-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_1509400-1644707

-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_11-snap.389-T1
Valid prediction for snap_scaffold_11-snap.375-T1
Valid prediction for HiQ_model.g17579.t1
Valid prediction for snap_scaffold_11-snap.384-T1
Valid prediction for snap_scaffold_11-snap.363-T1
Valid prediction for Augustus_model.g17576.t1
Valid prediction for snap_scaffold_11-snap.390-T1
Valid prediction for GlimmerHMM_glimmerT_26534-T1
Valid prediction for snap_scaffold_11-snap.382-T1
Valid prediction for GlimmerHMM_glimmerT_26540-T1
Valid prediction for snap_scaffold_11-snap.392-T1
Valid prediction for snap_scaffold_11-snap.370-T1
Valid prediction for GlimmerHMM_glimmerT_26542-T1
Valid prediction for snap_scaffold_11-snap.393-T1
Valid prediction for snap_scaffold_11-snap.373-T1
Valid prediction for snap_scaffold_11-snap.364-T1
Valid prediction for GlimmerHMM_glimmerT_26528-T1
Valid prediction for snap_scaffold_11-snap.374-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_26535-T1
Valid prediction for HiQ_model.g17578.t1
Valid prediction for GlimmerHMM_glimmerT_26545-T1
Valid prediction for GlimmerHMM_glimmerT_26525-T1
Valid prediction for snap_scaffold_11-snap.381-T1
Valid prediction for GlimmerHMM_glimmerT_26549-T1
Valid prediction for Augustus_model.g17571.t1
Valid prediction for CodingQuarry_transcript_7978-T1
Valid prediction for GlimmerHMM_glimmerT_26541-T1
Couldn't classify 120616, 120776
Sorry, prediction pasa_asmbl_5340.p1 fails validation.
(ATG)	 AG	119272-119301	GT	AGG
(GTC)	 AG	119501-119548	GT	AAG
(AGT)	 AG	119658-119790	GT	AGG
(GTG)	 AG	120616-120776	GA	GGG
-recovered pasa_asmbl_5340.p1, initial, 119272, 119301
-recovered pasa_asmbl_5340.p1, internal, 119272, 119301
-recovered pasa_asmbl_5340.p1, internal, 119501, 119548
-recovered pasa_asmbl_5340.p1, internal, 119658, 119790
Valid prediction for Augustus_model.g17581.t1
Valid prediction for snap_scaffold_11-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_26531-T1
Couldn't classify 121521, 122001
Sorry, prediction pasa_asmbl_5341.p1 fails validation.
(CAG)	 CC	121521-122001	GT	CGG
(GAA)	 AG	122092-122181	GT	AGG
(AGA)	 AG	122326-122408	GT	CGG
(GCT)	 AG	122767-122862	GT	AGG
(TTG)	 AG	123035-123145	CG	AGC
-recovered pasa_asmbl_5341.p1, terminal, 123035, 123145
-recovered pasa_asmbl_5341.p1, internal, 122092, 122181
-recovered pasa_asmbl_5341.p1, internal, 122326, 122408
-recovered pasa_asmbl_5341.p1, internal, 122767, 122862
Valid prediction for Augustus_model.g17583.t1
Valid prediction for GlimmerHMM_glimmerT_26546-T1
Valid prediction for GlimmerHMM_glimmerT_26543-T1
Valid prediction for snap_scaffold_11-snap.387-T1
Couldn't classify 84214, 84357
Sorry, prediction pasa_asmbl_5338.p1 fails validation.
(GGA)	 AC	84214-84357	GT	AGG
(ATT)	 AG	86189-86277	GT	CAG
(GTA)	 AG	87471-87527	GT	GCG
(GTT)	 AG	88166-88240	GT	ATG
(TTA)	 AG	88882-89263	GT	AGG
(ATT)	 AG	91098-91207	GT	CGG
(TCC)	 AG	91951-92023	TC	GAT
-recovered pasa_asmbl_5338.p1, terminal, 91951, 92023
-recovered pasa_asmbl_5338.p1, internal, 86189, 86277
-recovered pasa_asmbl_5338.p1, internal, 87471, 87527
-recovered pasa_asmbl_5338.p1, internal, 88166, 88240
-recovered pasa_asmbl_5338.p1, internal, 88882, 89263
-recovered pasa_asmbl_5338.p1, internal, 91098, 91207
Valid prediction for CodingQuarry_transcript_7977-T1
Valid prediction for pasa_asmbl_6353.p1
Valid prediction for snap_scaffold_11-snap.379-T1
Valid prediction for GlimmerHMM_glimmerT_26548-T1
Valid prediction for snap_scaffold_11-snap.385-T1
Valid prediction for Augustus_model.g17582.t1
Valid prediction for snap_scaffold_11-snap.376-T1
Valid prediction for snap_scaffold_11-snap.394-T1
Valid prediction for GlimmerHMM_glimmerT_26537-T1
Valid prediction for GlimmerHMM_glimmerT_26538-T1
Valid prediction for snap_scaffold_11-snap.380-T1
Valid prediction for snap_scaffold_11-snap.396-T1
Valid prediction for snap_scaffold_11-snap.360-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.368-T1
Valid prediction for snap_scaffold_11-snap.399-T1
Valid prediction for GlimmerHMM_glimmerT_26547-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_11-snap.372-T1
Valid prediction for snap_scaffold_11-snap.361-T1
Valid prediction for snap_scaffold_11-snap.366-T1
Valid prediction for GlimmerHMM_glimmerT_26544-T1
Valid prediction for snap_scaffold_11-snap.369-T1
Valid prediction for snap_scaffold_11-snap.371-T1
Valid prediction for snap_scaffold_11-snap.388-T1
Valid prediction for Augustus_model.g17574.t1
Couldn't classify 64340, 64481
Couldn't classify 65359, 65468
Sorry, prediction pasa_asmbl_6440.p1 fails validation.
(TTC)	 AG	64340-64481	GT	CGG
(GAG)	 AG	64938-65059	GT	CAG
(TCT)	 AG	65145-65220	GT	GGG
(CAC)	 AG	65359-65468	GT	TGG
-recovered pasa_asmbl_6440.p1, internal, 64340, 64481
-recovered pasa_asmbl_6440.p1, internal, 64938, 65059
-recovered pasa_asmbl_6440.p1, internal, 65145, 65220
-recovered pasa_asmbl_6440.p1, internal, 65359, 65468
Valid prediction for snap_scaffold_11-snap.377-T1
Valid prediction for snap_scaffold_11-snap.398-T1
Valid prediction for Augustus_model.g17577.t1
Couldn't classify 72512, 72642
Couldn't classify 72826, 72936
Couldn't classify 73081, 73135
Sorry, prediction CodingQuarry_transcript_7976-T1 fails validation.
(ATG)	 AA	72512-72642	CT	ACC
(CTG)	 AC	72826-72936	CT	ACC
(CTG)	 AC	73081-73135	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_26536-T1
Valid prediction for Augustus_model.g17572.t1
Valid prediction for snap_scaffold_11-snap.395-T1
Valid prediction for snap_scaffold_11-snap.391-T1
Valid prediction for GlimmerHMM_glimmerT_26539-T1
Valid prediction for snap_scaffold_11-snap.383-T1
Valid prediction for snap_scaffold_11-snap.359-T1
Valid prediction for Augustus_model.g17573.t1
Valid prediction for GlimmerHMM_glimmerT_26530-T1
Valid prediction for snap_scaffold_11-snap.386-T1
Valid prediction for pasa_asmbl_6444.p1
Valid prediction for GlimmerHMM_glimmerT_26526-T1
Valid prediction for snap_scaffold_11-snap.378-T1
Valid prediction for snap_scaffold_11-snap.367-T1
Valid prediction for GlimmerHMM_glimmerT_26550-T1
Couldn't classify 61580, 61681
Couldn't classify 62704, 62933
Sorry, prediction pasa_asmbl_6441.p1 fails validation.
(CAG)	 AG	61580-61681	GT	CGG
(CTG)	 AG	62317-62497	GT	CGG
(AGA)	 AG	62704-62933	AT	ACA
-recovered pasa_asmbl_6441.p1, internal, 61580, 61681
-recovered pasa_asmbl_6441.p1, internal, 62317, 62497
Couldn't classify 2358, 2480
Sorry, prediction pasa_asmbl_7322.p1 fails validation.
(TAC)	 GG	2358-2480	GT	AGG
(GGA)	 AG	3516-3549	GT	AGG
(CCC)	 AG	3628-3667	GT	GTG
(GCA)	 AG	3807-3868	GT	CAG
(AGA)	 AG	3978-4052	GT	AGG
(GTG)	 AG	4287-4342	GT	AGG
(ACG)	 AG	5090-5198	GT	AGG
(CAG)	 AG	5616-5783	GT	AGG
(TGT)	 AG	5922-6007	GT	GGG
(GTC)	 AG	6387-6484	GT	AGG
(TAA)	 AG	7915-8045	GT	CGG
(TCA)	 AG	8720-8793	GT	AGG
(GGT)	 AG	8903-8986	GT	AAG
(GCC)	 AG	10054-10221	GT	AGG
(GTG)	 AG	10699-10833	AC	GAA
-recovered pasa_asmbl_7322.p1, terminal, 10699, 10833
-recovered pasa_asmbl_7322.p1, internal, 3516, 3549
-recovered pasa_asmbl_7322.p1, internal, 3628, 3667
-recovered pasa_asmbl_7322.p1, internal, 3807, 3868
-recovered pasa_asmbl_7322.p1, internal, 3978, 4052
-recovered pasa_asmbl_7322.p1, internal, 4287, 4342
-recovered pasa_asmbl_7322.p1, internal, 5090, 5198
-recovered pasa_asmbl_7322.p1, internal, 5616, 5783
-recovered pasa_asmbl_7322.p1, internal, 5922, 6007
-recovered pasa_asmbl_7322.p1, internal, 6387, 6484
-recovered pasa_asmbl_7322.p1, internal, 7915, 8045
-recovered pasa_asmbl_7322.p1, internal, 8720, 8793
-recovered pasa_asmbl_7322.p1, internal, 8903, 8986
-recovered pasa_asmbl_7322.p1, internal, 10054, 10221
Valid prediction for GlimmerHMM_glimmerT_26533-T1
Valid prediction for GlimmerHMM_glimmerT_26532-T1
Couldn't classify 72512, 72642
Couldn't classify 73007, 73061
Sorry, prediction CodingQuarry_transcript_7974-T1 fails validation.
(ATG)	 AA	72512-72642	CT	ACC
(CTG)	 AC	73007-73061	GA	GAG
Valid prediction for snap_scaffold_11-snap.362-T1
Valid prediction for Augustus_model.g17580.t1
Valid prediction for GlimmerHMM_glimmerT_26529-T1
Valid prediction for GlimmerHMM_glimmerT_26527-T1
Couldn't classify 69267, 69309
Sorry, prediction pasa_asmbl_6439.p1 fails validation.
(ATG)	 AG	66769-66822	GT	AGG
(GTG)	 AG	67526-67655	GT	AGG
(GTC)	 AG	67778-67836	GT	AGG
(CTG)	 AG	67974-68063	GT	AGG
(GTG)	 AG	68251-68426	GT	TGG
(TTT)	 AG	69267-69309	CT	AGC
-recovered pasa_asmbl_6439.p1, initial, 66769, 66822
-recovered pasa_asmbl_6439.p1, internal, 66769, 66822
-recovered pasa_asmbl_6439.p1, internal, 67526, 67655
-recovered pasa_asmbl_6439.p1, internal, 67778, 67836
-recovered pasa_asmbl_6439.p1, internal, 67974, 68063
-recovered pasa_asmbl_6439.p1, internal, 68251, 68426
Valid prediction for snap_scaffold_11-snap.397-T1
Couldn't classify 72512, 72642
Couldn't classify 72682, 72736
Sorry, prediction CodingQuarry_transcript_7975-T1 fails validation.
(ATG)	 AA	72512-72642	CT	ACC
(CTT)	 AC	72682-72736	GA	GAG
Valid prediction for Augustus_model.g17575.t1
Valid prediction for HiQ_model.g17584.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4978, rend_intergenic: 4325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6491, rend_intergenic: 4999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19525, rend_intergenic: 12361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32342, rend_intergenic: 27882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40241, rend_intergenic: 35124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51194, rend_intergenic: 48723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78837, rend_intergenic: 65947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88177, rend_intergenic: 86588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95042, rend_intergenic: 94104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99545, rend_intergenic: 96382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105973, rend_intergenic: 102813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118261, rend_intergenic: 115878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123145, rend_intergenic: 119654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132340, rend_intergenic: 125098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 135308
-exon list size: 357


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.1    
3.3    
3.6    
3.9    
4.2    
4.5    
4.7    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.7    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
24.0    
24.2    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.5    
34.8    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.5    
43.7    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.3    
56.5    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.8    
59.1    
59.3    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.2    
65.5    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.2    
68.5    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.9    
72.1    
72.4    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.8    
76.0    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.3    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.4    
96.7    
96.9    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 4978, rend_intergenic: 4325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6491, rend_intergenic: 4999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19525, rend_intergenic: 12361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32342, rend_intergenic: 27882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40241, rend_intergenic: 35124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51194, rend_intergenic: 48723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78837, rend_intergenic: 65947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88177, rend_intergenic: 86588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95042, rend_intergenic: 94104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99545, rend_intergenic: 96382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105973, rend_intergenic: 102813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118261, rend_intergenic: 115878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123145, rend_intergenic: 119654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132340, rend_intergenic: 125098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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