-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_7178733-7384144

-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: +)Couldn't classify 149060, 149352
Sorry, prediction pasa_asmbl_40155.p1 fails validation.
(TGC)	 AG	149060-149352	GT	AGG
(TGC)	 AG	149519-149654	GT	CTG
(AGC)	 AG	150310-150552	CC	GAC
-recovered pasa_asmbl_40155.p1, terminal, 150310, 150552
-recovered pasa_asmbl_40155.p1, internal, 149060, 149352
-recovered pasa_asmbl_40155.p1, internal, 149519, 149654
Valid prediction for HiQ_model.g4433.t1
Valid prediction for GlimmerHMM_glimmerT_6801-T1
Valid prediction for CodingQuarry_transcript_46203-T1
Valid prediction for Augustus_model.g4435.t1
Valid prediction for snap_scaffold_3-snap.1457-T1
Valid prediction for GlimmerHMM_glimmerT_6792-T1
Valid prediction for snap_scaffold_3-snap.1474-T1
Valid prediction for snap_scaffold_3-snap.1464-T1
Valid prediction for GlimmerHMM_glimmerT_6798-T1
Valid prediction for snap_scaffold_3-snap.1462-T1
Valid prediction for GlimmerHMM_glimmerT_6784-T1
Valid prediction for Augustus_model.g4426.t1
Valid prediction for snap_scaffold_3-snap.1466-T1
Valid prediction for GlimmerHMM_glimmerT_6793-T1
Valid prediction for snap_scaffold_3-snap.1475-T1
Couldn't classify 169915, 169980
Couldn't classify 173224, 173265
Sorry, prediction pasa_asmbl_40158.p1 fails validation.
(CCG)	 CT	169915-169980	GT	AGG
(GGC)	 AG	170068-170132	GT	AGG
(GCT)	 AG	170773-170889	GT	AGG
(TGA)	 AG	171802-171883	GT	AGG
(GCT)	 AG	172007-172084	GT	TAG
(TTC)	 AG	172202-172264	GT	CGG
(CGT)	 AG	173224-173265	CA	CCC
-recovered pasa_asmbl_40158.p1, terminal, 170773, 170889
-recovered pasa_asmbl_40158.p1, internal, 170068, 170132
-recovered pasa_asmbl_40158.p1, internal, 170773, 170889
-recovered pasa_asmbl_40158.p1, internal, 171802, 171883
-recovered pasa_asmbl_40158.p1, internal, 172007, 172084
-recovered pasa_asmbl_40158.p1, internal, 172202, 172264
Valid prediction for GlimmerHMM_glimmerT_6797-T1
Valid prediction for pasa_asmbl_40156.p1
Valid prediction for HiQ_model.g4421.t1
Valid prediction for snap_scaffold_3-snap.1491-T1
Valid prediction for snap_scaffold_3-snap.1459-T1
Valid prediction for GlimmerHMM_glimmerT_6777-T1
Valid prediction for Augustus_model.g4422.t1
Valid prediction for GlimmerHMM_glimmerT_6795-T1
Valid prediction for snap_scaffold_3-snap.1483-T1
Valid prediction for GlimmerHMM_glimmerT_6781-T1
Valid prediction for GlimmerHMM_glimmerT_6789-T1
Valid prediction for snap_scaffold_3-snap.1490-T1
Valid prediction for snap_scaffold_3-snap.1456-T1
Valid prediction for GlimmerHMM_glimmerT_6790-T1
Valid prediction for Augustus_model.g4434.t1
Valid prediction for Augustus_model.g4436.t1
Valid prediction for snap_scaffold_3-snap.1478-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_6785-T1
Valid prediction for Augustus_model.g4425.t1
Valid prediction for snap_scaffold_3-snap.1463-T1
Couldn't classify 20057, 20285
Sorry, prediction pasa_asmbl_40150.p1 fails validation.
(AGC)	 AC	20057-20285	GT	AGG
(CTC)	 AG	20482-20567	GT	GAG
(GGT)	 AG	20762-20936	GT	AGG
(ACA)	 AG	21057-21126	GT	AGG
(GAT)	 AG	21256-21370	GT	AGG
(ATC)	 AG	21506-21604	TC	GAT
add_exon() Sorry, pasa_asmbl_40150.p1 20762-20936-terminal-3 is invalid.
-recovered pasa_asmbl_40150.p1, terminal, 20762, 20936
-recovered pasa_asmbl_40150.p1, terminal, 21506, 21604
-recovered pasa_asmbl_40150.p1, internal, 20482, 20567
-recovered pasa_asmbl_40150.p1, internal, 20762, 20936
-recovered pasa_asmbl_40150.p1, internal, 21057, 21126
-recovered pasa_asmbl_40150.p1, internal, 21256, 21370
Valid prediction for GlimmerHMM_glimmerT_6778-T1
Couldn't classify 136593, 136617
Couldn't classify 140491, 140548
Sorry, prediction pasa_asmbl_40153.p1 fails validation.
(CTC)	 CC	136593-136617	GT	ATG
(CTG)	 AG	138441-138561	GT	AGG
(TGG)	 AG	138791-138878	GT	GGG
(GAT)	 AG	139039-139127	GT	TGG
(GTT)	 AG	140491-140548	GA	GAG
-recovered pasa_asmbl_40153.p1, internal, 138441, 138561
-recovered pasa_asmbl_40153.p1, internal, 138791, 138878
-recovered pasa_asmbl_40153.p1, internal, 139039, 139127
Valid prediction for GlimmerHMM_glimmerT_6800-T1
Valid prediction for snap_scaffold_3-snap.1487-T1
Valid prediction for snap_scaffold_3-snap.1484-T1
Valid prediction for GlimmerHMM_glimmerT_6796-T1
Valid prediction for Augustus_model.g4432.t1
Valid prediction for Augustus_model.g4430.t1
Valid prediction for snap_scaffold_3-snap.1480-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_6782-T1
Valid prediction for GlimmerHMM_glimmerT_6799-T1
Valid prediction for CodingQuarry_transcript_46200-T1
Valid prediction for snap_scaffold_3-snap.1460-T1
Valid prediction for snap_scaffold_3-snap.1489-T1
Valid prediction for pasa_asmbl_38956.p1
Valid prediction for GlimmerHMM_glimmerT_6791-T1
Valid prediction for Augustus_model.g4428.t1
Valid prediction for GlimmerHMM_glimmerT_6787-T1
Valid prediction for GlimmerHMM_glimmerT_6794-T1
Valid prediction for GlimmerHMM_glimmerT_6780-T1
Valid prediction for Augustus_model.g4424.t1
Valid prediction for GlimmerHMM_glimmerT_6786-T1
Valid prediction for snap_scaffold_3-snap.1492-T1
Valid prediction for Augustus_model.g4431.t1
Valid prediction for snap_scaffold_3-snap.1485-T1
Valid prediction for snap_scaffold_3-snap.1471-T1
Valid prediction for snap_scaffold_3-snap.1469-T1
Valid prediction for snap_scaffold_3-snap.1486-T1
Valid prediction for Augustus_model.g4429.t1
Valid prediction for snap_scaffold_3-snap.1476-T1
Valid prediction for GlimmerHMM_glimmerT_6788-T1
Valid prediction for snap_scaffold_3-snap.1473-T1
Valid prediction for snap_scaffold_3-snap.1470-T1
Valid prediction for snap_scaffold_3-snap.1467-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.1479-T1
Valid prediction for snap_scaffold_3-snap.1461-T1
Valid prediction for GlimmerHMM_glimmerT_6776-T1
Valid prediction for snap_scaffold_3-snap.1454-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g4420.t1
Valid prediction for GlimmerHMM_glimmerT_6783-T1
Valid prediction for snap_scaffold_3-snap.1477-T1
Valid prediction for Augustus_model.g4419.t1
Valid prediction for snap_scaffold_3-snap.1468-T1
Valid prediction for GlimmerHMM_glimmerT_6779-T1
Valid prediction for pasa_asmbl_38963.p1
Valid prediction for snap_scaffold_3-snap.1465-T1
Valid prediction for pasa_asmbl_38959.p1
Valid prediction for CodingQuarry_transcript_46201-T1
Valid prediction for snap_scaffold_3-snap.1481-T1
Valid prediction for Augustus_model.g4427.t1
Valid prediction for Augustus_model.g4423.t1
Valid prediction for snap_scaffold_3-snap.1488-T1
Valid prediction for snap_scaffold_3-snap.1482-T1
Valid prediction for snap_scaffold_3-snap.1455-T1
Valid prediction for snap_scaffold_3-snap.1458-T1
Valid prediction for snap_scaffold_3-snap.1472-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31818, rend_intergenic: 27478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70754, rend_intergenic: 66100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129527, rend_intergenic: 124571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135341, rend_intergenic: 129773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150552, rend_intergenic: 136014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165903, rend_intergenic: 159100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172305, rend_intergenic: 167987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185853, rend_intergenic: 180401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191605, rend_intergenic: 188496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199649, rend_intergenic: 192391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203664, rend_intergenic: 201451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205412
-exon list size: 379


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.7    
5.0    
5.2    
5.5    
5.8    
6.0    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.9    
8.1    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
10.0    
10.2    
10.5    
10.8    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.1    
13.4    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.2    
15.5    
15.7    
16.0    
16.3    
16.5    
16.8    
17.1    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.5    
21.8    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.2    
35.4    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.5    
41.7    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.3    
58.5    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.6    
64.8    
65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.2    
78.5    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 31818, rend_intergenic: 27478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70754, rend_intergenic: 66100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129527, rend_intergenic: 124571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135341, rend_intergenic: 129773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150552, rend_intergenic: 136014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165903, rend_intergenic: 159100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172305, rend_intergenic: 167987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185853, rend_intergenic: 180401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191605, rend_intergenic: 188496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199649, rend_intergenic: 192391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203664, rend_intergenic: 201451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support