-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_6195111-6401399

-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 GlimmerHMM_glimmerT_9694-T1
Valid prediction for snap_scaffold_4-snap.1331-T1
Valid prediction for snap_scaffold_4-snap.1354-T1
Valid prediction for snap_scaffold_4-snap.1364-T1
Valid prediction for HiQ_model.g6346.t1
Valid prediction for GeneMark_model.15805_t
Valid prediction for GeneMark_model.15789_t
Valid prediction for GlimmerHMM_glimmerT_9703-T1
Valid prediction for GeneMark_model.15804_t
Valid prediction for GeneMark_model.15791_t
Valid prediction for Augustus_model.g6344.t1
Valid prediction for snap_scaffold_4-snap.1351-T1
Valid prediction for snap_scaffold_4-snap.1361-T1
Valid prediction for pasa_asmbl_42735.p1
Valid prediction for GlimmerHMM_glimmerT_9685-T1
Valid prediction for Augustus_model.g6345.t1
Valid prediction for snap_scaffold_4-snap.1345-T1
Valid prediction for GlimmerHMM_glimmerT_9697-T1
Valid prediction for GlimmerHMM_glimmerT_9705-T1
Valid prediction for GeneMark_model.15795_t
Valid prediction for HiQ_model.g6334.t1
Valid prediction for snap_scaffold_4-snap.1353-T1
Valid prediction for GeneMark_model.15785_t
Couldn't classify 55851, 56015
Sorry, prediction pasa_asmbl_42713.p1 fails validation.
(AGA)	 TC	55851-56015	GT	AGG
(AAT)	 AG	56787-56889	GT	TGG
(CAA)	 AG	56979-57058	GT	AGG
(GTG)	 AG	57187-57290	GT	AAG
(GTC)	 AG	57473-57602	GT	AGG
(ATC)	 AG	57731-57827	GT	AGG
(GTA)	 AG	58980-59133	GT	AGG
(TCA)	 AG	59407-59494	GT	AGG
(GTG)	 AG	59597-59653	CA	GAC
add_exon() Sorry, pasa_asmbl_42713.p1 57187-57290-terminal-2 is invalid.
-recovered pasa_asmbl_42713.p1, terminal, 57187, 57290
-recovered pasa_asmbl_42713.p1, terminal, 59597, 59653
-recovered pasa_asmbl_42713.p1, internal, 56787, 56889
-recovered pasa_asmbl_42713.p1, internal, 56979, 57058
-recovered pasa_asmbl_42713.p1, internal, 57187, 57290
-recovered pasa_asmbl_42713.p1, internal, 57473, 57602
-recovered pasa_asmbl_42713.p1, internal, 57731, 57827
-recovered pasa_asmbl_42713.p1, internal, 58980, 59133
-recovered pasa_asmbl_42713.p1, internal, 59407, 59494
Valid prediction for GlimmerHMM_glimmerT_9715-T1
Valid prediction for snap_scaffold_4-snap.1352-T1
Valid prediction for GlimmerHMM_glimmerT_9706-T1
Valid prediction for snap_scaffold_4-snap.1355-T1
Valid prediction for Augustus_model.g6337.t1
Valid prediction for Augustus_model.g6336.t1
Valid prediction for Augustus_model.g6353.t1
Valid prediction for snap_scaffold_4-snap.1357-T1
Valid prediction for snap_scaffold_4-snap.1332-T1
Valid prediction for Augustus_model.g6342.t1
Valid prediction for snap_scaffold_4-snap.1340-T1
Valid prediction for Augustus_model.g6348.t1
Valid prediction for GeneMark_model.15782_t
Valid prediction for Augustus_model.g6333.t1
Valid prediction for CodingQuarry_transcript_48918-T1
Valid prediction for snap_scaffold_4-snap.1334-T1
Valid prediction for GlimmerHMM_glimmerT_9693-T1
Couldn't classify 38218, 38343
Couldn't classify 39616, 39705
Sorry, prediction pasa_asmbl_42708.p1 fails validation.
(TAT)	 CC	38218-38343	GT	AGG
(ATG)	 AG	38711-38840	GT	CGG
(AGA)	 AG	39408-39520	GT	AAG
(GTT)	 AG	39616-39705	AT	CCA
-recovered pasa_asmbl_42708.p1, initial, 38711, 38840
-recovered pasa_asmbl_42708.p1, internal, 38711, 38840
-recovered pasa_asmbl_42708.p1, internal, 39408, 39520
Valid prediction for GlimmerHMM_glimmerT_9698-T1
Valid prediction for snap_scaffold_4-snap.1329-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.1338-T1
Valid prediction for CodingQuarry_transcript_48917-T1
Valid prediction for Augustus_model.g6330.t1
Valid prediction for pasa_asmbl_42716.p1
Valid prediction for GlimmerHMM_glimmerT_9686-T1
Valid prediction for pasa_asmbl_42734.p1
Valid prediction for GeneMark_model.15788_t
Valid prediction for CodingQuarry_transcript_48914-T1
Valid prediction for HiQ_model.g6340.t1
Valid prediction for snap_scaffold_4-snap.1356-T1
Valid prediction for GeneMark_model.15783_t
Valid prediction for GlimmerHMM_glimmerT_9699-T1
Valid prediction for GeneMark_model.15801_t
Valid prediction for GeneMark_model.15787_t
Valid prediction for snap_scaffold_4-snap.1350-T1
Valid prediction for CodingQuarry_transcript_48919-T1
Valid prediction for GeneMark_model.15793_t
Valid prediction for snap_scaffold_4-snap.1336-T1
Valid prediction for GeneMark_model.15796_t
Valid prediction for GlimmerHMM_glimmerT_9700-T1
Valid prediction for GeneMark_model.15784_t
Valid prediction for GlimmerHMM_glimmerT_9701-T1
Valid prediction for GlimmerHMM_glimmerT_9691-T1
Valid prediction for snap_scaffold_4-snap.1344-T1
Valid prediction for Augustus_model.g6332.t1
Couldn't classify 35016, 35138
Sorry, prediction pasa_asmbl_42706.p1 fails validation.
(ATG)	 CC	30027-30212	GT	AGG
(GGC)	 AG	30877-31022	GT	AGG
(GTA)	 AG	31730-31814	GT	TGG
(TGT)	 AG	32088-32188	GT	AGG
(TGC)	 AG	32337-32529	GC	AGG
(GTT)	 AG	32787-32939	GT	GGG
(GTC)	 AG	34120-34233	GT	AGG
(GCA)	 AG	35016-35138	GA	GGG
-recovered pasa_asmbl_42706.p1, initial, 30027, 30212
-recovered pasa_asmbl_42706.p1, internal, 30877, 31022
-recovered pasa_asmbl_42706.p1, internal, 31730, 31814
-recovered pasa_asmbl_42706.p1, internal, 32088, 32188
-recovered pasa_asmbl_42706.p1, internal, 32337, 32529
-recovered pasa_asmbl_42706.p1, internal, 32787, 32939
-recovered pasa_asmbl_42706.p1, internal, 34120, 34233
Valid prediction for GlimmerHMM_glimmerT_9688-T1
Valid prediction for snap_scaffold_4-snap.1333-T1
Couldn't classify 104188, 104390
Sorry, prediction pasa_asmbl_42718.p1 fails validation.
(GAC)	 CA	104188-104390	GT	AGG
(CTA)	 AG	104826-104941	GT	CTG
(ATT)	 AG	105490-105539	GT	AGG
(CGT)	 AG	105639-105731	GT	GGG
(CTG)	 AG	107857-107950	GT	AGG
(TTC)	 AG	108266-108450	GT	GGG
(CCT)	 AG	109134-109316	GT	AGG
(ATC)	 AG	109702-109845	GT	AGG
(GAT)	 AG	110036-110125	AA	GAA
-recovered pasa_asmbl_42718.p1, terminal, 110036, 110125
-recovered pasa_asmbl_42718.p1, internal, 104826, 104941
-recovered pasa_asmbl_42718.p1, internal, 105490, 105539
-recovered pasa_asmbl_42718.p1, internal, 105639, 105731
-recovered pasa_asmbl_42718.p1, internal, 107857, 107950
-recovered pasa_asmbl_42718.p1, internal, 108266, 108450
-recovered pasa_asmbl_42718.p1, internal, 109134, 109316
-recovered pasa_asmbl_42718.p1, internal, 109702, 109845
Valid prediction for snap_scaffold_4-snap.1341-T1
Valid prediction for GlimmerHMM_glimmerT_9704-T1
Valid prediction for HiQ_model.g6331.t1
Valid prediction for GeneMark_model.15799_t
Valid prediction for GlimmerHMM_glimmerT_9687-T1
Valid prediction for GeneMark_model.15790_t
Valid prediction for Augustus_model.g6354.t1
Valid prediction for pasa_asmbl_42728.p1
Valid prediction for GeneMark_model.15798_t
Valid prediction for GlimmerHMM_glimmerT_9708-T1
Couldn't classify 49176, 49253
Sorry, prediction pasa_asmbl_42709.p1 fails validation.
(AGC)	 AC	49176-49253	GT	AGG
(CTG)	 AG	49403-49513	GT	AGG
(GTG)	 AG	50715-50855	GT	AGG
(GTG)	 AG	51055-51135	GT	AGG
(GTG)	 AG	51363-51464	GT	AGG
(CCC)	 AG	51748-51927	GT	AGG
(ATC)	 AG	52513-52637	GT	AGG
(ATA)	 AG	52764-52767	AG	AGA
-recovered pasa_asmbl_42709.p1, terminal, 52764, 52767
-recovered pasa_asmbl_42709.p1, internal, 49403, 49513
-recovered pasa_asmbl_42709.p1, internal, 50715, 50855
-recovered pasa_asmbl_42709.p1, internal, 51055, 51135
-recovered pasa_asmbl_42709.p1, internal, 51363, 51464
-recovered pasa_asmbl_42709.p1, internal, 51748, 51927
-recovered pasa_asmbl_42709.p1, internal, 52513, 52637
Valid prediction for HiQ_model.g6335.t1
Valid prediction for GeneMark_model.15781_t
Valid prediction for Augustus_model.g6347.t1
Valid prediction for GlimmerHMM_glimmerT_9709-T1
Valid prediction for GeneMark_model.15792_t
Valid prediction for GlimmerHMM_glimmerT_9683-T1
Valid prediction for HiQ_model.g6339.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 snap_scaffold_4-snap.1346-T1
Valid prediction for GlimmerHMM_glimmerT_9690-T1
Valid prediction for snap_scaffold_4-snap.1359-T1
Valid prediction for snap_scaffold_4-snap.1330-T1
Valid prediction for GeneMark_model.15786_t
Valid prediction for snap_scaffold_4-snap.1358-T1
Valid prediction for Augustus_model.g6355.t1
Valid prediction for GlimmerHMM_glimmerT_9712-T1
Valid prediction for GlimmerHMM_glimmerT_9714-T1
Valid prediction for GlimmerHMM_glimmerT_9710-T1
Valid prediction for GeneMark_model.15800_t
Valid prediction for Augustus_model.g6350.t1
Valid prediction for CodingQuarry_transcript_48916-T1
Valid prediction for Augustus_model.g6351.t1
Valid prediction for GlimmerHMM_glimmerT_9689-T1
Valid prediction for snap_scaffold_4-snap.1349-T1
Valid prediction for Augustus_model.g6352.t1
Valid prediction for snap_scaffold_4-snap.1348-T1
Valid prediction for snap_scaffold_4-snap.1343-T1
Valid prediction for snap_scaffold_4-snap.1342-T1
Valid prediction for GlimmerHMM_glimmerT_9695-T1
Valid prediction for GlimmerHMM_glimmerT_9684-T1
Valid prediction for GlimmerHMM_glimmerT_9702-T1
Valid prediction for GlimmerHMM_glimmerT_9707-T1
Valid prediction for snap_scaffold_4-snap.1362-T1
Valid prediction for GlimmerHMM_glimmerT_9713-T1
Valid prediction for snap_scaffold_4-snap.1366-T1
Valid prediction for Augustus_model.g6343.t1
Valid prediction for GlimmerHMM_glimmerT_9692-T1
Valid prediction for pasa_asmbl_41408.p1
Valid prediction for snap_scaffold_4-snap.1365-T1
Valid prediction for GlimmerHMM_glimmerT_9696-T1
Valid prediction for GeneMark_model.15794_t
Valid prediction for Augustus_model.g6349.t1
Valid prediction for snap_scaffold_4-snap.1363-T1
Valid prediction for snap_scaffold_4-snap.1339-T1
Valid prediction for snap_scaffold_4-snap.1337-T1
Valid prediction for GlimmerHMM_glimmerT_9711-T1
Valid prediction for Augustus_model.g6341.t1
Valid prediction for snap_scaffold_4-snap.1360-T1
Valid prediction for HiQ_model.g6338.t1
Valid prediction for GeneMark_model.15803_t
Valid prediction for snap_scaffold_4-snap.1347-T1
Valid prediction for snap_scaffold_4-snap.1335-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 172747, rend_intergenic: 171466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206289
-exon list size: 385


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.8    
3.1    
3.4    
3.6    
3.9    
4.1    
4.4    
4.7    
4.9    
5.2    
5.4    
5.7    
5.9    
6.2    
6.5    
6.7    
7.0    
7.2    
7.5    
7.8    
8.0    
8.3    
8.5    
8.8    
9.0    
9.3    
9.6    
9.8    
10.1    
10.3    
10.6    
10.9    
11.1    
11.4    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.5    
15.8    
16.0    
16.3    
16.5    
16.8    
17.1    
17.3    
17.6    
17.8    
18.1    
18.3    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
22.0    
22.2    
22.5    
22.7    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
31.0    
31.3    
31.5    
31.8    
32.0    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.0    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.6    
63.8    
64.1    
64.3    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
68.0    
68.2    
68.5    
68.7    
69.0    
69.3    
69.5    
69.8    
70.0    
70.3    
70.5    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.3    
77.5    
77.8    
78.0    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.2    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.4    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 172747, rend_intergenic: 171466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support