-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_1512726-1723428

-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_2-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_3230-T1
Valid prediction for snap_scaffold_2-snap.385-T1
Valid prediction for GlimmerHMM_glimmerT_3228-T1
Valid prediction for snap_scaffold_2-snap.364-T1
Valid prediction for Augustus_model.g2193.t1
Valid prediction for snap_scaffold_2-snap.388-T1
Valid prediction for snap_scaffold_2-snap.394-T1
Valid prediction for snap_scaffold_2-snap.378-T1
Valid prediction for snap_scaffold_2-snap.359-T1
Valid prediction for CodingQuarry_transcript_28463-T1
Valid prediction for GlimmerHMM_glimmerT_3241-T1
Valid prediction for GlimmerHMM_glimmerT_3235-T1
Valid prediction for GlimmerHMM_glimmerT_3231-T1
Valid prediction for CodingQuarry_transcript_28465-T1
Valid prediction for GlimmerHMM_glimmerT_3240-T1
Valid prediction for Augustus_model.g2180.t1
Valid prediction for GlimmerHMM_glimmerT_3233-T1
Valid prediction for Augustus_model.g2188.t1
Valid prediction for snap_scaffold_2-snap.368-T1
Valid prediction for GlimmerHMM_glimmerT_3232-T1
Valid prediction for snap_scaffold_2-snap.383-T1
Valid prediction for snap_scaffold_2-snap.398-T1
Valid prediction for snap_scaffold_2-snap.392-T1
Valid prediction for snap_scaffold_2-snap.355-T1
Valid prediction for snap_scaffold_2-snap.350-T1
Valid prediction for Augustus_model.g2190.t1
Valid prediction for snap_scaffold_2-snap.367-T1
Valid prediction for Augustus_model.g2189.t1
Valid prediction for snap_scaffold_2-snap.390-T1
Valid prediction for Augustus_model.g2182.t1
Valid prediction for snap_scaffold_2-snap.381-T1
Valid prediction for GlimmerHMM_glimmerT_3252-T1
Valid prediction for snap_scaffold_2-snap.391-T1
Valid prediction for snap_scaffold_2-snap.399-T1
Valid prediction for pasa_asmbl_24211.p1
Valid prediction for Augustus_model.g2181.t1
Valid prediction for GlimmerHMM_glimmerT_3249-T1
Valid prediction for snap_scaffold_2-snap.363-T1
Valid prediction for HiQ_model.g2184.t1
Valid prediction for Augustus_model.g2192.t1
Valid prediction for snap_scaffold_2-snap.354-T1
Valid prediction for GlimmerHMM_glimmerT_3242-T1
Valid prediction for snap_scaffold_2-snap.386-T1
Valid prediction for snap_scaffold_2-snap.372-T1
Valid prediction for snap_scaffold_2-snap.360-T1
Valid prediction for snap_scaffold_2-snap.356-T1
Valid prediction for GlimmerHMM_glimmerT_3227-T1
Valid prediction for GlimmerHMM_glimmerT_3225-T1
Valid prediction for snap_scaffold_2-snap.362-T1
Valid prediction for snap_scaffold_2-snap.369-T1
Valid prediction for GlimmerHMM_glimmerT_3251-T1
Valid prediction for GlimmerHMM_glimmerT_3248-T1
Valid prediction for snap_scaffold_2-snap.351-T1
Valid prediction for CodingQuarry_transcript_28464-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_2-snap.397-T1
Valid prediction for snap_scaffold_2-snap.352-T1
Valid prediction for snap_scaffold_2-snap.382-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3237-T1
Couldn't classify 73659, 73988
Couldn't classify 79600, 79650
Sorry, prediction pasa_asmbl_22865.p1 fails validation.
(CGG)	 TC	73659-73988	GT	AGG
(GCA)	 AG	74168-74320	GT	AGG
(CTG)	 AG	74917-75092	GT	AGG
(GTT)	 AG	75350-75443	GT	GGG
(GTC)	 AG	76931-77008	GT	AGG
(GTG)	 AG	77251-77385	GT	AGG
(ATG)	 AG	77669-77781	GT	AGG
(GTT)	 AG	78355-78496	GT	AGG
(GTG)	 AG	79056-79346	GT	AGG
(ACC)	 AG	79600-79650	GC	AGG
-recovered pasa_asmbl_22865.p1, initial, 77669, 77781
-recovered pasa_asmbl_22865.p1, internal, 74168, 74320
-recovered pasa_asmbl_22865.p1, internal, 74917, 75092
-recovered pasa_asmbl_22865.p1, internal, 75350, 75443
-recovered pasa_asmbl_22865.p1, internal, 76931, 77008
-recovered pasa_asmbl_22865.p1, internal, 77251, 77385
-recovered pasa_asmbl_22865.p1, internal, 77669, 77781
-recovered pasa_asmbl_22865.p1, internal, 78355, 78496
-recovered pasa_asmbl_22865.p1, internal, 79056, 79346
-recovered pasa_asmbl_22865.p1, internal, 79600, 79650
Valid prediction for snap_scaffold_2-snap.358-T1
Valid prediction for snap_scaffold_2-snap.370-T1
Valid prediction for snap_scaffold_2-snap.384-T1
Valid prediction for GlimmerHMM_glimmerT_3236-T1
Valid prediction for GlimmerHMM_glimmerT_3246-T1
Valid prediction for snap_scaffold_2-snap.393-T1
Valid prediction for GlimmerHMM_glimmerT_3244-T1
Valid prediction for snap_scaffold_2-snap.371-T1
Valid prediction for GlimmerHMM_glimmerT_3234-T1
Valid prediction for snap_scaffold_2-snap.361-T1
Valid prediction for snap_scaffold_2-snap.349-T1
Valid prediction for snap_scaffold_2-snap.375-T1
Valid prediction for GlimmerHMM_glimmerT_3247-T1
Valid prediction for Augustus_model.g2187.t1
Couldn't classify 70995, 71140
Couldn't classify 71567, 71735
Sorry, prediction pasa_asmbl_24021.p3 fails validation.
(GGT)	 GG	70995-71140	GT	AAG
(GTT)	 AG	71567-71735	AA	CCA
Valid prediction for GlimmerHMM_glimmerT_3226-T1
Valid prediction for snap_scaffold_2-snap.379-T1
Valid prediction for snap_scaffold_2-snap.373-T1
Valid prediction for snap_scaffold_2-snap.389-T1
Valid prediction for GlimmerHMM_glimmerT_3239-T1
Valid prediction for snap_scaffold_2-snap.374-T1
Valid prediction for snap_scaffold_2-snap.387-T1
Valid prediction for snap_scaffold_2-snap.380-T1
Couldn't classify 122342, 122386
Couldn't classify 123435, 123559
Sorry, prediction pasa_asmbl_22855.p1 fails validation.
(TTC)	 TC	122342-122386	GT	AGG
(TCT)	 AG	122485-122627	GT	AGG
(CCC)	 AG	122902-123176	GT	AGG
(GAG)	 AG	123435-123559	GG	GGG
-recovered pasa_asmbl_22855.p1, internal, 122485, 122627
-recovered pasa_asmbl_22855.p1, internal, 122902, 123176
Valid prediction for snap_scaffold_2-snap.396-T1
Valid prediction for Augustus_model.g2183.t1
Couldn't classify 121250, 121741
Sorry, prediction pasa_asmbl_22856.p1 fails validation.
(ATG)	 AG	121250-121741	TT	GCT
Valid prediction for GlimmerHMM_glimmerT_3243-T1
Valid prediction for snap_scaffold_2-snap.395-T1
Valid prediction for snap_scaffold_2-snap.376-T1
Valid prediction for GlimmerHMM_glimmerT_3250-T1
Valid prediction for HiQ_model.g2185.t1
Valid prediction for Augustus_model.g2186.t1
Valid prediction for GlimmerHMM_glimmerT_3238-T1
Valid prediction for snap_scaffold_2-snap.377-T1
Valid prediction for GlimmerHMM_glimmerT_3224-T1
Valid prediction for snap_scaffold_2-snap.357-T1
Valid prediction for snap_scaffold_2-snap.353-T1
Valid prediction for Augustus_model.g2191.t1
Couldn't classify 107607, 109634
Sorry, prediction pasa_asmbl_22860.p1 fails validation.
(ATG)	 CC	105421-106232	GT	AGG
(TCA)	 AG	106550-106602	GT	AGG
(GTG)	 AG	106690-106772	GT	GGG
(GTG)	 AG	107607-109634	GA	TGG
-recovered pasa_asmbl_22860.p1, initial, 105421, 106232
-recovered pasa_asmbl_22860.p1, internal, 106550, 106602
-recovered pasa_asmbl_22860.p1, internal, 106690, 106772
Valid prediction for snap_scaffold_2-snap.366-T1
Valid prediction for GlimmerHMM_glimmerT_3229-T1
Valid prediction for GlimmerHMM_glimmerT_3245-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8246, rend_intergenic: 4615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17622, rend_intergenic: 14044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41978, rend_intergenic: 40220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50989, rend_intergenic: 46801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68990, rend_intergenic: 67372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94150, rend_intergenic: 91955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111236, rend_intergenic: 109471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118226, rend_intergenic: 112183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131227, rend_intergenic: 127885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133808, rend_intergenic: 131349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134835, rend_intergenic: 133922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152657, rend_intergenic: 135515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169017, rend_intergenic: 165839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185405, rend_intergenic: 183626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210703
-exon list size: 366


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.3    
3.5    
3.8    
4.1    
4.3    
4.6    
4.9    
5.2    
5.4    
5.7    
6.0    
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6.5    
6.8    
7.1    
7.3    
7.6    
7.9    
8.2    
8.4    
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9.5    
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10.1    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.6    
13.9    
14.1    
14.4    
14.7    
14.9    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.8    
17.1    
17.4    
17.7    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.7    
20.9    
21.2    
21.5    
21.7    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.1    
35.3    
35.6    
35.9    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.1    
64.4    
64.7    
64.9    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.4    
70.7    
70.9    
71.2    
71.5    
71.7    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.5    
78.8    
79.1    
79.3    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.3    
82.6    
82.9    
83.2    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.7    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 8246, rend_intergenic: 4615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17622, rend_intergenic: 14044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41978, rend_intergenic: 40220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50989, rend_intergenic: 46801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68990, rend_intergenic: 67372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94150, rend_intergenic: 91955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111236, rend_intergenic: 109471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118226, rend_intergenic: 112183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131227, rend_intergenic: 127885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133808, rend_intergenic: 131349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134835, rend_intergenic: 133922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152657, rend_intergenic: 135515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169017, rend_intergenic: 165839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185405, rend_intergenic: 183626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support