-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_5690835-5911037

-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 pasa_asmbl_46979.p1
Couldn't classify 218725, 218793
Couldn't classify 219123, 219299
Sorry, prediction pasa_asmbl_47894.p1 fails validation.
(CTG)	 TC	218725-218793	GT	AGG
(GAC)	 AG	218896-218976	GT	AGG
(GGT)	 AG	219123-219299	CT	TGC
-recovered pasa_asmbl_47894.p1, internal, 218896, 218976
Valid prediction for Augustus_model.g9739.t1
Valid prediction for GlimmerHMM_glimmerT_14705-T1
Valid prediction for HiQ_model.g9734.t1
Valid prediction for Augustus_model.g9744.t1
Valid prediction for snap_scaffold_6-snap.1319-T1
Valid prediction for snap_scaffold_6-snap.1313-T1
Valid prediction for GlimmerHMM_glimmerT_14704-T1
Couldn't classify 122530, 122586
Sorry, prediction pasa_asmbl_47945.p1 fails validation.
(ATG)	 CA	121792-121859	GT	CAG
(GTC)	 AG	122125-122164	GT	AGG
(GTG)	 AG	122249-122446	GT	TTG
(GGT)	 AG	122530-122586	AA	GAA
-recovered pasa_asmbl_47945.p1, initial, 121792, 121859
-recovered pasa_asmbl_47945.p1, internal, 122125, 122164
-recovered pasa_asmbl_47945.p1, internal, 122249, 122446
Valid prediction for snap_scaffold_6-snap.1321-T1
Valid prediction for snap_scaffold_6-snap.1305-T1
Valid prediction for snap_scaffold_6-snap.1315-T1
Valid prediction for snap_scaffold_6-snap.1311-T1
Valid prediction for GlimmerHMM_glimmerT_14710-T1
Valid prediction for snap_scaffold_6-snap.1318-T1
Valid prediction for GlimmerHMM_glimmerT_14708-T1
Valid prediction for CodingQuarry_transcript_55061-T1
Valid prediction for GlimmerHMM_glimmerT_14694-T1
Valid prediction for snap_scaffold_6-snap.1328-T1
Valid prediction for snap_scaffold_6-snap.1323-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for pasa_asmbl_46973.p1
Valid prediction for Augustus_model.g9745.t1
Valid prediction for Augustus_model.g9743.t1
Valid prediction for GlimmerHMM_glimmerT_14713-T1
Valid prediction for GlimmerHMM_glimmerT_14695-T1
Valid prediction for snap_scaffold_6-snap.1327-T1
Valid prediction for GlimmerHMM_glimmerT_14698-T1
Valid prediction for HiQ_model.g9733.t1
Valid prediction for GlimmerHMM_glimmerT_14703-T1
Valid prediction for GlimmerHMM_glimmerT_14702-T1
Valid prediction for snap_scaffold_6-snap.1307-T1
Valid prediction for GlimmerHMM_glimmerT_14716-T1
Valid prediction for GlimmerHMM_glimmerT_14715-T1
Valid prediction for GlimmerHMM_glimmerT_14707-T1
Valid prediction for snap_scaffold_6-snap.1306-T1
Valid prediction for GlimmerHMM_glimmerT_14701-T1
Valid prediction for CodingQuarry_transcript_55062-T1
Valid prediction for snap_scaffold_6-snap.1312-T1
Valid prediction for GlimmerHMM_glimmerT_14697-T1
Valid prediction for Augustus_model.g9737.t1
Valid prediction for GlimmerHMM_glimmerT_14714-T1
Valid prediction for Augustus_model.g9746.t1
Valid prediction for Augustus_model.g9742.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_14700-T1
Valid prediction for snap_scaffold_6-snap.1308-T1
Valid prediction for snap_scaffold_6-snap.1309-T1
Valid prediction for snap_scaffold_6-snap.1324-T1
Couldn't classify 121770, 122423
Sorry, prediction pasa_asmbl_48435.p1 fails validation.
(AGC)	 GC	121770-122423	AG	ACA
Valid prediction for Augustus_model.g9736.t1
Valid prediction for GlimmerHMM_glimmerT_14717-T1
Valid prediction for GlimmerHMM_glimmerT_14711-T1
Valid prediction for GlimmerHMM_glimmerT_14706-T1
Valid prediction for Augustus_model.g9732.t1
Valid prediction for GlimmerHMM_glimmerT_14696-T1
Valid prediction for GlimmerHMM_glimmerT_14709-T1
Valid prediction for Augustus_model.g9740.t1
Valid prediction for Augustus_model.g9741.t1
Valid prediction for snap_scaffold_6-snap.1331-T1
Valid prediction for GlimmerHMM_glimmerT_14712-T1
Valid prediction for snap_scaffold_6-snap.1317-T1
Valid prediction for GlimmerHMM_glimmerT_14699-T1
Couldn't classify 133087, 133178
Sorry, prediction pasa_asmbl_48432.p2 fails validation.
(CCA)	 AC	133087-133178	GT	AGG
(ACA)	 AG	134857-135006	GT	AGG
(GTA)	 AG	135116-135242	CA	GAC
-recovered pasa_asmbl_48432.p2, terminal, 135116, 135242
-recovered pasa_asmbl_48432.p2, internal, 134857, 135006
Valid prediction for snap_scaffold_6-snap.1326-T1
Valid prediction for Augustus_model.g9747.t1
Valid prediction for Augustus_model.g9735.t1
Valid prediction for snap_scaffold_6-snap.1314-T1
Valid prediction for snap_scaffold_6-snap.1322-T1
Valid prediction for snap_scaffold_6-snap.1320-T1
Valid prediction for snap_scaffold_6-snap.1329-T1
Valid prediction for snap_scaffold_6-snap.1325-T1
Couldn't classify 132618, 132783
Sorry, prediction pasa_asmbl_48434.p1 fails validation.
(ATG)	 CC	127540-127625	GT	GTG
(CGA)	 AG	128785-128881	GT	CTG
(CGC)	 AG	130222-130359	GT	TGG
(GAG)	 AG	131984-132519	GT	AGG
(TAG)	 AG	132618-132783	TG	GGT
-recovered pasa_asmbl_48434.p1, initial, 127540, 127625
-recovered pasa_asmbl_48434.p1, internal, 128785, 128881
-recovered pasa_asmbl_48434.p1, internal, 130222, 130359
-recovered pasa_asmbl_48434.p1, internal, 131984, 132519
Valid prediction for snap_scaffold_6-snap.1310-T1
Valid prediction for snap_scaffold_6-snap.1316-T1
Valid prediction for HiQ_model.g9738.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 157021, rend_intergenic: 153705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163778, rend_intergenic: 160981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184022, rend_intergenic: 182207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186680, rend_intergenic: 184142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201190, rend_intergenic: 187485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206276, rend_intergenic: 204438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220203
-exon list size: 268


building trellis

0.4    
0.7    
1.1    
1.5    
1.9    
2.2    
2.6    
3.0    
3.3    
3.7    
4.1    
4.4    
4.8    
5.2    
5.6    
5.9    
6.3    
6.7    
7.0    
7.4    
7.8    
8.1    
8.5    
8.9    
9.3    
9.6    
10.0    
10.4    
10.7    
11.1    
11.5    
11.9    
12.2    
12.6    
13.0    
13.3    
13.7    
14.1    
14.4    
14.8    
15.2    
15.6    
15.9    
16.3    
16.7    
17.0    
17.4    
17.8    
18.1    
18.5    
18.9    
19.3    
19.6    
20.0    
20.4    
20.7    
21.1    
21.5    
21.9    
22.2    
22.6    
23.0    
23.3    
23.7    
24.1    
24.4    
24.8    
25.2    
25.6    
25.9    
26.3    
26.7    
27.0    
27.4    
27.8    
28.1    
28.5    
28.9    
29.3    
29.6    
30.0    
30.4    
30.7    
31.1    
31.5    
31.9    
32.2    
32.6    
33.0    
33.3    
33.7    
34.1    
34.4    
34.8    
35.2    
35.6    
35.9    
36.3    
36.7    
37.0    
37.4    
37.8    
38.1    
38.5    
38.9    
39.3    
39.6    
40.0    
40.4    
40.7    
41.1    
41.5    
41.9    
42.2    
42.6    
43.0    
43.3    
43.7    
44.1    
44.4    
44.8    
45.2    
45.6    
45.9    
46.3    
46.7    
47.0    
47.4    
47.8    
48.1    
48.5    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.5    
51.9    
52.2    
52.6    
53.0    
53.3    
53.7    
54.1    
54.4    
54.8    
55.2    
55.6    
55.9    
56.3    
56.7    
57.0    
57.4    
57.8    
58.1    
58.5    
58.9    
59.3    
59.6    
60.0    
60.4    
60.7    
61.1    
61.5    
61.9    
62.2    
62.6    
63.0    
63.3    
63.7    
64.1    
64.4    
64.8    
65.2    
65.6    
65.9    
66.3    
66.7    
67.0    
67.4    
67.8    
68.1    
68.5    
68.9    
69.3    
69.6    
70.0    
70.4    
70.7    
71.1    
71.5    
71.9    
72.2    
72.6    
73.0    
73.3    
73.7    
74.1    
74.4    
74.8    
75.2    
75.6    
75.9    
76.3    
76.7    
77.0    
77.4    
77.8    
78.1    
78.5    
78.9    
79.3    
79.6    
80.0    
80.4    
80.7    
81.1    
81.5    
81.9    
82.2    
82.6    
83.0    
83.3    
83.7    
84.1    
84.4    
84.8    
85.2    
85.6    
85.9    
86.3    
86.7    
87.0    
87.4    
87.8    
88.1    
88.5    
88.9    
89.3    
89.6    
90.0    
90.4    
90.7    
91.1    
91.5    
91.9    
92.2    
92.6    
93.0    
93.3    
93.7    
94.1    
94.4    
94.8    
95.2    
95.6    
95.9    
96.3    
96.7    
97.0    
97.4    
97.8    
98.1    
98.5    
98.9    
99.3    
99.6    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 157021, rend_intergenic: 153705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163778, rend_intergenic: 160981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184022, rend_intergenic: 182207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186680, rend_intergenic: 184142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201190, rend_intergenic: 187485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206276, rend_intergenic: 204438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 29328
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 1888 - 29328
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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 1888 - 15117
-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

-building DP trellis

-building trellis in range 4066 - 15117
-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 15165 - 29328
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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

-building DP trellis

-building trellis in range 205712 - 220203
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-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 205712 - 218895
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-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 207813 - 218895
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support