-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_6350628-6595545

-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_22317-T1
Valid prediction for snap_scaffold_9-snap.1368-T1
Valid prediction for Augustus_model.g14849.t1
Valid prediction for GlimmerHMM_glimmerT_22339-T1
Valid prediction for snap_scaffold_9-snap.1335-T1
Valid prediction for Augustus_model.g14850.t1
Valid prediction for snap_scaffold_9-snap.1336-T1
Valid prediction for snap_scaffold_9-snap.1358-T1
Valid prediction for snap_scaffold_9-snap.1349-T1
Valid prediction for snap_scaffold_9-snap.1353-T1
Valid prediction for snap_scaffold_9-snap.1337-T1
Valid prediction for GlimmerHMM_glimmerT_22315-T1
Valid prediction for CodingQuarry_transcript_62206-T1
Valid prediction for snap_scaffold_9-snap.1345-T1
Valid prediction for GlimmerHMM_glimmerT_22334-T1
Valid prediction for snap_scaffold_9-snap.1366-T1
Valid prediction for Augustus_model.g14834.t1
Valid prediction for snap_scaffold_9-snap.1341-T1
Valid prediction for GlimmerHMM_glimmerT_22332-T1
Valid prediction for snap_scaffold_9-snap.1365-T1
Valid prediction for snap_scaffold_9-snap.1362-T1
Valid prediction for CodingQuarry_transcript_62205-T1
Valid prediction for GlimmerHMM_glimmerT_22336-T1
Valid prediction for snap_scaffold_9-snap.1355-T1
Valid prediction for GlimmerHMM_glimmerT_22329-T1
Couldn't classify 53410, 53571
Sorry, prediction pasa_asmbl_54095.p1 fails validation.
(GTC)	 GT	53410-53571	GT	TGG
(GTT)	 AG	53826-53879	GT	AGG
(AGG)	 AG	54149-54199	GT	AAG
(GAC)	 AG	54509-54613	GT	ACG
(GAA)	 AG	54936-54989	GT	AGG
(CAG)	 AG	55199-55279	GT	GAG
(TCC)	 AG	55412-55486	GT	AGG
(GGT)	 AG	55814-55975	GT	GGG
(GGC)	 AG	56133-56199	GT	CAG
(AAA)	 AG	56374-56482	GT	AGG
(GTT)	 AG	56736-56844	GT	AGG
(GTG)	 AG	57126-57209	AG	AGA
-recovered pasa_asmbl_54095.p1, terminal, 57126, 57209
-recovered pasa_asmbl_54095.p1, internal, 53826, 53879
-recovered pasa_asmbl_54095.p1, internal, 54149, 54199
-recovered pasa_asmbl_54095.p1, internal, 54509, 54613
-recovered pasa_asmbl_54095.p1, internal, 54936, 54989
-recovered pasa_asmbl_54095.p1, internal, 55199, 55279
-recovered pasa_asmbl_54095.p1, internal, 55412, 55486
-recovered pasa_asmbl_54095.p1, internal, 55814, 55975
-recovered pasa_asmbl_54095.p1, internal, 56133, 56199
-recovered pasa_asmbl_54095.p1, internal, 56374, 56482
-recovered pasa_asmbl_54095.p1, internal, 56736, 56844
Valid prediction for GlimmerHMM_glimmerT_22333-T1
Valid prediction for snap_scaffold_9-snap.1354-T1
Valid prediction for HiQ_model.g14836.t1
Valid prediction for Augustus_model.g14845.t1
Valid prediction for GlimmerHMM_glimmerT_22327-T1
Valid prediction for GlimmerHMM_glimmerT_22330-T1
Valid prediction for snap_scaffold_9-snap.1367-T1
Valid prediction for snap_scaffold_9-snap.1370-T1
Valid prediction for GlimmerHMM_glimmerT_22322-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_9-snap.1346-T1
Valid prediction for snap_scaffold_9-snap.1342-T1
Valid prediction for Augustus_model.g14842.t1
Valid prediction for snap_scaffold_9-snap.1363-T1
Valid prediction for Augustus_model.g14841.t1
Valid prediction for Augustus_model.g14847.t1
Valid prediction for snap_scaffold_9-snap.1356-T1
Valid prediction for GlimmerHMM_glimmerT_22326-T1
Valid prediction for HiQ_model.g14835.t1
Valid prediction for snap_scaffold_9-snap.1369-T1
Valid prediction for CodingQuarry_transcript_62207-T1
Valid prediction for snap_scaffold_9-snap.1352-T1
Valid prediction for GlimmerHMM_glimmerT_22338-T1
Valid prediction for GlimmerHMM_glimmerT_22324-T1
Valid prediction for snap_scaffold_9-snap.1351-T1
Valid prediction for pasa_asmbl_55053.p1
Valid prediction for Augustus_model.g14837.t1
Valid prediction for GlimmerHMM_glimmerT_22337-T1
Valid prediction for GlimmerHMM_glimmerT_22328-T1
Valid prediction for GlimmerHMM_glimmerT_22320-T1
Valid prediction for snap_scaffold_9-snap.1360-T1
Valid prediction for GlimmerHMM_glimmerT_22323-T1
Valid prediction for GlimmerHMM_glimmerT_22318-T1
Valid prediction for Augustus_model.g14852.t1
Valid prediction for GlimmerHMM_glimmerT_22319-T1
Valid prediction for CodingQuarry_transcript_62204-T1
Valid prediction for CodingQuarry_transcript_62203-T1
Valid prediction for Augustus_model.g14839.t1
Valid prediction for snap_scaffold_9-snap.1340-T1
Valid prediction for snap_scaffold_9-snap.1357-T1
Valid prediction for Augustus_model.g14848.t1
Valid prediction for HiQ_model.g14838.t1
Valid prediction for snap_scaffold_9-snap.1339-T1
Valid prediction for GlimmerHMM_glimmerT_22321-T1
Valid prediction for Augustus_model.g14846.t1
Valid prediction for snap_scaffold_9-snap.1344-T1
Valid prediction for snap_scaffold_9-snap.1350-T1
Valid prediction for Augustus_model.g14840.t1
Valid prediction for GlimmerHMM_glimmerT_22316-T1
Valid prediction for GlimmerHMM_glimmerT_22331-T1
Valid prediction for snap_scaffold_9-snap.1338-T1
Valid prediction for snap_scaffold_9-snap.1359-T1
Valid prediction for snap_scaffold_9-snap.1347-T1
Valid prediction for GlimmerHMM_glimmerT_22314-T1
Valid prediction for Augustus_model.g14844.t1
Valid prediction for GlimmerHMM_glimmerT_22313-T1
Valid prediction for GlimmerHMM_glimmerT_22325-T1
Valid prediction for snap_scaffold_9-snap.1364-T1
Valid prediction for snap_scaffold_9-snap.1348-T1
Valid prediction for snap_scaffold_9-snap.1361-T1
Valid prediction for pasa_asmbl_55056.p1
Valid prediction for GlimmerHMM_glimmerT_22335-T1
Valid prediction for Augustus_model.g14843.t1
Valid prediction for Augustus_model.g14851.t1
Valid prediction for snap_scaffold_9-snap.1343-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 54482, rend_intergenic: 51409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73855, rend_intergenic: 71254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84787, rend_intergenic: 82825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87437, rend_intergenic: 85105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108771, rend_intergenic: 107897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113446, rend_intergenic: 110887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236421, rend_intergenic: 231638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 244918
-exon list size: 329


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
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    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
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80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 54482, rend_intergenic: 51409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73855, rend_intergenic: 71254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84787, rend_intergenic: 82825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87437, rend_intergenic: 85105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108771, rend_intergenic: 107897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113446, rend_intergenic: 110887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236421, rend_intergenic: 231638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support