-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_5341553-5543364

-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.g31794.t1
Valid prediction for HiQ_model.g31793.t1
Valid prediction for snap_scaffold_21-snap.1080-T1
Valid prediction for pasa_asmbl_28565.p1
Valid prediction for snap_scaffold_21-snap.1082-T1
Valid prediction for Augustus_model.g31790.t1
Valid prediction for GlimmerHMM_glimmerT_47687-T1
Valid prediction for CodingQuarry_transcript_32541-T1
Valid prediction for HiQ_model.g31795.t1
Valid prediction for snap_scaffold_21-snap.1083-T1
Valid prediction for snap_scaffold_21-snap.1098-T1
Valid prediction for Augustus_model.g31788.t1
Couldn't classify 35163, 35552
Sorry, prediction pasa_asmbl_28564.p1 fails validation.
(CTG)	 CA	35163-35552	CT	GAC
Valid prediction for HiQ_model.g31810.t1
Valid prediction for GlimmerHMM_glimmerT_47674-T1
Valid prediction for Augustus_model.g31811.t1
Valid prediction for snap_scaffold_21-snap.1077-T1
Valid prediction for snap_scaffold_21-snap.1093-T1
Valid prediction for GlimmerHMM_glimmerT_47677-T1
Valid prediction for GlimmerHMM_glimmerT_47682-T1
Valid prediction for snap_scaffold_21-snap.1097-T1
Valid prediction for Augustus_model.g31796.t1
Valid prediction for snap_scaffold_21-snap.1064-T1
Valid prediction for GlimmerHMM_glimmerT_47680-T1
Valid prediction for CodingQuarry_transcript_32534-T1
Valid prediction for CodingQuarry_transcript_32536-T1
Valid prediction for GlimmerHMM_glimmerT_47675-T1
Valid prediction for snap_scaffold_21-snap.1087-T1
Valid prediction for pasa_asmbl_28568.p1
Valid prediction for snap_scaffold_21-snap.1059-T1
Valid prediction for snap_scaffold_21-snap.1075-T1
Valid prediction for Augustus_model.g31801.t1
Valid prediction for GlimmerHMM_glimmerT_47697-T1
Valid prediction for pasa_asmbl_28574.p1
Couldn't classify 95329, 95445
Sorry, prediction pasa_asmbl_28566.p1 fails validation.
(ACA)	 AC	95329-95445	GT	CGG
(ATA)	 AG	95585-95773	GT	AGG
(GAT)	 AG	95906-96424	AG	AGA
-recovered pasa_asmbl_28566.p1, terminal, 95906, 96424
-recovered pasa_asmbl_28566.p1, internal, 95585, 95773
Valid prediction for snap_scaffold_21-snap.1076-T1
Valid prediction for Augustus_model.g31787.t1
Valid prediction for snap_scaffold_21-snap.1070-T1
Valid prediction for HiQ_model.g31792.t1
Valid prediction for CodingQuarry_transcript_32537-T1
Valid prediction for GlimmerHMM_glimmerT_47681-T1
Valid prediction for pasa_asmbl_28573.p1
Valid prediction for CodingQuarry_transcript_32535-T1
Valid prediction for Augustus_model.g31807.t1
Valid prediction for snap_scaffold_21-snap.1065-T1
Valid prediction for GlimmerHMM_glimmerT_47670-T1
Valid prediction for snap_scaffold_21-snap.1090-T1
Valid prediction for snap_scaffold_21-snap.1069-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.1073-T1
Valid prediction for snap_scaffold_21-snap.1074-T1
Valid prediction for snap_scaffold_21-snap.1063-T1
Valid prediction for Augustus_model.g31808.t1
Valid prediction for GlimmerHMM_glimmerT_47671-T1
Valid prediction for GlimmerHMM_glimmerT_47679-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_47684-T1
Valid prediction for snap_scaffold_21-snap.1061-T1
Valid prediction for HiQ_model.g31798.t1
Valid prediction for snap_scaffold_21-snap.1086-T1
Valid prediction for GlimmerHMM_glimmerT_47696-T1
Valid prediction for CodingQuarry_transcript_32542-T1
Valid prediction for snap_scaffold_21-snap.1089-T1
Valid prediction for Augustus_model.g31802.t1
Valid prediction for Augustus_model.g31797.t1
Valid prediction for snap_scaffold_21-snap.1067-T1
Valid prediction for GlimmerHMM_glimmerT_47691-T1
Valid prediction for snap_scaffold_21-snap.1072-T1
Valid prediction for snap_scaffold_21-snap.1068-T1
Valid prediction for GlimmerHMM_glimmerT_47676-T1
Valid prediction for snap_scaffold_21-snap.1062-T1
Valid prediction for snap_scaffold_21-snap.1066-T1
Valid prediction for Augustus_model.g31803.t1
Valid prediction for snap_scaffold_21-snap.1071-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_47673-T1
Valid prediction for snap_scaffold_21-snap.1094-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.1084-T1
Valid prediction for HiQ_model.g31804.t1
Valid prediction for snap_scaffold_21-snap.1078-T1
Valid prediction for GlimmerHMM_glimmerT_47678-T1
Valid prediction for Augustus_model.g31805.t1
Valid prediction for Augustus_model.g31809.t1
Valid prediction for snap_scaffold_21-snap.1081-T1
Valid prediction for snap_scaffold_21-snap.1096-T1
Valid prediction for GlimmerHMM_glimmerT_47699-T1
Valid prediction for CodingQuarry_transcript_32543-T1
Valid prediction for snap_scaffold_21-snap.1079-T1
Valid prediction for GlimmerHMM_glimmerT_47683-T1
Valid prediction for pasa_asmbl_27676.p1
Valid prediction for CodingQuarry_transcript_32540-T1
Valid prediction for snap_scaffold_21-snap.1088-T1
Valid prediction for GlimmerHMM_glimmerT_47698-T1
Valid prediction for Augustus_model.g31789.t1
Valid prediction for GlimmerHMM_glimmerT_47690-T1
Valid prediction for GlimmerHMM_glimmerT_47672-T1
Valid prediction for Augustus_model.g31799.t1
Valid prediction for GlimmerHMM_glimmerT_47694-T1
Valid prediction for CodingQuarry_transcript_32538-T1
Valid prediction for GlimmerHMM_glimmerT_47685-T1
Valid prediction for GlimmerHMM_glimmerT_47695-T1
Valid prediction for snap_scaffold_21-snap.1091-T1
Valid prediction for GlimmerHMM_glimmerT_47689-T1
Valid prediction for GlimmerHMM_glimmerT_47688-T1
Valid prediction for CodingQuarry_transcript_32539-T1
Valid prediction for snap_scaffold_21-snap.1085-T1
Valid prediction for Augustus_model.g31791.t1
Valid prediction for snap_scaffold_21-snap.1100-T1
Valid prediction for HiQ_model.g31812.t1
Valid prediction for GlimmerHMM_glimmerT_47686-T1
Valid prediction for pasa_asmbl_27660.p1
Valid prediction for snap_scaffold_21-snap.1092-T1
Valid prediction for snap_scaffold_21-snap.1095-T1
Valid prediction for CodingQuarry_transcript_32533-T1
Couldn't classify 74135, 74320
Sorry, prediction pasa_asmbl_27657.p1 fails validation.
(CCA)	 GA	74135-74320	GT	GTG
(GTC)	 AG	74410-74581	GT	GGG
(GGA)	 AG	74699-74801	GT	AAG
(GAA)	 AG	74916-75060	AC	GAA
-recovered pasa_asmbl_27657.p1, terminal, 74916, 75060
-recovered pasa_asmbl_27657.p1, internal, 74410, 74581
-recovered pasa_asmbl_27657.p1, internal, 74699, 74801
Valid prediction for HiQ_model.g31813.t1
Valid prediction for Augustus_model.g31806.t1
Couldn't classify 22831, 22940
Sorry, prediction pasa_asmbl_27663.p2 fails validation.
(GTC)	 AC	22831-22940	GT	AGG
(ACA)	 AG	23988-24081	GT	AGG
(CTG)	 AG	24875-24941	GT	CAG
(TGA)	 AG	25351-25415	TG	AAT
-recovered pasa_asmbl_27663.p2, terminal, 25351, 25415
-recovered pasa_asmbl_27663.p2, internal, 23988, 24081
-recovered pasa_asmbl_27663.p2, internal, 24875, 24941
Valid prediction for Augustus_model.g31800.t1
Valid prediction for GlimmerHMM_glimmerT_47693-T1
Couldn't classify 167790, 167954
Sorry, prediction pasa_asmbl_27649.p1 fails validation.
(AAA)	 GT	167790-167954	GT	AGG
(GGT)	 AG	168874-168970	GT	TGG
(GGT)	 AG	169215-169284	GT	AGG
(GCA)	 AG	170007-170124	GT	TGG
(ATC)	 AG	170357-170464	AC	AGA
-recovered pasa_asmbl_27649.p1, terminal, 170357, 170464
-recovered pasa_asmbl_27649.p1, internal, 168874, 168970
-recovered pasa_asmbl_27649.p1, internal, 169215, 169284
-recovered pasa_asmbl_27649.p1, internal, 170007, 170124
Valid prediction for GlimmerHMM_glimmerT_47692-T1
Valid prediction for HiQ_model.g31786.t1
Valid prediction for snap_scaffold_21-snap.1099-T1
Valid prediction for snap_scaffold_21-snap.1060-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29909, rend_intergenic: 3116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71754, rend_intergenic: 67820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79843, rend_intergenic: 79042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133755, rend_intergenic: 132904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138506, rend_intergenic: 134616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141563, rend_intergenic: 139232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163595, rend_intergenic: 159384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164951, rend_intergenic: 164132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170236, rend_intergenic: 165473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173449, rend_intergenic: 170255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201812
-exon list size: 348


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 29909, rend_intergenic: 3116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71754, rend_intergenic: 67820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79843, rend_intergenic: 79042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133755, rend_intergenic: 132904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138506, rend_intergenic: 134616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141563, rend_intergenic: 139232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163595, rend_intergenic: 159384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164951, rend_intergenic: 164132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170236, rend_intergenic: 165473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173449, rend_intergenic: 170255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support