-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_7295156-7387064

-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 GeneMark_model.11474_t
Valid prediction for CodingQuarry_transcript_46090-T1
Valid prediction for HiQ_model.g4547.t1
Valid prediction for GeneMark_model.11480_t
Valid prediction for GlimmerHMM_glimmerT_6930-T1
Valid prediction for GeneMark_model.11483_t
Valid prediction for GeneMark_model.11481_t
Couldn't classify 53492, 53557
Couldn't classify 56801, 56842
Sorry, prediction pasa_asmbl_40117.p1 fails validation.
(CCG)	 CT	53492-53557	GT	AGG
(GGC)	 AG	53645-53709	GT	AGG
(GCT)	 AG	54350-54466	GT	AGG
(TGA)	 AG	55379-55460	GT	AGG
(GCT)	 AG	55584-55661	GT	TAG
(TTC)	 AG	55779-55841	GT	CGG
(CGT)	 AG	56801-56842	CA	CCC
-recovered pasa_asmbl_40117.p1, terminal, 54350, 54466
-recovered pasa_asmbl_40117.p1, internal, 53645, 53709
-recovered pasa_asmbl_40117.p1, internal, 54350, 54466
-recovered pasa_asmbl_40117.p1, internal, 55379, 55460
-recovered pasa_asmbl_40117.p1, internal, 55584, 55661
-recovered pasa_asmbl_40117.p1, internal, 55779, 55841
Valid prediction for snap_scaffold_3-snap.1488-T1
Valid prediction for GlimmerHMM_glimmerT_6934-T1
Valid prediction for GlimmerHMM_glimmerT_6935-T1
Valid prediction for GeneMark_model.11485_t
Valid prediction for GeneMark_model.11463_t
Valid prediction for GeneMark_model.11478_t
Valid prediction for Augustus_model.g4546.t1
Valid prediction for GeneMark_model.11465_t
Valid prediction for snap_scaffold_3-snap.1495-T1
Valid prediction for GlimmerHMM_glimmerT_6929-T1
Valid prediction for GeneMark_model.11469_t
Valid prediction for pasa_asmbl_40115.p1
Valid prediction for snap_scaffold_3-snap.1498-T1
Valid prediction for GlimmerHMM_glimmerT_6940-T1
Couldn't classify 20170, 20194
Couldn't classify 24068, 24125
Sorry, prediction pasa_asmbl_40112.p1 fails validation.
(CTC)	 CC	20170-20194	GT	ATG
(CTG)	 AG	22018-22138	GT	AGG
(TGG)	 AG	22368-22455	GT	GGG
(GAT)	 AG	22616-22704	GT	TGG
(GTT)	 AG	24068-24125	GA	GAG
-recovered pasa_asmbl_40112.p1, internal, 22018, 22138
-recovered pasa_asmbl_40112.p1, internal, 22368, 22455
-recovered pasa_asmbl_40112.p1, internal, 22616, 22704
Valid prediction for Augustus_model.g4550.t1
Valid prediction for snap_scaffold_3-snap.1492-T1
Valid prediction for GeneMark_model.11470_t
Valid prediction for snap_scaffold_3-snap.1491-T1
Valid prediction for GlimmerHMM_glimmerT_6933-T1
Valid prediction for GeneMark_model.11461_t
Valid prediction for Augustus_model.g4548.t1
Couldn't classify 32637, 32929
Sorry, prediction pasa_asmbl_40114.p1 fails validation.
(TGC)	 AG	32637-32929	GT	AGG
(TGC)	 AG	33096-33231	GT	CTG
(AGC)	 AG	33887-34129	CC	GAC
-recovered pasa_asmbl_40114.p1, terminal, 33887, 34129
-recovered pasa_asmbl_40114.p1, internal, 32637, 32929
-recovered pasa_asmbl_40114.p1, internal, 33096, 33231
Valid prediction for Augustus_model.g4549.t1
Valid prediction for GeneMark_model.11467_t
Valid prediction for GlimmerHMM_glimmerT_6932-T1
Valid prediction for GeneMark_model.11487_t
Valid prediction for snap_scaffold_3-snap.1484-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.11476_t
Valid prediction for GeneMark_model.11472_t
Valid prediction for GlimmerHMM_glimmerT_6936-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.11486_t
Valid prediction for snap_scaffold_3-snap.1496-T1
Valid prediction for GeneMark_model.11477_t
Valid prediction for GeneMark_model.11471_t
Valid prediction for GeneMark_model.11468_t
Valid prediction for GlimmerHMM_glimmerT_6937-T1
Valid prediction for snap_scaffold_3-snap.1489-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.11475_t
Valid prediction for GeneMark_model.11473_t
Valid prediction for GeneMark_model.11464_t
Valid prediction for Augustus_model.g4545.t1
Valid prediction for snap_scaffold_3-snap.1486-T1
Valid prediction for snap_scaffold_3-snap.1493-T1
Valid prediction for GeneMark_model.11479_t
Valid prediction for GlimmerHMM_glimmerT_6931-T1
Valid prediction for GeneMark_model.11462_t
Valid prediction for snap_scaffold_3-snap.1490-T1
Valid prediction for GlimmerHMM_glimmerT_6939-T1
Valid prediction for snap_scaffold_3-snap.1494-T1
Valid prediction for GlimmerHMM_glimmerT_6938-T1
Valid prediction for snap_scaffold_3-snap.1499-T1
Valid prediction for snap_scaffold_3-snap.1487-T1
Valid prediction for GeneMark_model.11466_t
Valid prediction for GlimmerHMM_glimmerT_6941-T1
Valid prediction for snap_scaffold_3-snap.1485-T1
Valid prediction for GeneMark_model.11484_t
Valid prediction for GlimmerHMM_glimmerT_6928-T1
Valid prediction for snap_scaffold_3-snap.1497-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34129, rend_intergenic: 8148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49480, rend_intergenic: 42677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55882, rend_intergenic: 51564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69430, rend_intergenic: 63978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80615, rend_intergenic: 72073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87241, rend_intergenic: 85028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 91909
-exon list size: 342


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 8 predictions from path traversal
Error with prediction: snap lend_intergenic: 34129, rend_intergenic: 8148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49480, rend_intergenic: 42677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55882, rend_intergenic: 51564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69430, rend_intergenic: 63978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80615, rend_intergenic: 72073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87241, rend_intergenic: 85028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 4 predictions persist after filtering for low support