valid prediction for snap_scaffold_6-snap.1397-T1
Valid prediction for GlimmerHMM_glimmerT_14758-T1
Valid prediction for snap_scaffold_6-snap.1391-T1
Valid prediction for GlimmerHMM_glimmerT_14766-T1
Valid prediction for GlimmerHMM_glimmerT_14760-T1
Valid prediction for snap_scaffold_6-snap.1407-T1
Valid prediction for snap_scaffold_6-snap.1375-T1
Valid prediction for Augustus_model.g9770.t1
Valid prediction for GlimmerHMM_glimmerT_14750-T1
Valid prediction for Augustus_model.g9777.t1
Valid prediction for GlimmerHMM_glimmerT_14767-T1
Valid prediction for GlimmerHMM_glimmerT_14763-T1
Valid prediction for snap_scaffold_6-snap.1406-T1
Valid prediction for snap_scaffold_6-snap.1393-T1
Valid prediction for GlimmerHMM_glimmerT_14746-T1
Valid prediction for snap_scaffold_6-snap.1401-T1
Valid prediction for snap_scaffold_6-snap.1399-T1
Valid prediction for snap_scaffold_6-snap.1402-T1
Valid prediction for GlimmerHMM_glimmerT_14755-T1
Valid prediction for snap_scaffold_6-snap.1383-T1
Valid prediction for snap_scaffold_6-snap.1385-T1
Valid prediction for snap_scaffold_6-snap.1388-T1
Valid prediction for GlimmerHMM_glimmerT_14761-T1
Valid prediction for Augustus_model.g9778.t1
Valid prediction for Augustus_model.g9774.t1
Valid prediction for snap_scaffold_6-snap.1386-T1
Valid prediction for GlimmerHMM_glimmerT_14764-T1
Valid prediction for snap_scaffold_6-snap.1403-T1
Valid prediction for GlimmerHMM_glimmerT_14768-T1
Valid prediction for snap_scaffold_6-snap.1409-T1
Valid prediction for snap_scaffold_6-snap.1395-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 80893, rend_intergenic: 70245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95236, rend_intergenic: 89861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106158, rend_intergenic: 105279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114843, rend_intergenic: 111573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140129, rend_intergenic: 137675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173952
-exon list size: 299


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.7    
3.0    
3.3    
3.7    
4.0    
4.3    
4.7    
5.0    
5.3    
5.6    
6.0    
6.3    
6.6    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
9.0    
9.3    
9.6    
10.0    
10.3    
10.6    
11.0    
11.3    
11.6    
12.0    
12.3    
12.6    
13.0    
13.3    
13.6    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.3    
16.6    
16.9    
17.3    
17.6    
17.9    
18.3    
18.6    
18.9    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.3    
21.6    
21.9    
22.3    
22.6    
22.9    
23.3    
23.6    
23.9    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.6    
26.9    
27.2    
27.6    
27.9    
28.2    
28.6    
28.9    
29.2    
29.6    
29.9    
30.2    
30.6    
30.9    
31.2    
31.6    
31.9    
32.2    
32.6    
32.9    
33.2    
33.6    
33.9    
34.2    
34.6    
34.9    
35.2    
35.5    
35.9    
36.2    
36.5    
36.9    
37.2    
37.5    
37.9    
38.2    
38.5    
38.9    
39.2    
39.5    
39.9    
40.2    
40.5    
40.9    
41.2    
41.5    
41.9    
42.2    
42.5    
42.9    
43.2    
43.5    
43.9    
44.2    
44.5    
44.9    
45.2    
45.5    
45.8    
46.2    
46.5    
46.8    
47.2    
47.5    
47.8    
48.2    
48.5    
48.8    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.2    
51.5    
51.8    
52.2    
52.5    
52.8    
53.2    
53.5    
53.8    
54.2    
54.5    
54.8    
55.1    
55.5    
55.8    
56.1    
56.5    
56.8    
57.1    
57.5    
57.8    
58.1    
58.5    
58.8    
59.1    
59.5    
59.8    
60.1    
60.5    
60.8    
61.1    
61.5    
61.8    
62.1    
62.5    
62.8    
63.1    
63.5    
63.8    
64.1    
64.5    
64.8    
65.1    
65.4    
65.8    
66.1    
66.4    
66.8    
67.1    
67.4    
67.8    
68.1    
68.4    
68.8    
69.1    
69.4    
69.8    
70.1    
70.4    
70.8    
71.1    
71.4    
71.8    
72.1    
72.4    
72.8    
73.1    
73.4    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.1    
76.4    
76.7    
77.1    
77.4    
77.7    
78.1    
78.4    
78.7    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.1    
81.4    
81.7    
82.1    
82.4    
82.7    
83.1    
83.4    
83.7    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.4    
86.7    
87.0    
87.4    
87.7    
88.0    
88.4    
88.7    
89.0    
89.4    
89.7    
90.0    
90.4    
90.7    
91.0    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.4    
93.7    
94.0    
94.4    
94.7    
95.0    
95.3    
95.7    
96.0    
96.3    
96.7    
97.0    
97.3    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 80893, rend_intergenic: 70245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95236, rend_intergenic: 89861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106158, rend_intergenic: 105279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114843, rend_intergenic: 111573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140129, rend_intergenic: 137675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support