-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_3923639-4134959

-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_24521-T1
Valid prediction for snap_scaffold_10-snap.870-T1
Valid prediction for GlimmerHMM_glimmerT_24512-T1
Valid prediction for snap_scaffold_10-snap.863-T1
Valid prediction for snap_scaffold_10-snap.841-T1
Valid prediction for HiQ_model.g16332.t1
Valid prediction for pasa_asmbl_3101.p1
Valid prediction for snap_scaffold_10-snap.871-T1
Valid prediction for snap_scaffold_10-snap.881-T1
Valid prediction for snap_scaffold_10-snap.862-T1
Couldn't classify 21310, 21623
Sorry, prediction pasa_asmbl_3094.p1 fails validation.
(AAC)	 CC	21310-21623	GT	AGG
(CAA)	 AG	21819-21861	GG	GAG
-recovered pasa_asmbl_3094.p1, terminal, 21819, 21861
Couldn't classify 105400, 107103
Sorry, prediction pasa_asmbl_3098.p1 fails validation.
(ATG)	 AC	105400-107103	AC	ACA
Valid prediction for GlimmerHMM_glimmerT_24509-T1
Valid prediction for HiQ_model.g16331.t1
Valid prediction for snap_scaffold_10-snap.860-T1
Valid prediction for snap_scaffold_10-snap.842-T1
Valid prediction for snap_scaffold_10-snap.855-T1
Valid prediction for snap_scaffold_10-snap.865-T1
Valid prediction for Augustus_model.g16325.t1
Valid prediction for CodingQuarry_transcript_5351-T1
Valid prediction for snap_scaffold_10-snap.849-T1
Valid prediction for snap_scaffold_10-snap.864-T1
Valid prediction for GlimmerHMM_glimmerT_24535-T1
Valid prediction for snap_scaffold_10-snap.852-T1
Valid prediction for CodingQuarry_transcript_5350-T1
Valid prediction for GlimmerHMM_glimmerT_24520-T1
Valid prediction for GlimmerHMM_glimmerT_24540-T1
Valid prediction for Augustus_model.g16339.t1
Valid prediction for snap_scaffold_10-snap.844-T1
Valid prediction for snap_scaffold_10-snap.883-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g16329.t1
Valid prediction for Augustus_model.g16336.t1
Couldn't classify 103893, 103962
Couldn't classify 104171, 104490
Sorry, prediction pasa_asmbl_3097.p1 fails validation.
(GGA)	 AT	103893-103962	GT	GGG
(AAT)	 AG	104171-104490	GA	GGG
Valid prediction for pasa_asmbl_3095.p1
Valid prediction for GlimmerHMM_glimmerT_24514-T1
Couldn't classify 107284, 109287
Sorry, prediction pasa_asmbl_3099.p1 fails validation.
(GTC)	 AT	107284-109287	GT	AGG
(GAC)	 AG	109511-109645	GT	AGG
(CAG)	 AG	111405-111796	GT	AAG
(CCT)	 AG	112705-112823	GT	AGG
(GTG)	 AG	114118-114309	GT	TGG
(ACC)	 AG	115300-115555	GT	AAG
(GTC)	 AG	115698-115834	GT	AGG
(AGG)	 AG	116419-116642	GT	AGG
(GTG)	 AG	116842-117097	GT	AGG
(TGT)	 AG	117230-117341	GT	ATG
(GAC)	 AG	117607-117823	AA	AAA
-recovered pasa_asmbl_3099.p1, terminal, 117607, 117823
-recovered pasa_asmbl_3099.p1, internal, 109511, 109645
-recovered pasa_asmbl_3099.p1, internal, 111405, 111796
-recovered pasa_asmbl_3099.p1, internal, 112705, 112823
-recovered pasa_asmbl_3099.p1, internal, 114118, 114309
-recovered pasa_asmbl_3099.p1, internal, 115300, 115555
-recovered pasa_asmbl_3099.p1, internal, 115698, 115834
-recovered pasa_asmbl_3099.p1, internal, 116419, 116642
-recovered pasa_asmbl_3099.p1, internal, 116842, 117097
-recovered pasa_asmbl_3099.p1, internal, 117230, 117341
Valid prediction for snap_scaffold_10-snap.878-T1
Valid prediction for GlimmerHMM_glimmerT_24533-T1
Valid prediction for snap_scaffold_10-snap.858-T1
Valid prediction for GlimmerHMM_glimmerT_24517-T1
Valid prediction for GlimmerHMM_glimmerT_24528-T1
Valid prediction for GlimmerHMM_glimmerT_24516-T1
Valid prediction for GlimmerHMM_glimmerT_24522-T1
Valid prediction for snap_scaffold_10-snap.885-T1
Valid prediction for GlimmerHMM_glimmerT_24532-T1
Valid prediction for HiQ_model.g16322.t1
Valid prediction for snap_scaffold_10-snap.875-T1
Valid prediction for GlimmerHMM_glimmerT_24530-T1
Valid prediction for Augustus_model.g16328.t1
Valid prediction for Augustus_model.g16324.t1
Valid prediction for snap_scaffold_10-snap.854-T1
Valid prediction for snap_scaffold_10-snap.877-T1
Valid prediction for GlimmerHMM_glimmerT_24518-T1
Valid prediction for CodingQuarry_transcript_5349-T1
Valid prediction for Augustus_model.g16330.t1
Valid prediction for GlimmerHMM_glimmerT_24539-T1
Valid prediction for GlimmerHMM_glimmerT_24527-T1
Valid prediction for snap_scaffold_10-snap.867-T1
Valid prediction for GlimmerHMM_glimmerT_24525-T1
Valid prediction for GlimmerHMM_glimmerT_24524-T1
Valid prediction for GlimmerHMM_glimmerT_24538-T1
Valid prediction for snap_scaffold_10-snap.846-T1
Couldn't classify 188905, 189505
Sorry, prediction pasa_asmbl_3105.p1 fails validation.
(AGG)	 CA	188905-189505	GT	AGG
(AGG)	 AG	189966-190637	GT	AGG
(TCT)	 AG	190832-190836	AG	AAA
-recovered pasa_asmbl_3105.p1, terminal, 190832, 190836
-recovered pasa_asmbl_3105.p1, internal, 189966, 190637
Valid prediction for HiQ_model.g16340.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 Augustus_model.g16327.t1
Valid prediction for pasa_asmbl_4241.p1
Valid prediction for HiQ_model.g16341.t1
Valid prediction for snap_scaffold_10-snap.876-T1
Valid prediction for snap_scaffold_10-snap.872-T1
Valid prediction for GlimmerHMM_glimmerT_24510-T1
Valid prediction for snap_scaffold_10-snap.840-T1
Valid prediction for Augustus_model.g16319.t1
Valid prediction for pasa_asmbl_4252.p1
Valid prediction for GlimmerHMM_glimmerT_24513-T1
Valid prediction for snap_scaffold_10-snap.856-T1
Valid prediction for GlimmerHMM_glimmerT_24523-T1
Valid prediction for GlimmerHMM_glimmerT_24537-T1
Valid prediction for GlimmerHMM_glimmerT_24536-T1
Valid prediction for snap_scaffold_10-snap.869-T1
Valid prediction for snap_scaffold_10-snap.884-T1
Valid prediction for snap_scaffold_10-snap.882-T1
Valid prediction for Augustus_model.g16338.t1
Valid prediction for snap_scaffold_10-snap.868-T1
Couldn't classify 196072, 196488
Couldn't classify 197860, 198009
Sorry, prediction pasa_asmbl_4248.p1 fails validation.
(TGC)	 AC	196072-196488	GT	AGG
(ATC)	 AG	197860-198009	CC	CCC
Valid prediction for Augustus_model.g16320.t1
Valid prediction for CodingQuarry_transcript_5353-T1
Valid prediction for GlimmerHMM_glimmerT_24526-T1
Valid prediction for Augustus_model.g16334.t1
Valid prediction for snap_scaffold_10-snap.850-T1
Valid prediction for Augustus_model.g16342.t1
Valid prediction for snap_scaffold_10-snap.847-T1
Valid prediction for GlimmerHMM_glimmerT_24519-T1
Valid prediction for GlimmerHMM_glimmerT_24531-T1
Valid prediction for Augustus_model.g16323.t1
Valid prediction for snap_scaffold_10-snap.873-T1
Valid prediction for Augustus_model.g16335.t1
Valid prediction for snap_scaffold_10-snap.851-T1
Valid prediction for Augustus_model.g16337.t1
Valid prediction for GlimmerHMM_glimmerT_24515-T1
Valid prediction for HiQ_model.g16333.t1
Valid prediction for snap_scaffold_10-snap.880-T1
Valid prediction for snap_scaffold_10-snap.853-T1
Valid prediction for snap_scaffold_10-snap.874-T1
Valid prediction for GlimmerHMM_glimmerT_24541-T1
Valid prediction for snap_scaffold_10-snap.848-T1
Valid prediction for snap_scaffold_10-snap.843-T1
Valid prediction for CodingQuarry_transcript_5352-T1
Valid prediction for snap_scaffold_10-snap.866-T1
Valid prediction for Augustus_model.g16326.t1
Valid prediction for snap_scaffold_10-snap.845-T1
Valid prediction for snap_scaffold_10-snap.879-T1
Valid prediction for GlimmerHMM_glimmerT_24529-T1
Couldn't classify 195740, 196014
Sorry, prediction pasa_asmbl_4249.p1 fails validation.
(ATG)	 GT	194292-194430	GT	TGG
(GTT)	 AG	195740-196014	CC	TGC
-recovered pasa_asmbl_4249.p1, initial, 194292, 194430
Valid prediction for pasa_asmbl_4259.p1
Valid prediction for snap_scaffold_10-snap.857-T1
Valid prediction for GlimmerHMM_glimmerT_24534-T1
Valid prediction for HiQ_model.g16321.t1
Valid prediction for GlimmerHMM_glimmerT_24511-T1
Valid prediction for snap_scaffold_10-snap.859-T1
Valid prediction for snap_scaffold_10-snap.861-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19073, rend_intergenic: 12353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21689, rend_intergenic: 19303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25284, rend_intergenic: 21834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40248, rend_intergenic: 30652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41880, rend_intergenic: 41221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50720, rend_intergenic: 42794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61563, rend_intergenic: 54649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68862, rend_intergenic: 62857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75497, rend_intergenic: 69864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84115, rend_intergenic: 75588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147648, rend_intergenic: 138499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154819, rend_intergenic: 147654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166684, rend_intergenic: 166474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169405, rend_intergenic: 166704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177480, rend_intergenic: 173408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182154, rend_intergenic: 182042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188805, rend_intergenic: 182448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199219, rend_intergenic: 191778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211321
-exon list size: 418


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.1    
2.4    
2.6    
2.9    
3.1    
3.3    
3.6    
3.8    
4.0    
4.3    
4.5    
4.8    
5.0    
5.2    
5.5    
5.7    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.3    
8.6    
8.8    
9.0    
9.3    
9.5    
9.8    
10.0    
10.2    
10.5    
10.7    
11.0    
11.2    
11.4    
11.7    
11.9    
12.1    
12.4    
12.6    
12.9    
13.1    
13.3    
13.6    
13.8    
14.0    
14.3    
14.5    
14.8    
15.0    
15.2    
15.5    
15.7    
16.0    
16.2    
16.4    
16.7    
16.9    
17.1    
17.4    
17.6    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.3    
28.6    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.4    
31.7    
31.9    
32.1    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
41.0    
41.2    
41.4    
41.7    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.2    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.4    
47.6    
47.9    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.4    
51.7    
51.9    
52.1    
52.4    
52.6    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.8    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.3    
58.6    
58.8    
59.0    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
61.0    
61.2    
61.4    
61.7    
61.9    
62.1    
62.4    
62.6    
62.9    
63.1    
63.3    
63.6    
63.8    
64.0    
64.3    
64.5    
64.8    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.9    
68.1    
68.3    
68.6    
68.8    
69.0    
69.3    
69.5    
69.8    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.4    
71.7    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.4    
82.6    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.3    
84.5    
84.8    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.4    
87.6    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.3    
89.5    
89.8    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.8    
95.0    
95.2    
95.5    
95.7    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 19073, rend_intergenic: 12353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21689, rend_intergenic: 19303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25284, rend_intergenic: 21834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40248, rend_intergenic: 30652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41880, rend_intergenic: 41221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50720, rend_intergenic: 42794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61563, rend_intergenic: 54649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68862, rend_intergenic: 62857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75497, rend_intergenic: 69864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84115, rend_intergenic: 75588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147648, rend_intergenic: 138499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154819, rend_intergenic: 147654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166684, rend_intergenic: 166474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169405, rend_intergenic: 166704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177480, rend_intergenic: 173408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182154, rend_intergenic: 182042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188805, rend_intergenic: 182448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199219, rend_intergenic: 191778  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