-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_1897828-2302000

-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_21-snap.351-T1
Valid prediction for snap_scaffold_21-snap.349-T1
Valid prediction for snap_scaffold_21-snap.383-T1
Valid prediction for snap_scaffold_21-snap.377-T1
Valid prediction for GlimmerHMM_glimmerT_47205-T1
Valid prediction for Augustus_model.g31438.t1
Valid prediction for snap_scaffold_21-snap.374-T1
Valid prediction for GlimmerHMM_glimmerT_47208-T1
Valid prediction for HiQ_model.g31437.t1
Valid prediction for GlimmerHMM_glimmerT_47181-T1
Valid prediction for GlimmerHMM_glimmerT_47187-T1
Couldn't classify 377450, 377629
Sorry, prediction pasa_asmbl_28375.p1 fails validation.
(ATG)	 TA	375459-375677	GT	TGG
(GTG)	 AG	377450-377629	CC	ACC
-recovered pasa_asmbl_28375.p1, initial, 375459, 375677
Valid prediction for Augustus_model.g31424.t1
Valid prediction for GlimmerHMM_glimmerT_47186-T1
Valid prediction for snap_scaffold_21-snap.356-T1
Valid prediction for snap_scaffold_21-snap.381-T1
Valid prediction for GlimmerHMM_glimmerT_47188-T1
Valid prediction for GlimmerHMM_glimmerT_47209-T1
Valid prediction for GlimmerHMM_glimmerT_47206-T1
Valid prediction for GlimmerHMM_glimmerT_47204-T1
Valid prediction for CodingQuarry_transcript_32450-T1
Valid prediction for snap_scaffold_21-snap.378-T1
Valid prediction for snap_scaffold_21-snap.352-T1
Couldn't classify 364788, 365030
Sorry, prediction pasa_asmbl_28372.p1 fails validation.
(AAA)	 AG	364788-365030	GT	AGG
(ACT)	 AG	365199-365368	GT	AAG
(GAC)	 AG	366082-366207	GT	AGG
(GTT)	 AG	366412-366498	GT	GGG
(GCG)	 AG	366669-366842	GT	AGG
(TGG)	 AG	367706-367895	GT	GGG
(GCT)	 AG	368468-368621	GT	AGG
(ACC)	 AG	368783-368881	GT	CGG
(ATG)	 AG	369426-369516	GT	AGG
(CAT)	 AG	369817-369921	GT	CTG
(GAA)	 AG	370127-370279	GT	AGG
(GGC)	 AG	370987-371109	GT	AGG
(GGT)	 AG	371245-371310	GT	AGG
(GAA)	 AG	372156-372236	GT	AGG
(GGT)	 AG	372378-372504	GT	AGG
(GTG)	 AG	372744-372862	GT	CAG
(GGG)	 AG	373754-373817	GT	GAG
-recovered pasa_asmbl_28372.p1, initial, 369426, 369516
-recovered pasa_asmbl_28372.p1, terminal, 373754, 373817
-recovered pasa_asmbl_28372.p1, internal, 364788, 365030
-recovered pasa_asmbl_28372.p1, internal, 365199, 365368
-recovered pasa_asmbl_28372.p1, internal, 366082, 366207
-recovered pasa_asmbl_28372.p1, internal, 366412, 366498
-recovered pasa_asmbl_28372.p1, internal, 366669, 366842
-recovered pasa_asmbl_28372.p1, internal, 367706, 367895
-recovered pasa_asmbl_28372.p1, internal, 368468, 368621
-recovered pasa_asmbl_28372.p1, internal, 368783, 368881
-recovered pasa_asmbl_28372.p1, internal, 369426, 369516
-recovered pasa_asmbl_28372.p1, internal, 369817, 369921
-recovered pasa_asmbl_28372.p1, internal, 370127, 370279
-recovered pasa_asmbl_28372.p1, internal, 370987, 371109
-recovered pasa_asmbl_28372.p1, internal, 371245, 371310
-recovered pasa_asmbl_28372.p1, internal, 372156, 372236
-recovered pasa_asmbl_28372.p1, internal, 372378, 372504
-recovered pasa_asmbl_28372.p1, internal, 372744, 372862
-recovered pasa_asmbl_28372.p1, internal, 373754, 373817
Valid prediction for GlimmerHMM_glimmerT_47210-T1
Valid prediction for snap_scaffold_21-snap.375-T1
Valid prediction for GlimmerHMM_glimmerT_47189-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.g31436.t1
Valid prediction for Augustus_model.g31432.t1
Valid prediction for GlimmerHMM_glimmerT_47207-T1
Valid prediction for Augustus_model.g31429.t1
Valid prediction for GlimmerHMM_glimmerT_47190-T1
Valid prediction for snap_scaffold_21-snap.379-T1
Valid prediction for snap_scaffold_21-snap.361-T1
Valid prediction for snap_scaffold_21-snap.357-T1
Valid prediction for GlimmerHMM_glimmerT_47185-T1
Valid prediction for HiQ_model.g31434.t1
Valid prediction for snap_scaffold_21-snap.346-T1
Valid prediction for snap_scaffold_21-snap.344-T1
Valid prediction for GlimmerHMM_glimmerT_47200-T1
Valid prediction for snap_scaffold_21-snap.354-T1
Valid prediction for pasa_asmbl_27434.p1
Valid prediction for GlimmerHMM_glimmerT_47191-T1
Valid prediction for snap_scaffold_21-snap.359-T1
Valid prediction for snap_scaffold_21-snap.376-T1
Valid prediction for snap_scaffold_21-snap.350-T1
Valid prediction for snap_scaffold_21-snap.358-T1
Couldn't classify 67664, 67832
Couldn't classify 68809, 68827
Sorry, prediction pasa_asmbl_28188.p1 fails validation.
(GTT)	 TA	67664-67832	GT	CGG
(GTG)	 AG	68037-68268	GT	AAG
(ATT)	 AG	68392-68474	GT	TAG
(TGA)	 AG	68573-68702	GT	TGG
(TTG)	 AG	68809-68827	CA	CAC
add_exon() Sorry, pasa_asmbl_28188.p1 68037-68268-terminal-3 is invalid.
-recovered pasa_asmbl_28188.p1, terminal, 68037, 68268
-recovered pasa_asmbl_28188.p1, internal, 68037, 68268
-recovered pasa_asmbl_28188.p1, internal, 68392, 68474
-recovered pasa_asmbl_28188.p1, internal, 68573, 68702
Valid prediction for snap_scaffold_21-snap.353-T1
Valid prediction for snap_scaffold_21-snap.369-T1
Valid prediction for GlimmerHMM_glimmerT_47199-T1
Valid prediction for snap_scaffold_21-snap.371-T1
Valid prediction for Augustus_model.g31433.t1
Valid prediction for snap_scaffold_21-snap.366-T1
Valid prediction for GlimmerHMM_glimmerT_47201-T1
Valid prediction for Augustus_model.g31428.t1
Valid prediction for Augustus_model.g31423.t1
Couldn't classify 120313, 120367
Sorry, prediction pasa_asmbl_27438.p1 fails validation.
(AAG)	 AA	120313-120367	GT	TGG
(CCT)	 AG	120606-120762	GT	AGG
(GAG)	 AG	121741-121900	GT	TGG
(GGC)	 AG	122199-122387	GT	CGG
(GTA)	 AG	122862-122924	GT	ATG
(GAG)	 AG	123304-123315	TC	GAT
-recovered pasa_asmbl_27438.p1, terminal, 123304, 123315
-recovered pasa_asmbl_27438.p1, internal, 120606, 120762
-recovered pasa_asmbl_27438.p1, internal, 121741, 121900
-recovered pasa_asmbl_27438.p1, internal, 122199, 122387
-recovered pasa_asmbl_27438.p1, internal, 122862, 122924
Valid prediction for snap_scaffold_21-snap.382-T1
Couldn't classify 113798, 113821
Couldn't classify 118965, 119009
Sorry, prediction pasa_asmbl_28197.p1 fails validation.
(GGC)	 GC	113798-113821	GT	TGG
(TTG)	 AG	114651-114848	GT	AGG
(TAC)	 AG	115755-115858	GT	AGG
(GAA)	 AG	116001-116061	GT	AGG
(GGC)	 AG	118103-118153	GT	AGG
(CAA)	 AG	118965-119009	GA	ATG
-recovered pasa_asmbl_28197.p1, internal, 114651, 114848
-recovered pasa_asmbl_28197.p1, internal, 115755, 115858
-recovered pasa_asmbl_28197.p1, internal, 116001, 116061
-recovered pasa_asmbl_28197.p1, internal, 118103, 118153
Valid prediction for snap_scaffold_21-snap.362-T1
Valid prediction for HiQ_model.g31426.t1
Valid prediction for CodingQuarry_transcript_32449-T1
Valid prediction for GlimmerHMM_glimmerT_47202-T1
Valid prediction for GlimmerHMM_glimmerT_47192-T1
Valid prediction for snap_scaffold_21-snap.365-T1
Valid prediction for snap_scaffold_21-snap.384-T1
Valid prediction for CodingQuarry_transcript_32448-T1
Valid prediction for snap_scaffold_21-snap.372-T1
Valid prediction for GlimmerHMM_glimmerT_47198-T1
Valid prediction for GlimmerHMM_glimmerT_47194-T1
Valid prediction for Augustus_model.g31422.t1
Valid prediction for GlimmerHMM_glimmerT_47203-T1
Valid prediction for snap_scaffold_21-snap.370-T1
Valid prediction for GlimmerHMM_glimmerT_47193-T1
Valid prediction for snap_scaffold_21-snap.360-T1
Couldn't classify 52868, 52951
Sorry, prediction pasa_asmbl_27443.p1 fails validation.
(GAG)	 CA	52868-52951	GT	AGG
(AAC)	 AG	55407-55955	CT	AAC
-recovered pasa_asmbl_27443.p1, terminal, 55407, 55955
Valid prediction for pasa_asmbl_27441.p1
Valid prediction for snap_scaffold_21-snap.373-T1
Valid prediction for GlimmerHMM_glimmerT_47182-T1
Valid prediction for snap_scaffold_21-snap.364-T1
Valid prediction for Augustus_model.g31431.t1
Valid prediction for snap_scaffold_21-snap.367-T1
Valid prediction for GlimmerHMM_glimmerT_47196-T1
Valid prediction for snap_scaffold_21-snap.385-T1
Valid prediction for snap_scaffold_21-snap.355-T1
Valid prediction for HiQ_model.g31435.t1
Valid prediction for GlimmerHMM_glimmerT_47197-T1
Valid prediction for snap_scaffold_21-snap.347-T1
Valid prediction for snap_scaffold_21-snap.368-T1
Valid prediction for pasa_asmbl_27432.p1
Valid prediction for pasa_asmbl_27433.p1
Valid prediction for GlimmerHMM_glimmerT_47184-T1
Valid prediction for Augustus_model.g31430.t1
Valid prediction for snap_scaffold_21-snap.343-T1
Valid prediction for Augustus_model.g31421.t1
Valid prediction for HiQ_model.g31427.t1
Valid prediction for snap_scaffold_21-snap.348-T1
Valid prediction for snap_scaffold_21-snap.345-T1
Valid prediction for GlimmerHMM_glimmerT_47183-T1
Valid prediction for snap_scaffold_21-snap.380-T1
Valid prediction for Augustus_model.g31425.t1
Valid prediction for snap_scaffold_21-snap.363-T1
Valid prediction for GlimmerHMM_glimmerT_47195-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 257203, rend_intergenic: 256054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 371639, rend_intergenic: 369403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 381057, rend_intergenic: 377402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 391623, rend_intergenic: 387571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 404173
-exon list size: 374


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.6    
10.9    
11.2    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.1    
23.4    
23.7    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.3    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.6    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.8    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.2    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.4    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.7    
71.0    
71.3    
71.5    
71.8    
72.1    
72.3    
72.6    
72.9    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.3    
76.6    
76.9    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.6    
85.9    
86.2    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.8    
89.1    
89.4    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 257203, rend_intergenic: 256054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 371639, rend_intergenic: 369403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 381057, rend_intergenic: 377402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 391623, rend_intergenic: 387571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 31831
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 1 - 15360
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 120 - 15360
-exon list size: 1


building trellis

33.3    
66.7    
-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 15388 - 31831
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 15388 - 31552
-exon list size: 1


building trellis

33.3    
66.7    
-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