-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_13869006-14071731

-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 CodingQuarry_transcript_57713-T1
Valid prediction for HiQ_model.g12430.t1
Valid prediction for snap_scaffold_7-snap.2611-T1
Valid prediction for snap_scaffold_7-snap.2633-T1
Valid prediction for snap_scaffold_7-snap.2620-T1
Valid prediction for CodingQuarry_transcript_57709-T1
Valid prediction for CodingQuarry_transcript_57710-T1
Valid prediction for snap_scaffold_7-snap.2598-T1
Valid prediction for Augustus_model.g12442.t1
Valid prediction for pasa_asmbl_50381.p1
Valid prediction for snap_scaffold_7-snap.2608-T1
Valid prediction for GlimmerHMM_glimmerT_18453-T1
Valid prediction for HiQ_model.g12436.t1
Valid prediction for CodingQuarry_transcript_57712-T1
Valid prediction for GlimmerHMM_glimmerT_18442-T1
Valid prediction for Augustus_model.g12434.t1
Valid prediction for snap_scaffold_7-snap.2599-T1
Valid prediction for snap_scaffold_7-snap.2610-T1
Valid prediction for GlimmerHMM_glimmerT_18439-T1
Valid prediction for CodingQuarry_transcript_57714-T1
Valid prediction for GlimmerHMM_glimmerT_18444-T1
Valid prediction for snap_scaffold_7-snap.2626-T1
Valid prediction for GlimmerHMM_glimmerT_18445-T1
Valid prediction for GlimmerHMM_glimmerT_18451-T1
Valid prediction for Augustus_model.g12441.t1
Valid prediction for HiQ_model.g12437.t1
Valid prediction for GlimmerHMM_glimmerT_18452-T1
Valid prediction for pasa_asmbl_50392.p1
Valid prediction for GlimmerHMM_glimmerT_18443-T1
Valid prediction for snap_scaffold_7-snap.2605-T1
Valid prediction for snap_scaffold_7-snap.2595-T1
Valid prediction for Augustus_model.g12443.t1
Valid prediction for snap_scaffold_7-snap.2631-T1
Valid prediction for snap_scaffold_7-snap.2609-T1
Valid prediction for snap_scaffold_7-snap.2603-T1
Couldn't classify 81108, 81158
Sorry, prediction pasa_asmbl_50385.p1 fails validation.
(ATG)	 AT	78315-78433	GT	AAG
(GAA)	 AG	78829-78889	GT	AGG
(CTT)	 AG	79003-79077	GT	TTG
(GTG)	 AG	79387-79492	GT	TGG
(ACA)	 AG	79595-79644	GT	AGG
(GTG)	 AG	79767-79830	GT	AGG
(CGT)	 AG	80137-80184	GT	TGG
(GTG)	 AG	80294-80407	GT	GGG
(TGA)	 AG	80591-80777	GT	CAG
(ATT)	 AG	80871-80922	GT	AGG
(ATC)	 AG	81108-81158	AT	AGA
-recovered pasa_asmbl_50385.p1, initial, 78315, 78433
-recovered pasa_asmbl_50385.p1, internal, 78829, 78889
-recovered pasa_asmbl_50385.p1, internal, 79003, 79077
-recovered pasa_asmbl_50385.p1, internal, 79387, 79492
-recovered pasa_asmbl_50385.p1, internal, 79595, 79644
-recovered pasa_asmbl_50385.p1, internal, 79767, 79830
-recovered pasa_asmbl_50385.p1, internal, 80137, 80184
-recovered pasa_asmbl_50385.p1, internal, 80294, 80407
-recovered pasa_asmbl_50385.p1, internal, 80591, 80777
-recovered pasa_asmbl_50385.p1, internal, 80871, 80922
Valid prediction for HiQ_model.g12431.t1
Valid prediction for GlimmerHMM_glimmerT_18448-T1
Valid prediction for CodingQuarry_transcript_57711-T1
Valid prediction for snap_scaffold_7-snap.2602-T1
Valid prediction for snap_scaffold_7-snap.2632-T1
Valid prediction for pasa_asmbl_50387.p1
Valid prediction for snap_scaffold_7-snap.2612-T1
Valid prediction for snap_scaffold_7-snap.2615-T1
Valid prediction for snap_scaffold_7-snap.2606-T1
Valid prediction for snap_scaffold_7-snap.2617-T1
Valid prediction for pasa_asmbl_50384.p1
Valid prediction for snap_scaffold_7-snap.2621-T1
Valid prediction for snap_scaffold_7-snap.2618-T1
Valid prediction for snap_scaffold_7-snap.2601-T1
Valid prediction for snap_scaffold_7-snap.2623-T1
Valid prediction for GlimmerHMM_glimmerT_18438-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.g12438.t1
Valid prediction for GlimmerHMM_glimmerT_18437-T1
Valid prediction for snap_scaffold_7-snap.2613-T1
Valid prediction for GlimmerHMM_glimmerT_18450-T1
Valid prediction for Augustus_model.g12440.t1
Valid prediction for GlimmerHMM_glimmerT_18441-T1
Valid prediction for GlimmerHMM_glimmerT_18440-T1
Valid prediction for snap_scaffold_7-snap.2624-T1
Valid prediction for snap_scaffold_7-snap.2630-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g12429.t1
Valid prediction for GlimmerHMM_glimmerT_18447-T1
Valid prediction for Augustus_model.g12433.t1
Valid prediction for GlimmerHMM_glimmerT_18446-T1
Couldn't classify 198171, 198286
Sorry, prediction pasa_asmbl_51329.p1 fails validation.
(ATG)	 AT	194228-194918	GT	TTG
(ATG)	 AG	197584-197637	GC	AGG
(CAC)	 AG	198171-198286	GC	TGG
-recovered pasa_asmbl_51329.p1, initial, 194228, 194918
add_exon() Sorry, pasa_asmbl_51329.p1 197584-197637-initial-1 is invalid.
-recovered pasa_asmbl_51329.p1, initial, 197584, 197637
-recovered pasa_asmbl_51329.p1, internal, 197584, 197637
-recovered pasa_asmbl_51329.p1, internal, 198171, 198286
Valid prediction for GlimmerHMM_glimmerT_18436-T1
Valid prediction for Augustus_model.g12432.t1
Couldn't classify 198596, 199945
Sorry, prediction pasa_asmbl_51328.p1 fails validation.
(CCT)	 TC	198596-199945	GC	CTG
Valid prediction for GlimmerHMM_glimmerT_18449-T1
Valid prediction for Augustus_model.g12439.t1
Valid prediction for snap_scaffold_7-snap.2593-T1
Valid prediction for snap_scaffold_7-snap.2629-T1
Valid prediction for snap_scaffold_7-snap.2628-T1
Valid prediction for snap_scaffold_7-snap.2616-T1
Valid prediction for snap_scaffold_7-snap.2614-T1
Valid prediction for snap_scaffold_7-snap.2596-T1
Valid prediction for snap_scaffold_7-snap.2604-T1
Valid prediction for snap_scaffold_7-snap.2597-T1
Valid prediction for Augustus_model.g12428.t1
Valid prediction for snap_scaffold_7-snap.2600-T1
Valid prediction for Augustus_model.g12435.t1
Valid prediction for snap_scaffold_7-snap.2619-T1
Valid prediction for snap_scaffold_7-snap.2592-T1
Valid prediction for snap_scaffold_7-snap.2627-T1
Valid prediction for snap_scaffold_7-snap.2622-T1
Valid prediction for snap_scaffold_7-snap.2607-T1
Valid prediction for snap_scaffold_7-snap.2625-T1
Valid prediction for snap_scaffold_7-snap.2594-T1
Couldn't classify 105324, 105417
Sorry, prediction pasa_asmbl_51333.p1 fails validation.
(ATG)	 AC	100909-101011	GT	AGG
(TTT)	 AG	101723-101787	GT	TGG
(GTG)	 AG	101952-102053	GT	AGG
(ACG)	 AG	103514-103628	GT	CGG
(GAG)	 AG	103720-103807	GT	AGG
(AAG)	 AG	105324-105417	GT	CGG
-recovered pasa_asmbl_51333.p1, initial, 100909, 101011
-recovered pasa_asmbl_51333.p1, internal, 101723, 101787
-recovered pasa_asmbl_51333.p1, internal, 101952, 102053
-recovered pasa_asmbl_51333.p1, internal, 103514, 103628
-recovered pasa_asmbl_51333.p1, internal, 103720, 103807
-recovered pasa_asmbl_51333.p1, internal, 105324, 105417

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18725, rend_intergenic: 15517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52456, rend_intergenic: 28335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56762, rend_intergenic: 52759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63715, rend_intergenic: 57918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71416, rend_intergenic: 66501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109041, rend_intergenic: 103785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130127, rend_intergenic: 122942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133597, rend_intergenic: 131153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152402, rend_intergenic: 146435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174956, rend_intergenic: 155188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193646, rend_intergenic: 178467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202726
-exon list size: 414


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.2    
2.4    
2.6    
2.9    
3.1    
3.4    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.0    
5.3    
5.5    
5.8    
6.0    
6.2    
6.5    
6.7    
7.0    
7.2    
7.5    
7.7    
7.9    
8.2    
8.4    
8.7    
8.9    
9.1    
9.4    
9.6    
9.9    
10.1    
10.3    
10.6    
10.8    
11.1    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.7    
13.0    
13.2    
13.5    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.1    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.8    
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    
27.2    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.0    
44.2    
44.5    
44.7    
45.0    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.6    
46.9    
47.1    
47.4    
47.6    
47.8    
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    
52.2    
52.4    
52.6    
52.9    
53.1    
53.4    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.0    
55.3    
55.5    
55.8    
56.0    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.7    
63.0    
63.2    
63.5    
63.7    
63.9    
64.2    
64.4    
64.7    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.8    
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    
77.2    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.9    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.6    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 18725, rend_intergenic: 15517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52456, rend_intergenic: 28335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56762, rend_intergenic: 52759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63715, rend_intergenic: 57918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71416, rend_intergenic: 66501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109041, rend_intergenic: 103785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130127, rend_intergenic: 122942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133597, rend_intergenic: 131153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152402, rend_intergenic: 146435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174956, rend_intergenic: 155188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193646, rend_intergenic: 178467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 180149 - 202726
-exon list size: 24


building trellis

3.8    
7.7    
11.5    
15.4    
19.2    
23.1    
26.9    
30.8    
34.6    
38.5    
42.3    
46.2    
50.0    
53.8    
57.7    
61.5    
65.4    
69.2    
73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-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 180617 - 202726
-exon list size: 20


building trellis

4.5    
9.1    
13.6    
18.2    
22.7    
27.3    
31.8    
36.4    
40.9    
45.5    
50.0    
54.5    
59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
95.5    
-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 180617 - 202393
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-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 180617 - 200293
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-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 180617 - 194390
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-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 184039 - 194390
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-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