-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_10769057-10906420

-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.g6594.t1
Valid prediction for Augustus_model.g6587.t1
Valid prediction for snap_scaffold_4-snap.2309-T1
Valid prediction for snap_scaffold_4-snap.2304-T1
Valid prediction for GlimmerHMM_glimmerT_10143-T1
Valid prediction for Augustus_model.g6588.t1
Valid prediction for snap_scaffold_4-snap.2338-T1
Couldn't classify 78708, 78857
Sorry, prediction pasa_asmbl_41670.p1 fails validation.
(GAC)	 AG	78708-78857	GT	AGG
(GGT)	 AG	79073-79257	GT	CTG
(GAA)	 AG	80332-81014	GT	AGG
(TGT)	 AG	82587-82746	GT	AGG
(GTC)	 AG	84240-84567	TA	AAT
-recovered pasa_asmbl_41670.p1, terminal, 84240, 84567
-recovered pasa_asmbl_41670.p1, internal, 78708, 78857
-recovered pasa_asmbl_41670.p1, internal, 79073, 79257
-recovered pasa_asmbl_41670.p1, internal, 80332, 81014
-recovered pasa_asmbl_41670.p1, internal, 82587, 82746
Valid prediction for snap_scaffold_4-snap.2337-T1
Valid prediction for GlimmerHMM_glimmerT_10162-T1
Valid prediction for snap_scaffold_4-snap.2311-T1
Valid prediction for Augustus_model.g6596.t1
Valid prediction for snap_scaffold_4-snap.2320-T1
Valid prediction for pasa_asmbl_41676.p1
Valid prediction for HiQ_model.g6597.t1
Valid prediction for Augustus_model.g6602.t1
Valid prediction for Augustus_model.g6589.t1
Valid prediction for snap_scaffold_4-snap.2307-T1
Valid prediction for Augustus_model.g6598.t1
Valid prediction for snap_scaffold_4-snap.2327-T1
Valid prediction for GlimmerHMM_glimmerT_10151-T1
Valid prediction for snap_scaffold_4-snap.2312-T1
Valid prediction for CodingQuarry_transcript_49121-T1
Valid prediction for CodingQuarry_transcript_49122-T1
Valid prediction for GlimmerHMM_glimmerT_10156-T1
Valid prediction for snap_scaffold_4-snap.2322-T1
Valid prediction for GlimmerHMM_glimmerT_10139-T1
Valid prediction for snap_scaffold_4-snap.2333-T1
Valid prediction for GlimmerHMM_glimmerT_10146-T1
Valid prediction for GlimmerHMM_glimmerT_10155-T1
Valid prediction for snap_scaffold_4-snap.2313-T1
Valid prediction for snap_scaffold_4-snap.2310-T1
Valid prediction for GlimmerHMM_glimmerT_10160-T1
Valid prediction for snap_scaffold_4-snap.2335-T1
Valid prediction for GlimmerHMM_glimmerT_10148-T1
Valid prediction for snap_scaffold_4-snap.2302-T1
Valid prediction for snap_scaffold_4-snap.2326-T1
Valid prediction for GlimmerHMM_glimmerT_10164-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_10149-T1
Valid prediction for snap_scaffold_4-snap.2305-T1
Couldn't classify 93038, 93281
Sorry, prediction pasa_asmbl_41680.p1 fails validation.
(GTC)	 AC	93038-93281	GT	AAG
(ACA)	 AG	93633-94606	GA	AGG
-recovered pasa_asmbl_41680.p1, terminal, 93633, 94606
Valid prediction for snap_scaffold_4-snap.2317-T1
Valid prediction for Augustus_model.g6592.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_10153-T1
Valid prediction for GlimmerHMM_glimmerT_10140-T1
Valid prediction for pasa_asmbl_43510.p1
Valid prediction for snap_scaffold_4-snap.2316-T1
Valid prediction for snap_scaffold_4-snap.2314-T1
Valid prediction for Augustus_model.g6599.t1
Valid prediction for snap_scaffold_4-snap.2332-T1
Valid prediction for GlimmerHMM_glimmerT_10144-T1
Valid prediction for Augustus_model.g6605.t1
Valid prediction for CodingQuarry_transcript_49124-T1
Valid prediction for Augustus_model.g6591.t1
Valid prediction for snap_scaffold_4-snap.2331-T1
Valid prediction for GlimmerHMM_glimmerT_10157-T1
Valid prediction for GlimmerHMM_glimmerT_10152-T1
Valid prediction for GlimmerHMM_glimmerT_10142-T1
Valid prediction for HiQ_model.g6600.t1
Valid prediction for snap_scaffold_4-snap.2324-T1
Valid prediction for Augustus_model.g6595.t1
Valid prediction for snap_scaffold_4-snap.2321-T1
Valid prediction for GlimmerHMM_glimmerT_10141-T1
Valid prediction for snap_scaffold_4-snap.2319-T1
Valid prediction for GlimmerHMM_glimmerT_10161-T1
Valid prediction for snap_scaffold_4-snap.2318-T1
Valid prediction for GlimmerHMM_glimmerT_10163-T1
Valid prediction for Augustus_model.g6590.t1
Valid prediction for Augustus_model.g6593.t1
Valid prediction for GlimmerHMM_glimmerT_10158-T1
Valid prediction for snap_scaffold_4-snap.2328-T1
Valid prediction for snap_scaffold_4-snap.2329-T1
Valid prediction for GlimmerHMM_glimmerT_10145-T1
Valid prediction for GlimmerHMM_glimmerT_10150-T1
Valid prediction for snap_scaffold_4-snap.2330-T1
Valid prediction for CodingQuarry_transcript_49123-T1
Valid prediction for GlimmerHMM_glimmerT_10159-T1
Valid prediction for GlimmerHMM_glimmerT_10147-T1
Valid prediction for Augustus_model.g6604.t1
Valid prediction for snap_scaffold_4-snap.2308-T1
Valid prediction for GlimmerHMM_glimmerT_10165-T1
Valid prediction for pasa_asmbl_42861.p1
Valid prediction for snap_scaffold_4-snap.2323-T1
Valid prediction for snap_scaffold_4-snap.2306-T1
Valid prediction for Augustus_model.g6603.t1
Valid prediction for snap_scaffold_4-snap.2334-T1
Valid prediction for snap_scaffold_4-snap.2315-T1
Valid prediction for snap_scaffold_4-snap.2336-T1
Valid prediction for snap_scaffold_4-snap.2325-T1
Valid prediction for Augustus_model.g6601.t1
Valid prediction for snap_scaffold_4-snap.2303-T1
Valid prediction for GlimmerHMM_glimmerT_10154-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13275, rend_intergenic: 9646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20914, rend_intergenic: 17955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21989, rend_intergenic: 21210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27170, rend_intergenic: 24614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30740, rend_intergenic: 27366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50331, rend_intergenic: 37797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66159, rend_intergenic: 61924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68187, rend_intergenic: 66331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72801, rend_intergenic: 70764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84936, rend_intergenic: 76096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109865, rend_intergenic: 108979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112116, rend_intergenic: 109893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137055, rend_intergenic: 119572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 137364
-exon list size: 335


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    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
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    
21.4    
21.7    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
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    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
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    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
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    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
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 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 13275, rend_intergenic: 9646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20914, rend_intergenic: 17955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21989, rend_intergenic: 21210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27170, rend_intergenic: 24614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30740, rend_intergenic: 27366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50331, rend_intergenic: 37797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66159, rend_intergenic: 61924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68187, rend_intergenic: 66331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72801, rend_intergenic: 70764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84936, rend_intergenic: 76096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109865, rend_intergenic: 108979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112116, rend_intergenic: 109893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137055, rend_intergenic: 119572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13158
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 11936
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 11722
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 11153
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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