-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_15742610-15965884

-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 GeneMark_model.32112_t
Valid prediction for snap_scaffold_7-snap.3008-T1
Valid prediction for GeneMark_model.32088_t
Valid prediction for GeneMark_model.32105_t
Valid prediction for snap_scaffold_7-snap.3023-T1
Valid prediction for GlimmerHMM_glimmerT_19074-T1
Valid prediction for snap_scaffold_7-snap.3028-T1
Valid prediction for snap_scaffold_7-snap.3003-T1
Valid prediction for snap_scaffold_7-snap.3029-T1
Valid prediction for GeneMark_model.32099_t
Valid prediction for Augustus_model.g12916.t1
Valid prediction for snap_scaffold_7-snap.2999-T1
Valid prediction for Augustus_model.g12903.t1
Valid prediction for GeneMark_model.32083_t
Valid prediction for snap_scaffold_7-snap.3002-T1
Valid prediction for GeneMark_model.32122_t
Valid prediction for Augustus_model.g12913.t1
Valid prediction for snap_scaffold_7-snap.3016-T1
Valid prediction for snap_scaffold_7-snap.3032-T1
Valid prediction for snap_scaffold_7-snap.3019-T1
Valid prediction for snap_scaffold_7-snap.2996-T1
Valid prediction for GeneMark_model.32127_t
Valid prediction for GlimmerHMM_glimmerT_19087-T1
Valid prediction for GeneMark_model.32141_t
Valid prediction for GeneMark_model.32106_t
Valid prediction for Augustus_model.g12914.t1
Valid prediction for GeneMark_model.32093_t
Valid prediction for snap_scaffold_7-snap.3021-T1
Valid prediction for GeneMark_model.32125_t
Valid prediction for snap_scaffold_7-snap.3010-T1
Valid prediction for GeneMark_model.32118_t
Valid prediction for GeneMark_model.32131_t
Valid prediction for GlimmerHMM_glimmerT_19078-T1
Valid prediction for GlimmerHMM_glimmerT_19084-T1
Valid prediction for GeneMark_model.32103_t
Valid prediction for GlimmerHMM_glimmerT_19075-T1
Valid prediction for snap_scaffold_7-snap.3005-T1
Valid prediction for GeneMark_model.32100_t
Valid prediction for GeneMark_model.32108_t
Valid prediction for GeneMark_model.32113_t
Valid prediction for GeneMark_model.32138_t
Valid prediction for GeneMark_model.32115_t
Valid prediction for GeneMark_model.32135_t
Valid prediction for GlimmerHMM_glimmerT_19072-T1
Valid prediction for GeneMark_model.32085_t
Valid prediction for GeneMark_model.32120_t
Valid prediction for GeneMark_model.32133_t
Valid prediction for GeneMark_model.32102_t
Valid prediction for GlimmerHMM_glimmerT_19077-T1
Valid prediction for GeneMark_model.32116_t
Valid prediction for GeneMark_model.32089_t
Valid prediction for GeneMark_model.32136_t
Valid prediction for GeneMark_model.32084_t
Valid prediction for snap_scaffold_7-snap.3026-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.32097_t
Valid prediction for GlimmerHMM_glimmerT_19069-T1
Valid prediction for GeneMark_model.32124_t
Valid prediction for GeneMark_model.32140_t
Valid prediction for GeneMark_model.32110_t
Valid prediction for GlimmerHMM_glimmerT_19085-T1
Valid prediction for snap_scaffold_7-snap.3011-T1
Valid prediction for GeneMark_model.32129_t
Valid prediction for snap_scaffold_7-snap.3027-T1
Sorry, intron length (9) is less than minimum required (10)

-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 GlimmerHMM_glimmerT_19079-T1
Valid prediction for snap_scaffold_7-snap.3001-T1
Valid prediction for GlimmerHMM_glimmerT_19070-T1
Valid prediction for GeneMark_model.32139_t
Valid prediction for snap_scaffold_7-snap.3007-T1
Valid prediction for GeneMark_model.32109_t
Valid prediction for snap_scaffold_7-snap.3000-T1
Valid prediction for snap_scaffold_7-snap.3006-T1
Valid prediction for GlimmerHMM_glimmerT_19073-T1
Valid prediction for GlimmerHMM_glimmerT_19068-T1
Valid prediction for GeneMark_model.32137_t
Valid prediction for Augustus_model.g12908.t1
Valid prediction for GeneMark_model.32087_t
Valid prediction for GlimmerHMM_glimmerT_19080-T1
Valid prediction for snap_scaffold_7-snap.3025-T1
Valid prediction for snap_scaffold_7-snap.3030-T1
Valid prediction for pasa_asmbl_50206.p1
Couldn't classify 19075, 19605
Sorry, prediction pasa_asmbl_50213.p1 fails validation.
(GAA)	 TG	19075-19605	CA	GAC
Valid prediction for GlimmerHMM_glimmerT_19081-T1
Valid prediction for GeneMark_model.32082_t
Valid prediction for snap_scaffold_7-snap.3013-T1
Valid prediction for GlimmerHMM_glimmerT_19086-T1
Valid prediction for GeneMark_model.32090_t
Valid prediction for GlimmerHMM_glimmerT_19071-T1
Valid prediction for GeneMark_model.32114_t
Valid prediction for Augustus_model.g12904.t1
Valid prediction for snap_scaffold_7-snap.2995-T1
Valid prediction for Augustus_model.g12905.t1
Valid prediction for GeneMark_model.32091_t
Valid prediction for Augustus_model.g12910.t1
Valid prediction for GeneMark_model.32104_t
Valid prediction for Augustus_model.g12906.t1
Couldn't classify 38047, 38092
Sorry, prediction pasa_asmbl_50211.p1 fails validation.
(GTG)	 AG	38047-38092	GT	CGG
(TCA)	 AG	39972-40069	GT	CTG
(GTT)	 AG	40172-40303	GT	AGG
(CAG)	 AG	40526-40672	GT	TGG
(ATG)	 AG	41297-41365	GT	TGG
(GAA)	 AG	42194-42258	GT	AGG
(TGA)	 AG	42691-42844	GT	CGG
(GAC)	 AG	45437-45793	TC	GAT
-recovered pasa_asmbl_50211.p1, initial, 41297, 41365
-recovered pasa_asmbl_50211.p1, terminal, 45437, 45793
-recovered pasa_asmbl_50211.p1, internal, 38047, 38092
-recovered pasa_asmbl_50211.p1, internal, 39972, 40069
-recovered pasa_asmbl_50211.p1, internal, 40172, 40303
-recovered pasa_asmbl_50211.p1, internal, 40526, 40672
-recovered pasa_asmbl_50211.p1, internal, 41297, 41365
-recovered pasa_asmbl_50211.p1, internal, 42194, 42258
-recovered pasa_asmbl_50211.p1, internal, 42691, 42844
Valid prediction for GlimmerHMM_glimmerT_19076-T1
Valid prediction for GeneMark_model.32081_t
Valid prediction for GeneMark_model.32123_t
Valid prediction for snap_scaffold_7-snap.3022-T1
Valid prediction for GeneMark_model.32134_t
Valid prediction for snap_scaffold_7-snap.2997-T1
Valid prediction for GeneMark_model.32095_t
Valid prediction for GeneMark_model.32096_t
Valid prediction for Augustus_model.g12907.t1
Valid prediction for snap_scaffold_7-snap.2998-T1
Valid prediction for GeneMark_model.32126_t
Valid prediction for snap_scaffold_7-snap.3017-T1
Valid prediction for Augustus_model.g12909.t1
Valid prediction for GeneMark_model.32098_t
Valid prediction for Augustus_model.g12915.t1
Valid prediction for Augustus_model.g12901.t1
Valid prediction for GlimmerHMM_glimmerT_19082-T1
Valid prediction for snap_scaffold_7-snap.3015-T1
Valid prediction for snap_scaffold_7-snap.3009-T1
Valid prediction for GeneMark_model.32117_t
Valid prediction for GeneMark_model.32101_t
Valid prediction for GlimmerHMM_glimmerT_19067-T1
Valid prediction for GeneMark_model.32130_t
Valid prediction for GeneMark_model.32092_t
Couldn't classify 70576, 71006
Couldn't classify 76544, 76652
Sorry, prediction pasa_asmbl_50207.p1 fails validation.
(ACA)	 GT	70576-71006	GT	CGG
(GTT)	 AG	71333-71637	GT	AGG
(ATG)	 AG	71963-72093	GT	AGG
(TCT)	 AG	72324-72419	GT	CGG
(GCC)	 AG	72609-72776	GT	AGG
(TTG)	 AG	72970-73106	GT	AGG
(TAT)	 AG	74510-74621	GT	CTG
(AAC)	 AG	74966-75196	GT	CGG
(TCG)	 AG	75386-75497	GT	AGG
(TGA)	 AG	75735-75832	GT	GTG
(GTG)	 AG	75988-76064	GT	AGG
(AGG)	 AG	76544-76652	AA	GCA
add_exon() Sorry, pasa_asmbl_50207.p1 71963-72093-initial-1 is invalid.
-recovered pasa_asmbl_50207.p1, initial, 71963, 72093
-recovered pasa_asmbl_50207.p1, internal, 71333, 71637
-recovered pasa_asmbl_50207.p1, internal, 71963, 72093
-recovered pasa_asmbl_50207.p1, internal, 72324, 72419
-recovered pasa_asmbl_50207.p1, internal, 72609, 72776
-recovered pasa_asmbl_50207.p1, internal, 72970, 73106
-recovered pasa_asmbl_50207.p1, internal, 74510, 74621
-recovered pasa_asmbl_50207.p1, internal, 74966, 75196
-recovered pasa_asmbl_50207.p1, internal, 75386, 75497
-recovered pasa_asmbl_50207.p1, internal, 75735, 75832
-recovered pasa_asmbl_50207.p1, internal, 75988, 76064
Valid prediction for GeneMark_model.32107_t
Couldn't classify 69606, 69923
Sorry, prediction pasa_asmbl_50208.p1 fails validation.
(ATG)	 GC	69606-69923	AG	GGA
Valid prediction for snap_scaffold_7-snap.3014-T1
Valid prediction for Augustus_model.g12912.t1
Valid prediction for Augustus_model.g12911.t1
Valid prediction for Augustus_model.g12902.t1
Valid prediction for GeneMark_model.32094_t
Valid prediction for GeneMark_model.32119_t
Valid prediction for snap_scaffold_7-snap.3004-T1
Valid prediction for Augustus_model.g12900.t1
Valid prediction for snap_scaffold_7-snap.3024-T1
Valid prediction for snap_scaffold_7-snap.3020-T1
Valid prediction for pasa_asmbl_50209.p1
Valid prediction for snap_scaffold_7-snap.3018-T1
Valid prediction for snap_scaffold_7-snap.3012-T1
Valid prediction for GlimmerHMM_glimmerT_19083-T1
Valid prediction for GeneMark_model.32111_t
Couldn't classify 55505, 55605
Couldn't classify 56336, 56540
Sorry, prediction pasa_asmbl_50372.p2 fails validation.
(GCA)	 CA	55505-55605	GT	AAG
(GAT)	 AG	56336-56540	GT	CGG
-recovered pasa_asmbl_50372.p2, internal, 56336, 56540
Valid prediction for GeneMark_model.32121_t
Valid prediction for CodingQuarry_transcript_57586-T1
Valid prediction for snap_scaffold_7-snap.3031-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 66637, rend_intergenic: 66634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67168, rend_intergenic: 62153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76652, rend_intergenic: 72344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88677, rend_intergenic: 85963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91770, rend_intergenic: 89794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141438, rend_intergenic: 136451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153670, rend_intergenic: 143181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159768, rend_intergenic: 158413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163544, rend_intergenic: 161798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172982, rend_intergenic: 164006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187759, rend_intergenic: 178919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 223275
-exon list size: 639


building trellis

0.2    
0.3    
0.5    
0.6    
0.8    
0.9    
1.1    
1.2    
1.4    
1.6    
1.7    
1.9    
2.0    
2.2    
2.3    
2.5    
2.7    
2.8    
3.0    
3.1    
3.3    
3.4    
3.6    
3.7    
3.9    
4.1    
4.2    
4.4    
4.5    
4.7    
4.8    
5.0    
5.1    
5.3    
5.5    
5.6    
5.8    
5.9    
6.1    
6.2    
6.4    
6.6    
6.7    
6.9    
7.0    
7.2    
7.3    
7.5    
7.6    
7.8    
8.0    
8.1    
8.3    
8.4    
8.6    
8.7    
8.9    
9.0    
9.2    
9.4    
9.5    
9.7    
9.8    
10.0    
10.1    
10.3    
10.5    
10.6    
10.8    
10.9    
11.1    
11.2    
11.4    
11.5    
11.7    
11.9    
12.0    
12.2    
12.3    
12.5    
12.6    
12.8    
12.9    
13.1    
13.3    
13.4    
13.6    
13.7    
13.9    
14.0    
14.2    
14.4    
14.5    
14.7    
14.8    
15.0    
15.1    
15.3    
15.4    
15.6    
15.8    
15.9    
16.1    
16.2    
16.4    
16.5    
16.7    
16.8    
17.0    
17.2    
17.3    
17.5    
17.6    
17.8    
17.9    
18.1    
18.3    
18.4    
18.6    
18.7    
18.9    
19.0    
19.2    
19.3    
19.5    
19.7    
19.8    
20.0    
20.1    
20.3    
20.4    
20.6    
20.7    
20.9    
21.1    
21.2    
21.4    
21.5    
21.7    
21.8    
22.0    
22.2    
22.3    
22.5    
22.6    
22.8    
22.9    
23.1    
23.2    
23.4    
23.6    
23.7    
23.9    
24.0    
24.2    
24.3    
24.5    
24.6    
24.8    
25.0    
25.1    
25.3    
25.4    
25.6    
25.7    
25.9    
26.1    
26.2    
26.4    
26.5    
26.7    
26.8    
27.0    
27.1    
27.3    
27.5    
27.6    
27.8    
27.9    
28.1    
28.2    
28.4    
28.5    
28.7    
28.9    
29.0    
29.2    
29.3    
29.5    
29.6    
29.8    
30.0    
30.1    
30.3    
30.4    
30.6    
30.7    
30.9    
31.0    
31.2    
31.4    
31.5    
31.7    
31.8    
32.0    
32.1    
32.3    
32.4    
32.6    
32.8    
32.9    
33.1    
33.2    
33.4    
33.5    
33.7    
33.9    
34.0    
34.2    
34.3    
34.5    
34.6    
34.8    
34.9    
35.1    
35.3    
35.4    
35.6    
35.7    
35.9    
36.0    
36.2    
36.3    
36.5    
36.7    
36.8    
37.0    
37.1    
37.3    
37.4    
37.6    
37.8    
37.9    
38.1    
38.2    
38.4    
38.5    
38.7    
38.8    
39.0    
39.2    
39.3    
39.5    
39.6    
39.8    
39.9    
40.1    
40.2    
40.4    
40.6    
40.7    
40.9    
41.0    
41.2    
41.3    
41.5    
41.7    
41.8    
42.0    
42.1    
42.3    
42.4    
42.6    
42.7    
42.9    
43.1    
43.2    
43.4    
43.5    
43.7    
43.8    
44.0    
44.1    
44.3    
44.5    
44.6    
44.8    
44.9    
45.1    
45.2    
45.4    
45.6    
45.7    
45.9    
46.0    
46.2    
46.3    
46.5    
46.6    
46.8    
47.0    
47.1    
47.3    
47.4    
47.6    
47.7    
47.9    
48.0    
48.2    
48.4    
48.5    
48.7    
48.8    
49.0    
49.1    
49.3    
49.5    
49.6    
49.8    
49.9    
50.1    
50.2    
50.4    
50.5    
50.7    
50.9    
51.0    
51.2    
51.3    
51.5    
51.6    
51.8    
52.0    
52.1    
52.3    
52.4    
52.6    
52.7    
52.9    
53.0    
53.2    
53.4    
53.5    
53.7    
53.8    
54.0    
54.1    
54.3    
54.4    
54.6    
54.8    
54.9    
55.1    
55.2    
55.4    
55.5    
55.7    
55.9    
56.0    
56.2    
56.3    
56.5    
56.6    
56.8    
56.9    
57.1    
57.3    
57.4    
57.6    
57.7    
57.9    
58.0    
58.2    
58.3    
58.5    
58.7    
58.8    
59.0    
59.1    
59.3    
59.4    
59.6    
59.8    
59.9    
60.1    
60.2    
60.4    
60.5    
60.7    
60.8    
61.0    
61.2    
61.3    
61.5    
61.6    
61.8    
61.9    
62.1    
62.2    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.7    
63.8    
64.0    
64.1    
64.3    
64.4    
64.6    
64.7    
64.9    
65.1    
65.2    
65.4    
65.5    
65.7    
65.8    
66.0    
66.1    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
69.0    
69.1    
69.3    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.5    
71.6    
71.8    
71.9    
72.1    
72.2    
72.4    
72.5    
72.7    
72.9    
73.0    
73.2    
73.3    
73.5    
73.6    
73.8    
73.9    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.4    
75.5    
75.7    
75.8    
76.0    
76.1    
76.3    
76.4    
76.6    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.2    
80.3    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 30 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 66637, rend_intergenic: 66634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67168, rend_intergenic: 62153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76652, rend_intergenic: 72344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88677, rend_intergenic: 85963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91770, rend_intergenic: 89794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141438, rend_intergenic: 136451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153670, rend_intergenic: 143181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159768, rend_intergenic: 158413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163544, rend_intergenic: 161798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172982, rend_intergenic: 164006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187759, rend_intergenic: 178919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support