-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_8487736-8746556

-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 snap_scaffold_5-snap.1618-T1
Valid prediction for snap_scaffold_5-snap.1617-T1
Valid prediction for Augustus_model.g8095.t1
Valid prediction for Augustus_model.g8091.t1
Valid prediction for snap_scaffold_5-snap.1634-T1
Valid prediction for GlimmerHMM_glimmerT_12327-T1
Valid prediction for snap_scaffold_5-snap.1643-T1
Valid prediction for GlimmerHMM_glimmerT_12304-T1
Valid prediction for snap_scaffold_5-snap.1611-T1
Valid prediction for GlimmerHMM_glimmerT_12305-T1
Couldn't classify 69305, 69438
Sorry, prediction pasa_asmbl_45553.p1 fails validation.
(CAG)	 TG	69305-69438	GT	AGG
(GTG)	 AG	69537-69591	GT	AGG
(CCA)	 AG	69786-69878	GT	AGG
(GGT)	 AG	70089-70223	GT	AAG
(GTT)	 AG	70365-70466	GT	AGG
(GGG)	 AG	70663-70818	GT	CGG
(AGT)	 AG	71018-71140	GT	GAG
-recovered pasa_asmbl_45553.p1, terminal, 71018, 71140
-recovered pasa_asmbl_45553.p1, internal, 69537, 69591
-recovered pasa_asmbl_45553.p1, internal, 69786, 69878
-recovered pasa_asmbl_45553.p1, internal, 70089, 70223
-recovered pasa_asmbl_45553.p1, internal, 70365, 70466
-recovered pasa_asmbl_45553.p1, internal, 70663, 70818
-recovered pasa_asmbl_45553.p1, internal, 71018, 71140
Valid prediction for snap_scaffold_5-snap.1615-T1
Valid prediction for GlimmerHMM_glimmerT_12306-T1
Couldn't classify 163181, 163798
Sorry, prediction pasa_asmbl_45559.p1 fails validation.
(CCA)	 CA	163181-163798	GG	AAG
Valid prediction for Augustus_model.g8097.t1
Valid prediction for GlimmerHMM_glimmerT_12319-T1
Valid prediction for GlimmerHMM_glimmerT_12310-T1
Valid prediction for snap_scaffold_5-snap.1631-T1
Valid prediction for snap_scaffold_5-snap.1638-T1
Valid prediction for GlimmerHMM_glimmerT_12311-T1
Valid prediction for HiQ_model.g8106.t1
Valid prediction for Augustus_model.g8089.t1
Valid prediction for GlimmerHMM_glimmerT_12307-T1
Valid prediction for snap_scaffold_5-snap.1639-T1
Couldn't classify 48917, 49056
Sorry, prediction pasa_asmbl_45552.p1 fails validation.
(GTG)	 AC	48917-49056	GT	AGG
(AGT)	 AG	49364-49434	GT	TGG
(GCC)	 AG	49536-49637	GT	GGG
(ATT)	 AG	49751-49890	CA	GAC
-recovered pasa_asmbl_45552.p1, terminal, 49751, 49890
-recovered pasa_asmbl_45552.p1, internal, 49364, 49434
-recovered pasa_asmbl_45552.p1, internal, 49536, 49637
Valid prediction for GlimmerHMM_glimmerT_12318-T1
Valid prediction for Augustus_model.g8096.t1
Valid prediction for Augustus_model.g8101.t1
Valid prediction for Augustus_model.g8102.t1
Valid prediction for snap_scaffold_5-snap.1628-T1
Valid prediction for GlimmerHMM_glimmerT_12323-T1
Valid prediction for snap_scaffold_5-snap.1641-T1
Valid prediction for GlimmerHMM_glimmerT_12313-T1
Valid prediction for snap_scaffold_5-snap.1626-T1
Valid prediction for Augustus_model.g8098.t1
Valid prediction for Augustus_model.g8104.t1
Valid prediction for Augustus_model.g8099.t1
Valid prediction for snap_scaffold_5-snap.1633-T1
Valid prediction for pasa_asmbl_45561.p1
Valid prediction for snap_scaffold_5-snap.1630-T1
Valid prediction for snap_scaffold_5-snap.1616-T1
Valid prediction for GlimmerHMM_glimmerT_12315-T1
Valid prediction for snap_scaffold_5-snap.1612-T1
Valid prediction for Augustus_model.g8090.t1
Valid prediction for Augustus_model.g8103.t1
Valid prediction for CodingQuarry_transcript_52150-T1
Valid prediction for snap_scaffold_5-snap.1623-T1
Valid prediction for GlimmerHMM_glimmerT_12317-T1
Valid prediction for Augustus_model.g8087.t1
Valid prediction for pasa_asmbl_45554.p1
Valid prediction for snap_scaffold_5-snap.1613-T1
Valid prediction for GlimmerHMM_glimmerT_12320-T1
Valid prediction for CodingQuarry_transcript_52153-T1
Valid prediction for GlimmerHMM_glimmerT_12316-T1
Valid prediction for Augustus_model.g8100.t1
Valid prediction for CodingQuarry_transcript_52152-T1
Valid prediction for CodingQuarry_transcript_52149-T1
Valid prediction for snap_scaffold_5-snap.1625-T1
Valid prediction for Augustus_model.g8110.t1
Valid prediction for snap_scaffold_5-snap.1649-T1
Valid prediction for Augustus_model.g8088.t1
Valid prediction for snap_scaffold_5-snap.1622-T1
Valid prediction for GlimmerHMM_glimmerT_12321-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_5-snap.1646-T1
Valid prediction for snap_scaffold_5-snap.1621-T1
Valid prediction for CodingQuarry_transcript_52144-T1
Valid prediction for snap_scaffold_5-snap.1624-T1
Valid prediction for GlimmerHMM_glimmerT_12326-T1
Valid prediction for Augustus_model.g8105.t1
Couldn't classify 65476, 65527
Sorry, prediction pasa_asmbl_44223.p1 fails validation.
(ACC)	 TG	65476-65527	GT	AAG
(CAT)	 AG	65651-65782	GC	AGG
(AGT)	 AG	65884-66012	GT	GAG
(CAT)	 AG	66131-66259	GT	GGG
(GCT)	 AG	66364-66492	GT	AGG
(TAT)	 AG	66579-66707	GT	TGG
(CCT)	 AG	66791-66919	GT	GAG
(AAT)	 AG	67024-67152	GT	AAG
(GTT)	 AG	67272-67400	GT	GGG
(GAG)	 AG	67487-67563	CA	AGC
-recovered pasa_asmbl_44223.p1, terminal, 67487, 67563
-recovered pasa_asmbl_44223.p1, internal, 65651, 65782
-recovered pasa_asmbl_44223.p1, internal, 65884, 66012
-recovered pasa_asmbl_44223.p1, internal, 66131, 66259
-recovered pasa_asmbl_44223.p1, internal, 66364, 66492
-recovered pasa_asmbl_44223.p1, internal, 66579, 66707
-recovered pasa_asmbl_44223.p1, internal, 66791, 66919
-recovered pasa_asmbl_44223.p1, internal, 67024, 67152
-recovered pasa_asmbl_44223.p1, internal, 67272, 67400
Valid prediction for snap_scaffold_5-snap.1648-T1
Couldn't classify 62887, 63018
Sorry, prediction pasa_asmbl_44977.p2 fails validation.
(ATG)	 GA	62381-62455	GT	GGG
(TGT)	 AG	62634-62762	GT	AGG
(CAT)	 AG	62887-63018	GT	AAG
-recovered pasa_asmbl_44977.p2, initial, 62381, 62455
-recovered pasa_asmbl_44977.p2, internal, 62634, 62762
-recovered pasa_asmbl_44977.p2, internal, 62887, 63018
Valid prediction for snap_scaffold_5-snap.1647-T1
Valid prediction for HiQ_model.g8111.t1
Valid prediction for HiQ_model.g8092.t1
Valid prediction for snap_scaffold_5-snap.1652-T1
Valid prediction for Augustus_model.g8112.t1
Valid prediction for CodingQuarry_transcript_52146-T1
Valid prediction for snap_scaffold_5-snap.1629-T1
Valid prediction for CodingQuarry_transcript_52143-T1
Valid prediction for CodingQuarry_transcript_52154-T1
Valid prediction for snap_scaffold_5-snap.1644-T1
Couldn't classify 10356, 10500
Sorry, prediction pasa_asmbl_44229.p1 fails validation.
(CAG)	 TG	10356-10500	GT	AGG
(AGA)	 AG	10661-10771	GT	AGG
(GGC)	 AG	10920-11013	GT	AGG
(GTT)	 AG	11164-11302	GT	AGG
(GTG)	 AG	11474-11671	TG	AGT
add_exon() Sorry, pasa_asmbl_44229.p1 10920-11013-terminal-3 is invalid.
-recovered pasa_asmbl_44229.p1, terminal, 10920, 11013
-recovered pasa_asmbl_44229.p1, terminal, 11474, 11671
-recovered pasa_asmbl_44229.p1, internal, 10661, 10771
-recovered pasa_asmbl_44229.p1, internal, 10920, 11013
-recovered pasa_asmbl_44229.p1, internal, 11164, 11302
Valid prediction for GlimmerHMM_glimmerT_12324-T1
Valid prediction for snap_scaffold_5-snap.1640-T1
Valid prediction for snap_scaffold_5-snap.1619-T1
Valid prediction for snap_scaffold_5-snap.1627-T1
Valid prediction for pasa_asmbl_44214.p1
Valid prediction for snap_scaffold_5-snap.1653-T1
Valid prediction for snap_scaffold_5-snap.1642-T1
Valid prediction for GlimmerHMM_glimmerT_12328-T1
Valid prediction for snap_scaffold_5-snap.1651-T1
Valid prediction for HiQ_model.g8093.t1
Valid prediction for CodingQuarry_transcript_52148-T1
Valid prediction for pasa_asmbl_44220.p1
Valid prediction for snap_scaffold_5-snap.1645-T1
Valid prediction for Augustus_model.g8109.t1
Valid prediction for snap_scaffold_5-snap.1637-T1
Valid prediction for Augustus_model.g8113.t1
Valid prediction for CodingQuarry_transcript_52147-T1
Valid prediction for CodingQuarry_transcript_52145-T1
Valid prediction for GlimmerHMM_glimmerT_12330-T1
Valid prediction for GlimmerHMM_glimmerT_12325-T1
Valid prediction for HiQ_model.g8094.t1
Valid prediction for pasa_asmbl_44222.p1
Valid prediction for GlimmerHMM_glimmerT_12309-T1
Valid prediction for GlimmerHMM_glimmerT_12322-T1
Valid prediction for CodingQuarry_transcript_52156-T1
Valid prediction for GlimmerHMM_glimmerT_12308-T1
Valid prediction for snap_scaffold_5-snap.1632-T1
Valid prediction for snap_scaffold_5-snap.1636-T1
Valid prediction for Augustus_model.g8108.t1
Valid prediction for snap_scaffold_5-snap.1650-T1
Valid prediction for CodingQuarry_transcript_52155-T1
Valid prediction for GlimmerHMM_glimmerT_12329-T1
Valid prediction for Augustus_model.g8107.t1
Couldn't classify 57488, 57554
Couldn't classify 58570, 58592
Sorry, prediction pasa_asmbl_44941.p1 fails validation.
(GGA)	 TC	57488-57554	GT	AGG
(ACA)	 AG	57761-57883	GT	CCG
(GTA)	 AG	58038-58175	GT	GGG
(ACT)	 AG	58311-58433	GT	TGG
(ATG)	 AG	58570-58592	AA	ACA
-recovered pasa_asmbl_44941.p1, internal, 57761, 57883
-recovered pasa_asmbl_44941.p1, internal, 58038, 58175
-recovered pasa_asmbl_44941.p1, internal, 58311, 58433
Valid prediction for GlimmerHMM_glimmerT_12312-T1
Valid prediction for snap_scaffold_5-snap.1620-T1
Valid prediction for GlimmerHMM_glimmerT_12314-T1
Valid prediction for snap_scaffold_5-snap.1635-T1
Valid prediction for snap_scaffold_5-snap.1614-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 49890, rend_intergenic: 43509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116813, rend_intergenic: 113000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129233, rend_intergenic: 128783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145094, rend_intergenic: 142206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163798, rend_intergenic: 162645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198516, rend_intergenic: 193522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209238, rend_intergenic: 208504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 258821
-exon list size: 391


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.3    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.4    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
83.0    
83.2    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 49890, rend_intergenic: 43509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116813, rend_intergenic: 113000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129233, rend_intergenic: 128783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145094, rend_intergenic: 142206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163798, rend_intergenic: 162645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198516, rend_intergenic: 193522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209238, rend_intergenic: 208504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10986
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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