-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_6043755-6207130

-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_3990-T1
Valid prediction for GeneMark_model.6555_t
Valid prediction for GeneMark_model.6545_t
Valid prediction for snap_scaffold_2-snap.1388-T1
Valid prediction for GeneMark_model.6544_t
Valid prediction for Augustus_model.g2667.t1
Valid prediction for snap_scaffold_2-snap.1392-T1
Valid prediction for snap_scaffold_2-snap.1376-T1
Valid prediction for Augustus_model.g2655.t1
Valid prediction for snap_scaffold_2-snap.1357-T1
Valid prediction for GlimmerHMM_glimmerT_4013-T1
Valid prediction for GlimmerHMM_glimmerT_4002-T1
Valid prediction for GeneMark_model.6536_t
Valid prediction for GeneMark_model.6548_t
Valid prediction for GeneMark_model.6535_t
Valid prediction for Augustus_model.g2669.t1
Valid prediction for snap_scaffold_2-snap.1374-T1
Valid prediction for GeneMark_model.6553_t
Valid prediction for GlimmerHMM_glimmerT_4012-T1
Valid prediction for pasa_asmbl_24473.p1
Valid prediction for snap_scaffold_2-snap.1364-T1
Valid prediction for GeneMark_model.6558_t
Valid prediction for snap_scaffold_2-snap.1361-T1
Valid prediction for GlimmerHMM_glimmerT_3998-T1
Valid prediction for Augustus_model.g2663.t1
Valid prediction for GeneMark_model.6542_t
Valid prediction for snap_scaffold_2-snap.1358-T1
Valid prediction for Augustus_model.g2656.t1
Valid prediction for GeneMark_model.6550_t
Valid prediction for GlimmerHMM_glimmerT_4014-T1
Valid prediction for GlimmerHMM_glimmerT_4005-T1
Valid prediction for GlimmerHMM_glimmerT_4007-T1
Valid prediction for GlimmerHMM_glimmerT_4000-T1
Valid prediction for Augustus_model.g2662.t1
Valid prediction for snap_scaffold_2-snap.1389-T1
Valid prediction for snap_scaffold_2-snap.1373-T1
Couldn't classify 141889, 141984
Couldn't classify 144832, 144926
Sorry, prediction pasa_asmbl_25382.p1 fails validation.
(GGG)	 CC	141889-141984	GT	GGG
(CAA)	 AG	142245-142362	GT	TGG
(GGT)	 AG	144832-144926	GG	TCG
-recovered pasa_asmbl_25382.p1, internal, 142245, 142362
Valid prediction for GeneMark_model.6560_t
Valid prediction for snap_scaffold_2-snap.1381-T1
Valid prediction for Augustus_model.g2668.t1
Valid prediction for GlimmerHMM_glimmerT_3996-T1
Valid prediction for GlimmerHMM_glimmerT_4009-T1
Valid prediction for Augustus_model.g2659.t1
Valid prediction for GlimmerHMM_glimmerT_4008-T1
Valid prediction for snap_scaffold_2-snap.1379-T1
Valid prediction for snap_scaffold_2-snap.1360-T1
Valid prediction for snap_scaffold_2-snap.1366-T1
Valid prediction for snap_scaffold_2-snap.1384-T1
Valid prediction for GeneMark_model.6532_t
Valid prediction for GlimmerHMM_glimmerT_4011-T1
Valid prediction for snap_scaffold_2-snap.1386-T1
Valid prediction for CodingQuarry_transcript_28512-T1
Valid prediction for GeneMark_model.6540_t
Valid prediction for snap_scaffold_2-snap.1356-T1
Valid prediction for GlimmerHMM_glimmerT_3992-T1
Valid prediction for HiQ_model.g2665.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.6533_t
Valid prediction for snap_scaffold_2-snap.1383-T1
Valid prediction for GlimmerHMM_glimmerT_3993-T1
Valid prediction for GeneMark_model.6547_t
Valid prediction for GeneMark_model.6541_t
Valid prediction for GeneMark_model.6552_t
Valid prediction for snap_scaffold_2-snap.1368-T1
Valid prediction for GeneMark_model.6551_t
Valid prediction for snap_scaffold_2-snap.1393-T1
Valid prediction for GlimmerHMM_glimmerT_4015-T1
Valid prediction for GeneMark_model.6546_t
Valid prediction for GlimmerHMM_glimmerT_3989-T1
Valid prediction for Augustus_model.g2658.t1
Valid prediction for GeneMark_model.6559_t
Valid prediction for GlimmerHMM_glimmerT_3994-T1
Valid prediction for GlimmerHMM_glimmerT_4003-T1
Valid prediction for snap_scaffold_2-snap.1359-T1
Valid prediction for GlimmerHMM_glimmerT_3995-T1
Valid prediction for GlimmerHMM_glimmerT_4001-T1
Valid prediction for snap_scaffold_2-snap.1371-T1
Valid prediction for GeneMark_model.6531_t
Valid prediction for snap_scaffold_2-snap.1365-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3991-T1
Valid prediction for Augustus_model.g2660.t1
Valid prediction for Augustus_model.g2661.t1
Valid prediction for snap_scaffold_2-snap.1378-T1
Valid prediction for GeneMark_model.6538_t
Valid prediction for snap_scaffold_2-snap.1369-T1
Valid prediction for CodingQuarry_transcript_28513-T1
Valid prediction for GeneMark_model.6556_t
Valid prediction for GeneMark_model.6539_t
Valid prediction for snap_scaffold_2-snap.1363-T1
Valid prediction for GlimmerHMM_glimmerT_3988-T1
Valid prediction for Augustus_model.g2657.t1
Valid prediction for GlimmerHMM_glimmerT_4010-T1
Valid prediction for snap_scaffold_2-snap.1362-T1
Valid prediction for Augustus_model.g2664.t1
Valid prediction for GlimmerHMM_glimmerT_3999-T1
Valid prediction for GeneMark_model.6549_t
Valid prediction for GlimmerHMM_glimmerT_3997-T1
Valid prediction for snap_scaffold_2-snap.1391-T1
Valid prediction for snap_scaffold_2-snap.1370-T1
Valid prediction for GlimmerHMM_glimmerT_4006-T1
Valid prediction for snap_scaffold_2-snap.1367-T1
Couldn't classify 86246, 86247
Sorry, prediction pasa_asmbl_23207.p1 fails validation.
(ATG)	 AC	86246-86247	GT	ATG
(GAG)	 AG	86344-86489	GT	TGG
(ACA)	 AG	86700-86852	GT	TGG
(GAT)	 AG	87242-87402	GT	CAG
(ATG)	 AG	87504-87568	GT	ACG
(GTT)	 AG	87993-88107	GT	TGG
(GAC)	 AG	88213-88322	GT	AGG
(TGG)	 AG	88465-88651	GT	TGG
(GTG)	 AG	89226-89288	GT	TAG
(ATG)	 AG	89449-89607	GT	AGG
(GTT)	 AG	89991-90062	CA	AGC
-recovered pasa_asmbl_23207.p1, initial, 87504, 87568
-recovered pasa_asmbl_23207.p1, initial, 89449, 89607
-recovered pasa_asmbl_23207.p1, terminal, 89991, 90062
-recovered pasa_asmbl_23207.p1, internal, 86344, 86489
-recovered pasa_asmbl_23207.p1, internal, 86700, 86852
-recovered pasa_asmbl_23207.p1, internal, 87242, 87402
-recovered pasa_asmbl_23207.p1, internal, 87504, 87568
-recovered pasa_asmbl_23207.p1, internal, 87993, 88107
-recovered pasa_asmbl_23207.p1, internal, 88213, 88322
-recovered pasa_asmbl_23207.p1, internal, 88465, 88651
-recovered pasa_asmbl_23207.p1, internal, 89226, 89288
-recovered pasa_asmbl_23207.p1, internal, 89449, 89607
Valid prediction for snap_scaffold_2-snap.1377-T1
Valid prediction for snap_scaffold_2-snap.1385-T1
Valid prediction for GeneMark_model.6543_t
Valid prediction for GeneMark_model.6530_t
Couldn't classify 116441, 116539
Sorry, prediction pasa_asmbl_23201.p1 fails validation.
(CCA)	 GG	116441-116539	GT	TGG
(GTA)	 AG	117764-117861	GT	TGG
(GAC)	 AG	119139-119298	GT	AGG
(GAT)	 AG	121841-121970	GT	AGG
(GTA)	 AG	123449-124116	CC	GAC
-recovered pasa_asmbl_23201.p1, terminal, 123449, 124116
-recovered pasa_asmbl_23201.p1, internal, 117764, 117861
-recovered pasa_asmbl_23201.p1, internal, 119139, 119298
-recovered pasa_asmbl_23201.p1, internal, 121841, 121970
Valid prediction for snap_scaffold_2-snap.1372-T1
Valid prediction for snap_scaffold_2-snap.1387-T1
Valid prediction for HiQ_model.g2666.t1
Valid prediction for snap_scaffold_2-snap.1380-T1
Valid prediction for snap_scaffold_2-snap.1390-T1
Valid prediction for snap_scaffold_2-snap.1375-T1
Valid prediction for GeneMark_model.6554_t
Valid prediction for GeneMark_model.6557_t
Valid prediction for snap_scaffold_2-snap.1382-T1
Valid prediction for GeneMark_model.6537_t
Valid prediction for GlimmerHMM_glimmerT_4004-T1
Valid prediction for GeneMark_model.6534_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 35517, rend_intergenic: 35514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11199, rend_intergenic: 9014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23038, rend_intergenic: 20768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81367, rend_intergenic: 80879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96018, rend_intergenic: 93983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119817, rend_intergenic: 116738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128734, rend_intergenic: 125679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140194, rend_intergenic: 131869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153390, rend_intergenic: 144828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163376
-exon list size: 409


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
1.9    
2.2    
2.4    
2.7    
2.9    
3.2    
3.4    
3.6    
3.9    
4.1    
4.4    
4.6    
4.9    
5.1    
5.4    
5.6    
5.8    
6.1    
6.3    
6.6    
6.8    
7.1    
7.3    
7.5    
7.8    
8.0    
8.3    
8.5    
8.8    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.5    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
12.9    
13.1    
13.4    
13.6    
13.9    
14.1    
14.4    
14.6    
14.8    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.5    
16.8    
17.0    
17.3    
17.5    
17.8    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.4    
23.6    
23.8    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
28.2    
28.5    
28.7    
29.0    
29.2    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.8    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.2    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.8    
71.0    
71.3    
71.5    
71.8    
72.0    
72.3    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.4    
76.6    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 22 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 35517, rend_intergenic: 35514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11199, rend_intergenic: 9014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23038, rend_intergenic: 20768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81367, rend_intergenic: 80879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96018, rend_intergenic: 93983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119817, rend_intergenic: 116738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128734, rend_intergenic: 125679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140194, rend_intergenic: 131869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153390, rend_intergenic: 144828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13945
-exon list size: 22


building trellis

4.2    
8.3    
12.5    
16.7    
20.8    
25.0    
29.2    
33.3    
37.5    
41.7    
45.8    
50.0    
54.2    
58.3    
62.5    
66.7    
70.8    
75.0    
79.2    
83.3    
87.5    
91.7    
95.8    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support