-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_17783054-18025201

-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_1-snap.3271-T1
Valid prediction for snap_scaffold_1-snap.3257-T1
Valid prediction for snap_scaffold_1-snap.3275-T1
Valid prediction for snap_scaffold_1-snap.3259-T1
Valid prediction for GlimmerHMM_glimmerT_2408-T1
Valid prediction for GlimmerHMM_glimmerT_2395-T1
Valid prediction for snap_scaffold_1-snap.3252-T1
Valid prediction for snap_scaffold_1-snap.3245-T1
Valid prediction for GlimmerHMM_glimmerT_2386-T1
Valid prediction for GlimmerHMM_glimmerT_2412-T1
Valid prediction for snap_scaffold_1-snap.3240-T1
Valid prediction for snap_scaffold_1-snap.3263-T1
Valid prediction for GlimmerHMM_glimmerT_2379-T1
Valid prediction for snap_scaffold_1-snap.3242-T1
Valid prediction for GlimmerHMM_glimmerT_2384-T1
Valid prediction for snap_scaffold_1-snap.3247-T1
Valid prediction for snap_scaffold_1-snap.3244-T1
Valid prediction for snap_scaffold_1-snap.3261-T1
Valid prediction for GlimmerHMM_glimmerT_2380-T1
Valid prediction for snap_scaffold_1-snap.3256-T1
Valid prediction for Augustus_model.g1759.t1
Valid prediction for GlimmerHMM_glimmerT_2382-T1
Valid prediction for snap_scaffold_1-snap.3249-T1
Valid prediction for GlimmerHMM_glimmerT_2392-T1
Valid prediction for Augustus_model.g1754.t1
Valid prediction for GlimmerHMM_glimmerT_2401-T1
Couldn't classify 131743, 131840
Sorry, prediction pasa_asmbl_2538.p1 fails validation.
(GGC)	 CA	131743-131840	GT	AGG
(TCT)	 AG	132207-132280	GT	CGG
(ACA)	 AG	132418-132494	GT	AGG
(GCG)	 AG	133023-133279	GT	GGG
(AGT)	 AG	134599-134659	GT	ATG
(GCC)	 AG	135000-135046	GT	AGG
(GTC)	 AG	135338-135446	CA	AGC
-recovered pasa_asmbl_2538.p1, terminal, 135338, 135446
-recovered pasa_asmbl_2538.p1, internal, 132207, 132280
-recovered pasa_asmbl_2538.p1, internal, 132418, 132494
-recovered pasa_asmbl_2538.p1, internal, 133023, 133279
-recovered pasa_asmbl_2538.p1, internal, 134599, 134659
-recovered pasa_asmbl_2538.p1, internal, 135000, 135046
Valid prediction for snap_scaffold_1-snap.3276-T1
Valid prediction for Augustus_model.g1762.t1
Valid prediction for snap_scaffold_1-snap.3255-T1
Valid prediction for Augustus_model.g1746.t1
Valid prediction for snap_scaffold_1-snap.3251-T1
Valid prediction for Augustus_model.g1751.t1
Valid prediction for GlimmerHMM_glimmerT_2403-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: -)Couldn't classify 102857, 103021
Sorry, prediction pasa_asmbl_1068.p1 fails validation.
(GAG)	 CA	102857-103021	GT	CTG
(TGT)	 AG	103289-103422	GT	AGG
(GCT)	 AG	103609-103792	AT	GAA
-recovered pasa_asmbl_1068.p1, terminal, 103609, 103792
-recovered pasa_asmbl_1068.p1, internal, 103289, 103422
Valid prediction for snap_scaffold_1-snap.3277-T1
Couldn't classify 48330, 48705
Couldn't classify 49511, 49585
Sorry, prediction pasa_asmbl_1074.p1 fails validation.
(GGA)	 CC	48330-48705	GT	AGG
(AGT)	 AG	49141-49304	GT	CTG
(TGT)	 AG	49511-49585	AC	TGA
-recovered pasa_asmbl_1074.p1, internal, 49141, 49304
Valid prediction for pasa_asmbl_1065.p1
Valid prediction for snap_scaffold_1-snap.3268-T1
Valid prediction for GlimmerHMM_glimmerT_2402-T1
Valid prediction for snap_scaffold_1-snap.3274-T1
Valid prediction for snap_scaffold_1-snap.3243-T1
Valid prediction for GlimmerHMM_glimmerT_2383-T1
Valid prediction for GlimmerHMM_glimmerT_2407-T1
Valid prediction for snap_scaffold_1-snap.3265-T1
Valid prediction for GlimmerHMM_glimmerT_2404-T1
Couldn't classify 92838, 93003
Couldn't classify 93437, 93579
Sorry, prediction pasa_asmbl_1070.p1 fails validation.
(CCC)	 AG	92838-93003	GT	AGG
(AGT)	 AG	93437-93579	GA	AAG
-recovered pasa_asmbl_1070.p1, internal, 92838, 93003
Valid prediction for HiQ_model.g1749.t1
Valid prediction for snap_scaffold_1-snap.3273-T1
Valid prediction for snap_scaffold_1-snap.3241-T1
Valid prediction for snap_scaffold_1-snap.3254-T1
Valid prediction for Augustus_model.g1752.t1
Couldn't classify 89677, 89872
Couldn't classify 90137, 90255
Sorry, prediction pasa_asmbl_1309.p1 fails validation.
(AAA)	 AC	89677-89872	GT	AGG
(ATG)	 AG	90137-90255	GT	AGG
add_exon() Sorry, pasa_asmbl_1309.p1 90137-90255-initial-1 is invalid.
-recovered pasa_asmbl_1309.p1, initial, 90137, 90255
-recovered pasa_asmbl_1309.p1, internal, 90137, 90255
Valid prediction for Augustus_model.g1755.t1
Valid prediction for GlimmerHMM_glimmerT_2396-T1
Valid prediction for snap_scaffold_1-snap.3248-T1
Valid prediction for Augustus_model.g1747.t1
Valid prediction for GlimmerHMM_glimmerT_2411-T1
Valid prediction for Augustus_model.g1758.t1
Valid prediction for snap_scaffold_1-snap.3267-T1
Valid prediction for Augustus_model.g1748.t1
Valid prediction for GlimmerHMM_glimmerT_2387-T1
Valid prediction for snap_scaffold_1-snap.3270-T1
Valid prediction for Augustus_model.g1750.t1
Valid prediction for GlimmerHMM_glimmerT_2405-T1
Valid prediction for GlimmerHMM_glimmerT_2399-T1
Valid prediction for snap_scaffold_1-snap.3278-T1
Valid prediction for snap_scaffold_1-snap.3260-T1
Valid prediction for GlimmerHMM_glimmerT_2409-T1
Couldn't classify 91025, 91157
Couldn't classify 92086, 92327
Sorry, prediction pasa_asmbl_1071.p1 fails validation.
(GGC)	 GC	91025-91157	GT	AGG
(TGT)	 AG	91497-91632	GT	TGG
(GAA)	 AG	91824-91933	GT	TGG
(GCG)	 AG	92086-92327	GG	AGG
-recovered pasa_asmbl_1071.p1, internal, 91497, 91632
-recovered pasa_asmbl_1071.p1, internal, 91824, 91933
Couldn't classify 99255, 99336
Couldn't classify 100195, 100202
Sorry, prediction pasa_asmbl_1069.p1 fails validation.
(GGG)	 GG	99255-99336	GT	AGG
(GGC)	 AG	99679-99930	GT	AGG
(ATG)	 AG	100195-100202	GT	GGG
-recovered pasa_asmbl_1069.p1, initial, 100195, 100202
-recovered pasa_asmbl_1069.p1, internal, 99679, 99930
-recovered pasa_asmbl_1069.p1, internal, 100195, 100202
Valid prediction for pasa_asmbl_1062.p1
Valid prediction for snap_scaffold_1-snap.3272-T1
Couldn't classify 92181, 92328
Couldn't classify 92527, 92690
Sorry, prediction pasa_asmbl_1296.p1 fails validation.
(GCA)	 AT	92181-92328	GT	GGG
(GCA)	 AG	92527-92690	CC	GAC
Valid prediction for GlimmerHMM_glimmerT_2391-T1
Valid prediction for snap_scaffold_1-snap.3253-T1
Valid prediction for snap_scaffold_1-snap.3269-T1
Valid prediction for CodingQuarry_transcript_2980-T1
Valid prediction for GlimmerHMM_glimmerT_2388-T1
Valid prediction for GlimmerHMM_glimmerT_2393-T1
Valid prediction for Augustus_model.g1761.t1
Valid prediction for GlimmerHMM_glimmerT_2390-T1
Valid prediction for snap_scaffold_1-snap.3246-T1
Valid prediction for GlimmerHMM_glimmerT_2397-T1
Valid prediction for Augustus_model.g1757.t1
Couldn't classify 80637, 80736
Couldn't classify 81654, 81734
Sorry, prediction pasa_asmbl_1376.p1 fails validation.
(CTC)	 GC	80637-80736	GT	AGG
(AGT)	 AG	81113-81276	GT	CTG
(TGT)	 AG	81654-81734	TG	ACT
-recovered pasa_asmbl_1376.p1, internal, 81113, 81276
Valid prediction for Augustus_model.g1756.t1
Valid prediction for snap_scaffold_1-snap.3262-T1
Valid prediction for GlimmerHMM_glimmerT_2381-T1
Valid prediction for snap_scaffold_1-snap.3266-T1
Valid prediction for GlimmerHMM_glimmerT_2394-T1
Valid prediction for snap_scaffold_1-snap.3250-T1
Valid prediction for GlimmerHMM_glimmerT_2385-T1
Valid prediction for snap_scaffold_1-snap.3258-T1
Valid prediction for GlimmerHMM_glimmerT_2410-T1
Valid prediction for GlimmerHMM_glimmerT_2398-T1
Valid prediction for snap_scaffold_1-snap.3264-T1
Valid prediction for GlimmerHMM_glimmerT_2389-T1
Valid prediction for Augustus_model.g1753.t1
Valid prediction for CodingQuarry_transcript_2981-T1
Valid prediction for Augustus_model.g1760.t1
Valid prediction for GlimmerHMM_glimmerT_2406-T1
Valid prediction for GlimmerHMM_glimmerT_2400-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21231, rend_intergenic: 8794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27426, rend_intergenic: 26303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32295, rend_intergenic: 29967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36087, rend_intergenic: 32470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37664, rend_intergenic: 36103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48833, rend_intergenic: 37826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73959, rend_intergenic: 71398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80001, rend_intergenic: 78481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92680, rend_intergenic: 82914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101580, rend_intergenic: 95989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112602, rend_intergenic: 104869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218696, rend_intergenic: 211534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223160, rend_intergenic: 221883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 37829, rend_intergenic: 37826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 242148
-exon list size: 407


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.4    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.2    
4.4    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.8    
7.1    
7.3    
7.6    
7.8    
8.1    
8.3    
8.6    
8.8    
9.0    
9.3    
9.5    
9.8    
10.0    
10.3    
10.5    
10.8    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.7    
13.0    
13.2    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.4    
15.6    
15.9    
16.1    
16.4    
16.6    
16.9    
17.1    
17.4    
17.6    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.8    
22.0    
22.2    
22.5    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
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    
44.3    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.3    
53.5    
53.8    
54.0    
54.3    
54.5    
54.8    
55.0    
55.3    
55.5    
55.7    
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    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.9    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.6    
63.8    
64.1    
64.3    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.2    
70.4    
70.7    
70.9    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.3    
73.6    
73.8    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
77.8    
78.0    
78.2    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.4    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.0    
87.3    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 21231, rend_intergenic: 8794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27426, rend_intergenic: 26303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32295, rend_intergenic: 29967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36087, rend_intergenic: 32470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37664, rend_intergenic: 36103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48833, rend_intergenic: 37826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73959, rend_intergenic: 71398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80001, rend_intergenic: 78481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92680, rend_intergenic: 82914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101580, rend_intergenic: 95989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112602, rend_intergenic: 104869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218696, rend_intergenic: 211534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223160, rend_intergenic: 221883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 37829, rend_intergenic: 37826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 15540
-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

-building DP trellis

-building trellis in range 228542 - 242148
-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