-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_13156127-13356623

-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_7-snap.2502-T1
Valid prediction for snap_scaffold_7-snap.2485-T1
Valid prediction for CodingQuarry_transcript_57690-T1
Valid prediction for snap_scaffold_7-snap.2494-T1
Valid prediction for GlimmerHMM_glimmerT_18377-T1
Valid prediction for snap_scaffold_7-snap.2476-T1
Valid prediction for snap_scaffold_7-snap.2498-T1
Valid prediction for pasa_asmbl_50331.p1
Valid prediction for GlimmerHMM_glimmerT_18366-T1
Valid prediction for snap_scaffold_7-snap.2482-T1
Valid prediction for GlimmerHMM_glimmerT_18361-T1
Valid prediction for CodingQuarry_transcript_57692-T1
Valid prediction for snap_scaffold_7-snap.2479-T1
Valid prediction for CodingQuarry_transcript_57695-T1
Valid prediction for CodingQuarry_transcript_57687-T1
Valid prediction for HiQ_model.g12379.t1
Valid prediction for GlimmerHMM_glimmerT_18363-T1
Valid prediction for GlimmerHMM_glimmerT_18365-T1
Valid prediction for snap_scaffold_7-snap.2493-T1
Valid prediction for Augustus_model.g12384.t1
Valid prediction for snap_scaffold_7-snap.2492-T1
Valid prediction for Augustus_model.g12390.t1
Valid prediction for GlimmerHMM_glimmerT_18373-T1
Valid prediction for snap_scaffold_7-snap.2490-T1
Valid prediction for Augustus_model.g12382.t1
Valid prediction for GlimmerHMM_glimmerT_18356-T1
Valid prediction for snap_scaffold_7-snap.2500-T1
Valid prediction for GlimmerHMM_glimmerT_18359-T1
Valid prediction for CodingQuarry_transcript_57693-T1
Valid prediction for HiQ_model.g12372.t1
Valid prediction for GlimmerHMM_glimmerT_18368-T1
Valid prediction for snap_scaffold_7-snap.2472-T1
Valid prediction for snap_scaffold_7-snap.2505-T1
Valid prediction for HiQ_model.g12377.t1
Valid prediction for snap_scaffold_7-snap.2496-T1
Valid prediction for Augustus_model.g12386.t1
Valid prediction for snap_scaffold_7-snap.2475-T1
Valid prediction for CodingQuarry_transcript_57691-T1
Valid prediction for pasa_asmbl_50333.p1
Valid prediction for Augustus_model.g12376.t1
Valid prediction for snap_scaffold_7-snap.2478-T1
Valid prediction for snap_scaffold_7-snap.2488-T1
Valid prediction for pasa_asmbl_50314.p1
Valid prediction for GlimmerHMM_glimmerT_18360-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_18371-T1
Valid prediction for snap_scaffold_7-snap.2473-T1
Valid prediction for pasa_asmbl_50313.p1
Couldn't classify 108713, 108820
Sorry, prediction pasa_asmbl_50569.p1 fails validation.
(GTA)	 AG	108713-108820	GT	TTG
(GTG)	 AG	109603-109764	GT	TGG
(GAT)	 AG	110219-110347	GT	TGG
(GTG)	 AG	110645-110719	GG	GAG
-recovered pasa_asmbl_50569.p1, terminal, 110645, 110719
-recovered pasa_asmbl_50569.p1, internal, 108713, 108820
-recovered pasa_asmbl_50569.p1, internal, 109603, 109764
-recovered pasa_asmbl_50569.p1, internal, 110219, 110347
Valid prediction for Augustus_model.g12381.t1
Valid prediction for snap_scaffold_7-snap.2481-T1
Valid prediction for snap_scaffold_7-snap.2483-T1
Valid prediction for snap_scaffold_7-snap.2469-T1
Couldn't classify 53892, 53902
Couldn't classify 57351, 58233
Sorry, prediction pasa_asmbl_50323.p1 fails validation.
(CAG)	 AC	53892-53902	GT	AAG
(ACT)	 AG	54030-54192	GT	AAG
(GTC)	 AG	54300-54584	GT	TGG
(AAT)	 AG	54731-54870	GT	AAG
(CGA)	 AG	54988-55093	GT	CTG
(GAG)	 AG	55324-55549	GT	AGG
(AAA)	 AG	55667-55728	GT	AGG
(AGT)	 AG	55913-56032	GT	ACG
(AAA)	 AG	56227-56374	GT	AGG
(GAT)	 AG	56975-57266	GC	AGG
(GCA)	 AG	57351-58233	GA	AGG
add_exon() Sorry, pasa_asmbl_50323.p1 56975-57266-terminal-3 is invalid.
-recovered pasa_asmbl_50323.p1, terminal, 56975, 57266
-recovered pasa_asmbl_50323.p1, internal, 54030, 54192
-recovered pasa_asmbl_50323.p1, internal, 54300, 54584
-recovered pasa_asmbl_50323.p1, internal, 54731, 54870
-recovered pasa_asmbl_50323.p1, internal, 54988, 55093
-recovered pasa_asmbl_50323.p1, internal, 55324, 55549
-recovered pasa_asmbl_50323.p1, internal, 55667, 55728
-recovered pasa_asmbl_50323.p1, internal, 55913, 56032
-recovered pasa_asmbl_50323.p1, internal, 56227, 56374
-recovered pasa_asmbl_50323.p1, internal, 56975, 57266
Valid prediction for pasa_asmbl_50336.p1
Valid prediction for snap_scaffold_7-snap.2504-T1
Valid prediction for snap_scaffold_7-snap.2484-T1
Valid prediction for snap_scaffold_7-snap.2470-T1
Valid prediction for GlimmerHMM_glimmerT_18378-T1
Valid prediction for HiQ_model.g12375.t1
Valid prediction for Augustus_model.g12389.t1
Valid prediction for snap_scaffold_7-snap.2506-T1
Valid prediction for HiQ_model.g12380.t1
Valid prediction for HiQ_model.g12383.t1
Couldn't classify 83073, 83115
Sorry, prediction pasa_asmbl_50335.p1 fails validation.
(CAG)	 AC	83073-83115	GT	AGG
(CCT)	 AG	85792-86144	GT	CGG
(ATG)	 AG	86658-86911	GT	AGG
(TCT)	 AG	87682-87858	GT	AGG
(CTT)	 AG	87952-88075	GT	AGG
(AAA)	 AG	88689-88814	GT	AGG
(GGG)	 AG	89018-89077	GG	GAG
-recovered pasa_asmbl_50335.p1, initial, 86658, 86911
-recovered pasa_asmbl_50335.p1, terminal, 89018, 89077
-recovered pasa_asmbl_50335.p1, internal, 85792, 86144
-recovered pasa_asmbl_50335.p1, internal, 86658, 86911
-recovered pasa_asmbl_50335.p1, internal, 87682, 87858
-recovered pasa_asmbl_50335.p1, internal, 87952, 88075
-recovered pasa_asmbl_50335.p1, internal, 88689, 88814
Valid prediction for CodingQuarry_transcript_57694-T1
Valid prediction for GlimmerHMM_glimmerT_18367-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 GlimmerHMM_glimmerT_18357-T1
Valid prediction for snap_scaffold_7-snap.2489-T1
Couldn't classify 181903, 182018
Sorry, prediction pasa_asmbl_51293.p1 fails validation.
(CTG)	 AG	181903-182018	GT	CGG
(CTG)	 AG	182446-182589	GT	TGG
(GCT)	 AG	182731-182851	TT	GAT
-recovered pasa_asmbl_51293.p1, terminal, 182731, 182851
-recovered pasa_asmbl_51293.p1, internal, 181903, 182018
-recovered pasa_asmbl_51293.p1, internal, 182446, 182589
Valid prediction for snap_scaffold_7-snap.2486-T1
Valid prediction for snap_scaffold_7-snap.2491-T1
Valid prediction for Augustus_model.g12385.t1
Valid prediction for snap_scaffold_7-snap.2503-T1
Valid prediction for snap_scaffold_7-snap.2499-T1
Valid prediction for snap_scaffold_7-snap.2501-T1
Valid prediction for GlimmerHMM_glimmerT_18375-T1
Valid prediction for GlimmerHMM_glimmerT_18376-T1
Valid prediction for snap_scaffold_7-snap.2495-T1
Valid prediction for snap_scaffold_7-snap.2487-T1
Valid prediction for HiQ_model.g12374.t1
Valid prediction for GlimmerHMM_glimmerT_18364-T1
Valid prediction for GlimmerHMM_glimmerT_18355-T1
Valid prediction for snap_scaffold_7-snap.2477-T1
Valid prediction for GlimmerHMM_glimmerT_18374-T1
Valid prediction for Augustus_model.g12378.t1
Valid prediction for CodingQuarry_transcript_57688-T1
Valid prediction for snap_scaffold_7-snap.2480-T1
Valid prediction for pasa_asmbl_51303.p1
Valid prediction for Augustus_model.g12373.t1
Valid prediction for snap_scaffold_7-snap.2474-T1
Couldn't classify 173513, 173529
Couldn't classify 179952, 180008
Sorry, prediction pasa_asmbl_51294.p1 fails validation.
(CAC)	 AC	173513-173529	GT	AGG
(GTT)	 AG	173639-173735	GT	GAG
(CAA)	 AG	173828-173935	GT	AGG
(TTG)	 AG	174399-174531	GT	CGG
(GCA)	 AG	175709-175797	GT	CTG
(CTG)	 AG	177955-178113	GT	CGG
(GAC)	 AG	178718-178792	GT	AGG
(GTT)	 AG	179952-180008	AA	ACA
-recovered pasa_asmbl_51294.p1, internal, 173639, 173735
-recovered pasa_asmbl_51294.p1, internal, 173828, 173935
-recovered pasa_asmbl_51294.p1, internal, 174399, 174531
-recovered pasa_asmbl_51294.p1, internal, 175709, 175797
-recovered pasa_asmbl_51294.p1, internal, 177955, 178113
-recovered pasa_asmbl_51294.p1, internal, 178718, 178792
Valid prediction for GlimmerHMM_glimmerT_18372-T1
Valid prediction for CodingQuarry_transcript_57689-T1
Valid prediction for snap_scaffold_7-snap.2471-T1
Valid prediction for Augustus_model.g12388.t1
Valid prediction for GlimmerHMM_glimmerT_18370-T1
Valid prediction for Augustus_model.g12387.t1
Valid prediction for GlimmerHMM_glimmerT_18358-T1
Valid prediction for snap_scaffold_7-snap.2497-T1
Valid prediction for pasa_asmbl_51297.p1
Couldn't classify 76867, 76901
Sorry, prediction pasa_asmbl_51304.p1 fails validation.
(ATG)	 AG	71402-71450	GT	AGG
(GCA)	 AG	71839-71976	GT	GCG
(TGA)	 AG	73662-73787	GT	AGG
(GCC)	 AG	74468-74701	GT	AGG
(AGA)	 AG	76867-76901	GT	AGG
-recovered pasa_asmbl_51304.p1, initial, 71402, 71450
-recovered pasa_asmbl_51304.p1, internal, 71402, 71450
-recovered pasa_asmbl_51304.p1, internal, 71839, 71976
-recovered pasa_asmbl_51304.p1, internal, 73662, 73787
-recovered pasa_asmbl_51304.p1, internal, 74468, 74701
-recovered pasa_asmbl_51304.p1, internal, 76867, 76901
Valid prediction for GlimmerHMM_glimmerT_18362-T1
Valid prediction for GlimmerHMM_glimmerT_18369-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32884, rend_intergenic: 22389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60449, rend_intergenic: 56941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104641, rend_intergenic: 101912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127111, rend_intergenic: 115531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139932, rend_intergenic: 138321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147297, rend_intergenic: 144140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152955, rend_intergenic: 152635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156659, rend_intergenic: 153065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160726, rend_intergenic: 158955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172549, rend_intergenic: 168043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185864, rend_intergenic: 184389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200497
-exon list size: 348


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 32884, rend_intergenic: 22389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60449, rend_intergenic: 56941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104641, rend_intergenic: 101912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127111, rend_intergenic: 115531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139932, rend_intergenic: 138321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147297, rend_intergenic: 144140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152955, rend_intergenic: 152635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156659, rend_intergenic: 153065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160726, rend_intergenic: 158955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172549, rend_intergenic: 168043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185864, rend_intergenic: 184389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support