-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_1-187942

-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.g21106.t1
Valid prediction for CodingQuarry_transcript_12784-T1
Valid prediction for HiQ_model.g21102.t1
Valid prediction for GlimmerHMM_glimmerT_31606-T1
Valid prediction for snap_scaffold_13-snap.17-T1
Valid prediction for snap_scaffold_13-snap.33-T1
Valid prediction for GeneMark_model.54404_t
Valid prediction for GlimmerHMM_glimmerT_31600-T1
Valid prediction for GeneMark_model.54411_t
Valid prediction for GlimmerHMM_glimmerT_31602-T1
Valid prediction for snap_scaffold_13-snap.19-T1
Valid prediction for snap_scaffold_13-snap.28-T1
Couldn't classify 1, 145
Sorry, prediction pasa_asmbl_10413.p1 fails validation.
(CCT)	 GA	1-145	GT	CGG
(GTG)	 AG	333-583	GT	AGG
(GCA)	 AG	776-859	TT	GAT
-recovered pasa_asmbl_10413.p1, terminal, 776, 859
-recovered pasa_asmbl_10413.p1, internal, 333, 583
Valid prediction for GeneMark_model.54393_t
Valid prediction for GeneMark_model.54384_t
Valid prediction for snap_scaffold_13-snap.2-T1
Valid prediction for pasa_asmbl_10425.p1
Couldn't classify 3619, 3688
Couldn't classify 4290, 4350
Sorry, prediction pasa_asmbl_10416.p1 fails validation.
(ATG)	 AA	1661-1697	GT	AGG
(GTA)	 AG	2080-2168	GT	AGG
(GGA)	 AG	2294-2361	GT	AGG
(ATT)	 AG	2514-2574	GT	AGG
(GAC)	 AG	2685-2741	GT	AGG
(TCA)	 AG	2875-2970	GT	GAG
(AAT)	 AG	3173-3247	GT	AGG
(GTG)	 AG	3338-3434	GT	AGG
(AGC)	 AG	3619-3688	AT	AGA
(ATT)	 AC	4290-4350	GT	AAG
(CCT)	 AG	4449-4529	GT	AGG
(AAT)	 AG	4698-4784	AT	AGA
-recovered pasa_asmbl_10416.p1, initial, 1661, 1697
-recovered pasa_asmbl_10416.p1, terminal, 4698, 4784
-recovered pasa_asmbl_10416.p1, internal, 2080, 2168
-recovered pasa_asmbl_10416.p1, internal, 2294, 2361
-recovered pasa_asmbl_10416.p1, internal, 2514, 2574
-recovered pasa_asmbl_10416.p1, internal, 2685, 2741
-recovered pasa_asmbl_10416.p1, internal, 2875, 2970
-recovered pasa_asmbl_10416.p1, internal, 3173, 3247
-recovered pasa_asmbl_10416.p1, internal, 3338, 3434
-recovered pasa_asmbl_10416.p1, internal, 4449, 4529
Valid prediction for pasa_asmbl_10428.p1
Valid prediction for GeneMark_model.54405_t
Valid prediction for Augustus_model.g21122.t1
Couldn't classify 31, 145
Sorry, prediction GeneMark_model.54380_t fails validation.
(AAT)	 AG	31-145	GT	CGG
(GGG)	 AG	357-583	GT	AGG
(CTT)	 AG	1571-1606	GG	AGG
-recovered GeneMark_model.54380_t, terminal, 1571, 1606
-recovered GeneMark_model.54380_t, internal, 31, 145
-recovered GeneMark_model.54380_t, internal, 357, 583
Valid prediction for GlimmerHMM_glimmerT_31609-T1
Valid prediction for snap_scaffold_13-snap.39-T1
Valid prediction for GeneMark_model.54394_t
Valid prediction for pasa_asmbl_10424.p1
Valid prediction for GlimmerHMM_glimmerT_31584-T1
add_exon() Sorry, GlimmerHMM_glimmerT_31584-T1 333-661-terminal-1 is invalid.
Valid prediction for Augustus_model.g21121.t1
Valid prediction for GeneMark_model.54388_t
Valid prediction for GeneMark_model.54399_t
Valid prediction for GlimmerHMM_glimmerT_31601-T1
Valid prediction for Augustus_model.g21113.t1
Valid prediction for snap_scaffold_13-snap.20-T1
Valid prediction for snap_scaffold_13-snap.21-T1
Valid prediction for HiQ_model.g21112.t1
Valid prediction for GlimmerHMM_glimmerT_31599-T1
Couldn't classify 3619, 3688
Couldn't classify 4290, 4350
Sorry, prediction CodingQuarry_transcript_12782-T1 fails validation.
(ATG)	 TC	2881-2970	GT	GAG
(AAT)	 AG	3173-3247	GT	AGG
(GTG)	 AG	3338-3434	GT	AGG
(AGC)	 AG	3619-3688	AT	AGA
(ATT)	 AC	4290-4350	GT	AAG
(CCT)	 AG	4449-4529	GT	AGG
(AAT)	 AG	4698-4784	AT	AGA
-recovered CodingQuarry_transcript_12782-T1, initial, 2881, 2970
-recovered CodingQuarry_transcript_12782-T1, terminal, 4698, 4784
-recovered CodingQuarry_transcript_12782-T1, internal, 3173, 3247
-recovered CodingQuarry_transcript_12782-T1, internal, 3338, 3434
-recovered CodingQuarry_transcript_12782-T1, internal, 4449, 4529
Valid prediction for GeneMark_model.54386_t
Valid prediction for CodingQuarry_transcript_12783-T1
Valid prediction for GlimmerHMM_glimmerT_31590-T1
Valid prediction for GeneMark_model.54403_t
Valid prediction for GlimmerHMM_glimmerT_31594-T1
Valid prediction for GeneMark_model.54401_t
Couldn't classify 31, 145
Sorry, prediction snap_scaffold_13-snap.1-T1 fails validation.
(AAT)	 AG	31-145	GT	CGG
(GTG)	 AG	333-583	GT	AGG
(GCA)	 AG	776-859	TT	GAT
-recovered snap_scaffold_13-snap.1-T1, terminal, 776, 859
-recovered snap_scaffold_13-snap.1-T1, internal, 31, 145
-recovered snap_scaffold_13-snap.1-T1, internal, 333, 583
Valid prediction for snap_scaffold_13-snap.22-T1
Valid prediction for snap_scaffold_13-snap.12-T1
Valid prediction for GlimmerHMM_glimmerT_31603-T1
Valid prediction for CodingQuarry_transcript_12786-T1
Valid prediction for GeneMark_model.54407_t
Valid prediction for GeneMark_model.54406_t
Couldn't classify 1, 145
Sorry, prediction HiQ_model.g21101.t1 fails validation.
(CCT)	 GA	1-145	GT	CGG
(GTG)	 AG	333-583	GT	AGG
(GCA)	 AG	776-859	TT	GAT
-recovered HiQ_model.g21101.t1, terminal, 776, 859
-recovered HiQ_model.g21101.t1, internal, 333, 583
Valid prediction for GlimmerHMM_glimmerT_31585-T1
Valid prediction for Augustus_model.g21111.t1
Valid prediction for CodingQuarry_transcript_12785-T1
Valid prediction for snap_scaffold_13-snap.30-T1
Valid prediction for GeneMark_model.54397_t
Valid prediction for Augustus_model.g21123.t1
Valid prediction for snap_scaffold_13-snap.18-T1
Valid prediction for snap_scaffold_13-snap.8-T1
Valid prediction for GeneMark_model.54392_t

-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.g21120.t1
Valid prediction for snap_scaffold_13-snap.25-T1
Valid prediction for snap_scaffold_13-snap.3-T1
Valid prediction for GeneMark_model.54387_t
Valid prediction for GlimmerHMM_glimmerT_31597-T1
Valid prediction for Augustus_model.g21116.t1
Valid prediction for Augustus_model.g21110.t1
Valid prediction for snap_scaffold_13-snap.35-T1
Valid prediction for snap_scaffold_13-snap.38-T1
Valid prediction for snap_scaffold_13-snap.7-T1
Valid prediction for snap_scaffold_13-snap.26-T1
Valid prediction for GeneMark_model.54398_t
Valid prediction for snap_scaffold_13-snap.34-T1
Valid prediction for Augustus_model.g21118.t1
Valid prediction for snap_scaffold_13-snap.11-T1
Valid prediction for snap_scaffold_13-snap.27-T1
Valid prediction for Augustus_model.g21115.t1
Valid prediction for GlimmerHMM_glimmerT_31604-T1
Valid prediction for GeneMark_model.54400_t
Valid prediction for GeneMark_model.54396_t
Valid prediction for Augustus_model.g21109.t1
Valid prediction for GeneMark_model.54389_t
Valid prediction for Augustus_model.g21105.t1
Valid prediction for snap_scaffold_13-snap.13-T1
Valid prediction for Augustus_model.g21114.t1
Valid prediction for snap_scaffold_13-snap.29-T1
Valid prediction for GlimmerHMM_glimmerT_31587-T1
Valid prediction for GeneMark_model.54410_t
Valid prediction for snap_scaffold_13-snap.14-T1
Valid prediction for GeneMark_model.54408_t
Valid prediction for GlimmerHMM_glimmerT_31598-T1
Valid prediction for GlimmerHMM_glimmerT_31593-T1
Valid prediction for GeneMark_model.54402_t
Valid prediction for snap_scaffold_13-snap.37-T1
Valid prediction for GlimmerHMM_glimmerT_31592-T1
Valid prediction for Augustus_model.g21107.t1
Valid prediction for GlimmerHMM_glimmerT_31596-T1
Valid prediction for Augustus_model.g21108.t1
Valid prediction for GeneMark_model.54391_t
Valid prediction for GlimmerHMM_glimmerT_31605-T1
Valid prediction for GeneMark_model.54409_t
Valid prediction for snap_scaffold_13-snap.16-T1
Valid prediction for Augustus_model.g21104.t1
Valid prediction for Augustus_model.g21119.t1
Valid prediction for GlimmerHMM_glimmerT_31610-T1
Valid prediction for snap_scaffold_13-snap.9-T1
Valid prediction for GeneMark_model.54395_t
Valid prediction for snap_scaffold_13-snap.24-T1
Valid prediction for GeneMark_model.54383_t
Valid prediction for GeneMark_model.54385_t
Valid prediction for snap_scaffold_13-snap.23-T1
Valid prediction for GlimmerHMM_glimmerT_31586-T1
Valid prediction for GlimmerHMM_glimmerT_31589-T1
Valid prediction for Augustus_model.g21117.t1
Valid prediction for GlimmerHMM_glimmerT_31595-T1
Valid prediction for snap_scaffold_13-snap.5-T1
Valid prediction for snap_scaffold_13-snap.32-T1
Valid prediction for GeneMark_model.54390_t
Valid prediction for Augustus_model.g21103.t1
Valid prediction for snap_scaffold_13-snap.36-T1
Valid prediction for snap_scaffold_13-snap.6-T1
Valid prediction for GlimmerHMM_glimmerT_31608-T1
Valid prediction for GlimmerHMM_glimmerT_31607-T1
Valid prediction for snap_scaffold_13-snap.4-T1
Valid prediction for snap_scaffold_13-snap.15-T1
Valid prediction for snap_scaffold_13-snap.31-T1
Valid prediction for GeneMark_model.54381_t
Valid prediction for GlimmerHMM_glimmerT_31591-T1
Valid prediction for snap_scaffold_13-snap.10-T1
Valid prediction for GlimmerHMM_glimmerT_31588-T1
Valid prediction for GeneMark_model.54382_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 108942, rend_intergenic: 102690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132062, rend_intergenic: 130547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 110743, rend_intergenic: 110740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187942
-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 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 108942, rend_intergenic: 102690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132062, rend_intergenic: 130547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 110743, rend_intergenic: 110740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 176354 - 187942
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 177447 - 187942
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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