-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_1-188888

-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 CodingQuarry_transcript_5235-T1
Valid prediction for snap_scaffold_10-snap.36-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.1-T1
Valid prediction for GeneMark_model.41793_t
Valid prediction for Augustus_model.g16358.t1
Valid prediction for GlimmerHMM_glimmerT_24414-T1
Valid prediction for GlimmerHMM_glimmerT_24420-T1
Valid prediction for Augustus_model.g16364.t1
Valid prediction for GlimmerHMM_glimmerT_24428-T1
Valid prediction for snap_scaffold_10-snap.17-T1
Valid prediction for Augustus_model.g16344.t1
Valid prediction for snap_scaffold_10-snap.34-T1
Valid prediction for GlimmerHMM_glimmerT_24430-T1
Valid prediction for GlimmerHMM_glimmerT_24441-T1
Valid prediction for Augustus_model.g16354.t1
Valid prediction for snap_scaffold_10-snap.8-T1
Valid prediction for GlimmerHMM_glimmerT_24434-T1
Valid prediction for snap_scaffold_10-snap.21-T1
Valid prediction for GlimmerHMM_glimmerT_24412-T1
Valid prediction for snap_scaffold_10-snap.18-T1
Valid prediction for CodingQuarry_transcript_5234-T1
Valid prediction for GlimmerHMM_glimmerT_24409-T1
Valid prediction for snap_scaffold_10-snap.30-T1
Valid prediction for GeneMark_model.41817_t
Valid prediction for GeneMark_model.41797_t
Couldn't classify 180222, 181112
Sorry, prediction pasa_asmbl_2832.p1 fails validation.
(CCG)	 AC	180222-181112	AG	CTA
Valid prediction for GeneMark_model.41808_t
Valid prediction for Augustus_model.g16351.t1
Valid prediction for snap_scaffold_10-snap.28-T1
Valid prediction for snap_scaffold_10-snap.15-T1
Valid prediction for snap_scaffold_10-snap.2-T1
Valid prediction for snap_scaffold_10-snap.26-T1
Valid prediction for GeneMark_model.41819_t
Couldn't classify 1241, 1378
Sorry, prediction GeneMark_model.41790_t fails validation.
(ACC)	 AG	1241-1378	GT	AGG
(TGT)	 AG	2280-2495	TT	AGT
-recovered GeneMark_model.41790_t, terminal, 2280, 2495
-recovered GeneMark_model.41790_t, internal, 1241, 1378
Couldn't classify 1213, 1378
Sorry, prediction Augustus_model.g16333.t1 fails validation.
(GTT)	 AG	1213-1378	GT	AGG
(TGT)	 AG	2280-2486	GT	AGG
(GGT)	 AG	2901-3083	GT	AGG
(GAG)	 AG	4575-4658	GT	AGG
(CCT)	 AG	4887-4919	CA	AAC
-recovered Augustus_model.g16333.t1, terminal, 4887, 4919
-recovered Augustus_model.g16333.t1, internal, 1213, 1378
-recovered Augustus_model.g16333.t1, internal, 2280, 2486
-recovered Augustus_model.g16333.t1, internal, 2901, 3083
-recovered Augustus_model.g16333.t1, internal, 4575, 4658
Valid prediction for GlimmerHMM_glimmerT_24419-T1
Valid prediction for snap_scaffold_10-snap.7-T1
Valid prediction for Augustus_model.g16352.t1
Valid prediction for Augustus_model.g16359.t1
Valid prediction for Augustus_model.g16335.t1
Valid prediction for Augustus_model.g16337.t1
Valid prediction for GeneMark_model.41803_t
Valid prediction for snap_scaffold_10-snap.41-T1
Couldn't classify 1199, 1378
Sorry, prediction pasa_asmbl_4127.p1 fails validation.
(AGG)	 TC	1199-1378	GT	AGG
(TGT)	 AG	2280-2486	GT	AGG
(GGT)	 AG	2901-3083	GT	AGG
(GAG)	 AG	4575-4658	GT	AGG
(CCT)	 AG	4887-4919	CA	AAC
-recovered pasa_asmbl_4127.p1, terminal, 4887, 4919
-recovered pasa_asmbl_4127.p1, internal, 2280, 2486
-recovered pasa_asmbl_4127.p1, internal, 2901, 3083
-recovered pasa_asmbl_4127.p1, internal, 4575, 4658
Couldn't classify 147193, 147335
Couldn't classify 155243, 155400
Sorry, prediction pasa_asmbl_4128.p1 fails validation.
(AGT)	 CC	147193-147335	GT	AGG
(CCG)	 AG	150179-150319	GT	AGG
(TGA)	 AG	152210-152310	GT	GGG
(GCG)	 AG	155243-155400	AG	AGA
-recovered pasa_asmbl_4128.p1, internal, 150179, 150319
-recovered pasa_asmbl_4128.p1, internal, 152210, 152310
Valid prediction for GeneMark_model.41809_t
Valid prediction for Augustus_model.g16357.t1
Valid prediction for snap_scaffold_10-snap.16-T1
Couldn't classify 163790, 164011
Sorry, prediction pasa_asmbl_4129.p1 fails validation.
(GAG)	 AG	163790-164011	GT	CGG
(GAC)	 AG	166186-166277	GT	CGG
(GGA)	 AG	166402-166524	GT	AGG
(TAA)	 AG	167052-167232	GA	GAG
-recovered pasa_asmbl_4129.p1, terminal, 167052, 167232
-recovered pasa_asmbl_4129.p1, internal, 163790, 164011
-recovered pasa_asmbl_4129.p1, internal, 166186, 166277
-recovered pasa_asmbl_4129.p1, internal, 166402, 166524
Valid prediction for GlimmerHMM_glimmerT_24437-T1
Valid prediction for GlimmerHMM_glimmerT_24411-T1
Valid prediction for snap_scaffold_10-snap.38-T1
Valid prediction for snap_scaffold_10-snap.35-T1
Valid prediction for GlimmerHMM_glimmerT_24435-T1
Valid prediction for Augustus_model.g16345.t1
Valid prediction for GeneMark_model.41813_t
Valid prediction for GlimmerHMM_glimmerT_24425-T1
Valid prediction for Augustus_model.g16347.t1
Valid prediction for snap_scaffold_10-snap.4-T1
Valid prediction for snap_scaffold_10-snap.40-T1
Valid prediction for HiQ_model.g16361.t1
Valid prediction for GeneMark_model.41815_t
Valid prediction for GlimmerHMM_glimmerT_24433-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_24418-T1
Valid prediction for snap_scaffold_10-snap.33-T1
Valid prediction for Augustus_model.g16340.t1
Valid prediction for Augustus_model.g16363.t1
Valid prediction for Augustus_model.g16362.t1
Valid prediction for snap_scaffold_10-snap.43-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.44-T1
Valid prediction for snap_scaffold_10-snap.20-T1
Valid prediction for snap_scaffold_10-snap.13-T1
Valid prediction for snap_scaffold_10-snap.19-T1
Valid prediction for snap_scaffold_10-snap.10-T1
Valid prediction for GeneMark_model.41821_t
Couldn't classify 152663, 152672
Couldn't classify 156553, 156672
Sorry, prediction pasa_asmbl_2828.p1 fails validation.
(TCT)	 CC	152663-152672	GT	TGG
(GTG)	 AG	152921-153017	GT	AGG
(GTA)	 AG	154758-154845	GT	TAG
(ATT)	 AG	154989-155069	GT	AGG
(AAG)	 AG	155160-155242	GT	AGG
(AGC)	 AG	156319-156424	GT	AGG
(GAG)	 AG	156553-156672	GT	AGG
-recovered pasa_asmbl_2828.p1, internal, 152921, 153017
-recovered pasa_asmbl_2828.p1, internal, 154758, 154845
-recovered pasa_asmbl_2828.p1, internal, 154989, 155069
-recovered pasa_asmbl_2828.p1, internal, 155160, 155242
-recovered pasa_asmbl_2828.p1, internal, 156319, 156424
-recovered pasa_asmbl_2828.p1, internal, 156553, 156672
Valid prediction for GeneMark_model.41805_t
Valid prediction for snap_scaffold_10-snap.14-T1
Valid prediction for GlimmerHMM_glimmerT_24440-T1
Valid prediction for GeneMark_model.41807_t
Valid prediction for GlimmerHMM_glimmerT_24438-T1
Valid prediction for GeneMark_model.41795_t
Valid prediction for Augustus_model.g16360.t1
Valid prediction for GeneMark_model.41816_t
Valid prediction for GlimmerHMM_glimmerT_24427-T1
Valid prediction for snap_scaffold_10-snap.11-T1
Valid prediction for GeneMark_model.41791_t
Valid prediction for GeneMark_model.41802_t
Valid prediction for snap_scaffold_10-snap.6-T1
Valid prediction for GeneMark_model.41794_t
Valid prediction for GlimmerHMM_glimmerT_24426-T1
Valid prediction for GeneMark_model.41822_t
Valid prediction for GlimmerHMM_glimmerT_24431-T1
Valid prediction for snap_scaffold_10-snap.27-T1
Valid prediction for GlimmerHMM_glimmerT_24416-T1
Valid prediction for GlimmerHMM_glimmerT_24442-T1
Valid prediction for Augustus_model.g16356.t1
Valid prediction for GlimmerHMM_glimmerT_24423-T1
Valid prediction for GlimmerHMM_glimmerT_24415-T1
Valid prediction for GeneMark_model.41814_t
Valid prediction for GeneMark_model.41810_t
Valid prediction for GlimmerHMM_glimmerT_24432-T1
Valid prediction for Augustus_model.g16346.t1
Valid prediction for Augustus_model.g16365.t1
Valid prediction for snap_scaffold_10-snap.37-T1
Valid prediction for Augustus_model.g16341.t1
Valid prediction for GlimmerHMM_glimmerT_24439-T1
Valid prediction for GlimmerHMM_glimmerT_24422-T1
Valid prediction for GeneMark_model.41820_t
Couldn't classify 163264, 163536
Couldn't classify 163669, 163758
Sorry, prediction pasa_asmbl_2827.p1 fails validation.
(ACC)	 AG	163264-163536	GT	AGG
(GCA)	 AG	163669-163758	AT	GGA
-recovered pasa_asmbl_2827.p1, internal, 163264, 163536
Couldn't classify 151973, 151989
Sorry, prediction pasa_asmbl_2829.p1 fails validation.
(ATG)	 AA	151167-151400	GT	ATG
(AAT)	 AG	151675-151810	GT	TGG
(TGG)	 AG	151973-151989	GA	GCG
-recovered pasa_asmbl_2829.p1, initial, 151167, 151400
-recovered pasa_asmbl_2829.p1, internal, 151675, 151810
Valid prediction for GeneMark_model.41804_t
Couldn't classify 142740, 142817
Couldn't classify 143911, 143923
Sorry, prediction pasa_asmbl_2830.p1 fails validation.
(CAC)	 TG	142740-142817	GT	TTG
(AGT)	 AG	143287-143455	GT	TGG
(AAA)	 AG	143538-143628	GT	GGG
(GAA)	 AG	143911-143923	AG	GCA
-recovered pasa_asmbl_2830.p1, internal, 143287, 143455
-recovered pasa_asmbl_2830.p1, internal, 143538, 143628
Valid prediction for Augustus_model.g16342.t1
Valid prediction for GeneMark_model.41799_t
Valid prediction for snap_scaffold_10-snap.31-T1
Valid prediction for Augustus_model.g16353.t1
Valid prediction for Augustus_model.g16350.t1
Valid prediction for Augustus_model.g16343.t1
Valid prediction for GeneMark_model.41818_t
Valid prediction for snap_scaffold_10-snap.5-T1
Valid prediction for snap_scaffold_10-snap.29-T1
Valid prediction for GlimmerHMM_glimmerT_24417-T1
Valid prediction for GlimmerHMM_glimmerT_24424-T1
Valid prediction for snap_scaffold_10-snap.24-T1
Valid prediction for Augustus_model.g16338.t1
Valid prediction for Augustus_model.g16336.t1
Valid prediction for snap_scaffold_10-snap.9-T1
Valid prediction for GeneMark_model.41792_t
Valid prediction for snap_scaffold_10-snap.12-T1
Valid prediction for GlimmerHMM_glimmerT_24436-T1
Valid prediction for snap_scaffold_10-snap.23-T1
Valid prediction for snap_scaffold_10-snap.22-T1
Valid prediction for Augustus_model.g16355.t1
Couldn't classify 3371, 4243
Sorry, prediction pasa_asmbl_4134.p1 fails validation.
(CGG)	 CA	3371-4243	NN	GGN
Valid prediction for Augustus_model.g16339.t1
Valid prediction for Augustus_model.g16349.t1
Couldn't classify 169591, 169788
Couldn't classify 173057, 173179
Sorry, prediction pasa_asmbl_2825.p1 fails validation.
(CGA)	 TA	169591-169788	GT	AGG
(ATT)	 AG	172214-172409	GT	AGG
(ACG)	 AG	172652-172758	GT	AGG
(GTG)	 AG	173057-173179	GG	TGG
-recovered pasa_asmbl_2825.p1, internal, 172214, 172409
-recovered pasa_asmbl_2825.p1, internal, 172652, 172758
Valid prediction for Augustus_model.g16334.t1
Valid prediction for Augustus_model.g16348.t1
Valid prediction for GlimmerHMM_glimmerT_24413-T1
Valid prediction for GlimmerHMM_glimmerT_24410-T1
Valid prediction for snap_scaffold_10-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_24421-T1
Valid prediction for snap_scaffold_10-snap.42-T1
Valid prediction for GeneMark_model.41800_t
Valid prediction for GeneMark_model.41798_t
Valid prediction for GlimmerHMM_glimmerT_24429-T1
Valid prediction for snap_scaffold_10-snap.32-T1
Valid prediction for GeneMark_model.41823_t
Valid prediction for snap_scaffold_10-snap.39-T1
Valid prediction for snap_scaffold_10-snap.25-T1
Couldn't classify 144224, 144427
Couldn't classify 144795, 144962
Sorry, prediction pasa_asmbl_4063.p1 fails validation.
(GAG)	 CA	144224-144427	GT	AGG
(ATT)	 AG	144795-144962	TA	GGT

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 188888
-exon list size: 412


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.2    
2.4    
2.7    
2.9    
3.1    
3.4    
3.6    
3.9    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
6.0    
6.3    
6.5    
6.8    
7.0    
7.2    
7.5    
7.7    
8.0    
8.2    
8.5    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.6    
11.8    
12.1    
12.3    
12.6    
12.8    
13.0    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.7    
15.0    
15.2    
15.5    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.1    
17.4    
17.6    
17.9    
18.1    
18.4    
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    
21.7    
22.0    
22.2    
22.5    
22.7    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.8    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.5    
27.8    
28.0    
28.3    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
30.0    
30.2    
30.4    
30.7    
30.9    
31.2    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.4    
37.7    
37.9    
38.2    
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    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.1    
46.4    
46.6    
46.9    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.1    
53.4    
53.6    
53.9    
54.1    
54.3    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
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    
61.8    
62.1    
62.3    
62.6    
62.8    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.8    
69.1    
69.3    
69.6    
69.8    
70.0    
70.3    
70.5    
70.8    
71.0    
71.3    
71.5    
71.7    
72.0    
72.2    
72.5    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.2    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.3    
77.5    
77.8    
78.0    
78.3    
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    
81.6    
81.9    
82.1    
82.4    
82.6    
82.9    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.5    
84.8    
85.0    
85.3    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
87.0    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.2    
93.5    
93.7    
94.0    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.1    
96.4    
96.6    
96.9    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 40 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support