-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_6811849-7131427

-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_7-snap.1404-T1
Valid prediction for snap_scaffold_7-snap.1426-T1
Valid prediction for snap_scaffold_7-snap.1435-T1
Valid prediction for GlimmerHMM_glimmerT_17592-T1
Valid prediction for CodingQuarry_transcript_57538-T1
Valid prediction for snap_scaffold_7-snap.1421-T1
Valid prediction for snap_scaffold_7-snap.1396-T1
Valid prediction for pasa_asmbl_49896.p1
Valid prediction for snap_scaffold_7-snap.1431-T1
Valid prediction for HiQ_model.g11798.t1
Couldn't classify 264626, 264768
Sorry, prediction pasa_asmbl_49892.p1 fails validation.
(ATG)	 TT	262902-263190	GT	AGG
(AAA)	 AG	263762-263985	GT	TGG
(GTT)	 AG	264224-264383	GT	TCG
(GGG)	 AG	264626-264768	CT	CCC
-recovered pasa_asmbl_49892.p1, initial, 262902, 263190
-recovered pasa_asmbl_49892.p1, internal, 263762, 263985
-recovered pasa_asmbl_49892.p1, internal, 264224, 264383
Valid prediction for GlimmerHMM_glimmerT_17588-T1
Valid prediction for snap_scaffold_7-snap.1434-T1
Valid prediction for GlimmerHMM_glimmerT_17604-T1
Valid prediction for GlimmerHMM_glimmerT_17587-T1
Valid prediction for snap_scaffold_7-snap.1429-T1
Valid prediction for Augustus_model.g11801.t1
Valid prediction for Augustus_model.g11785.t1
Valid prediction for snap_scaffold_7-snap.1393-T1
Valid prediction for pasa_asmbl_49890.p1
Valid prediction for HiQ_model.g11794.t1
Valid prediction for GlimmerHMM_glimmerT_17603-T1
Valid prediction for GlimmerHMM_glimmerT_17600-T1
Valid prediction for GlimmerHMM_glimmerT_17605-T1
Couldn't classify 295978, 296016
Sorry, prediction pasa_asmbl_49898.p1 fails validation.
(ACC)	 CC	295978-296016	GT	AGG
(AAC)	 AG	296342-296474	GT	GGG
(GTA)	 AG	296693-296840	GT	TCG
(ATA)	 AG	296937-297027	GT	ATG
(AAC)	 AG	297151-297264	AC	AGA
-recovered pasa_asmbl_49898.p1, terminal, 297151, 297264
-recovered pasa_asmbl_49898.p1, internal, 296342, 296474
-recovered pasa_asmbl_49898.p1, internal, 296693, 296840
-recovered pasa_asmbl_49898.p1, internal, 296937, 297027
Valid prediction for snap_scaffold_7-snap.1439-T1
Valid prediction for snap_scaffold_7-snap.1395-T1
Couldn't classify 89215, 89288
Couldn't classify 89804, 89830
Sorry, prediction pasa_asmbl_49878.p1 fails validation.
(AAG)	 AG	89215-89288	GC	AGG
(GTG)	 AG	89380-89490	GT	AGG
(GCA)	 AG	89592-89715	GT	AGG
(GCC)	 AG	89804-89830	TG	AGT
add_exon() Sorry, pasa_asmbl_49878.p1 89380-89490-terminal-1 is invalid.
-recovered pasa_asmbl_49878.p1, terminal, 89380, 89490
-recovered pasa_asmbl_49878.p1, internal, 89215, 89288
-recovered pasa_asmbl_49878.p1, internal, 89380, 89490
-recovered pasa_asmbl_49878.p1, internal, 89592, 89715
Valid prediction for Augustus_model.g11799.t1
Valid prediction for snap_scaffold_7-snap.1412-T1
Couldn't classify 167008, 167110
Sorry, prediction pasa_asmbl_49885.p1 fails validation.
(GAC)	 CA	167008-167110	GT	AGG
(ACT)	 AG	167408-168030	CA	AAC
-recovered pasa_asmbl_49885.p1, terminal, 167408, 168030
Valid prediction for snap_scaffold_7-snap.1401-T1
Valid prediction for snap_scaffold_7-snap.1403-T1
Valid prediction for GlimmerHMM_glimmerT_17597-T1
Couldn't classify 284198, 285031
Sorry, prediction pasa_asmbl_49895.p1 fails validation.
(GCC)	 GC	284198-285031	TA	GAT
Valid prediction for snap_scaffold_7-snap.1400-T1
Valid prediction for GlimmerHMM_glimmerT_17601-T1
Valid prediction for CodingQuarry_transcript_57544-T1
Couldn't classify 89930, 89956
Sorry, prediction pasa_asmbl_49879.p1 fails validation.
(CGC)	 TC	89930-89956	GT	AGG
(GGC)	 AG	90103-90251	GT	GGG
(GCA)	 AG	90341-90437	GT	CTG
(TTT)	 AG	91091-91123	GT	TGG
(AGA)	 AG	91239-91338	GT	AGG
(CTG)	 AG	91533-91621	GT	AAG
(AAC)	 AG	91875-91903	GT	ACG
(AGT)	 AG	92037-92110	GT	AGG
(ACC)	 AG	92198-92286	GT	AGG
(CAC)	 AG	92659-92750	GT	AGG
(AAC)	 AG	92910-92946	AC	AGA
-recovered pasa_asmbl_49879.p1, terminal, 92910, 92946
-recovered pasa_asmbl_49879.p1, internal, 90103, 90251
-recovered pasa_asmbl_49879.p1, internal, 90341, 90437
-recovered pasa_asmbl_49879.p1, internal, 91091, 91123
-recovered pasa_asmbl_49879.p1, internal, 91239, 91338
-recovered pasa_asmbl_49879.p1, internal, 91533, 91621
-recovered pasa_asmbl_49879.p1, internal, 91875, 91903
-recovered pasa_asmbl_49879.p1, internal, 92037, 92110
-recovered pasa_asmbl_49879.p1, internal, 92198, 92286
-recovered pasa_asmbl_49879.p1, internal, 92659, 92750
Valid prediction for Augustus_model.g11796.t1
Couldn't classify 276462, 276512
Couldn't classify 278033, 278213
Sorry, prediction pasa_asmbl_49893.p1 fails validation.
(TTC)	 GC	276462-276512	GT	CTG
(CTC)	 AG	277222-277322	GT	GGG
(ACT)	 AG	278033-278213	AC	CCA
-recovered pasa_asmbl_49893.p1, internal, 277222, 277322
Valid prediction for Augustus_model.g11800.t1
Valid prediction for snap_scaffold_7-snap.1413-T1
Valid prediction for CodingQuarry_transcript_57543-T1
Valid prediction for pasa_asmbl_49872.p1
Valid prediction for Augustus_model.g11782.t1
Valid prediction for Augustus_model.g11778.t1
Valid prediction for Augustus_model.g11795.t1
Valid prediction for pasa_asmbl_50583.p1
Valid prediction for GlimmerHMM_glimmerT_17589-T1
Valid prediction for pasa_asmbl_49875.p1
Valid prediction for Augustus_model.g11776.t1
Valid prediction for GlimmerHMM_glimmerT_17584-T1
Valid prediction for snap_scaffold_7-snap.1436-T1
Valid prediction for snap_scaffold_7-snap.1419-T1
Valid prediction for Augustus_model.g11791.t1
Valid prediction for HiQ_model.g11779.t1
Valid prediction for GlimmerHMM_glimmerT_17596-T1
Valid prediction for snap_scaffold_7-snap.1440-T1
Valid prediction for snap_scaffold_7-snap.1402-T1
Couldn't classify 185931, 186050
Couldn't classify 186263, 186475
Sorry, prediction pasa_asmbl_49886.p1 fails validation.
(ACA)	 GA	185931-186050	GT	ACG
(ATC)	 AG	186263-186475	GT	AGG
-recovered pasa_asmbl_49886.p1, internal, 186263, 186475
Valid prediction for Augustus_model.g11797.t1
Valid prediction for snap_scaffold_7-snap.1430-T1
Valid prediction for HiQ_model.g11790.t1
Valid prediction for HiQ_model.g11780.t1
Valid prediction for CodingQuarry_transcript_57539-T1
Valid prediction for snap_scaffold_7-snap.1420-T1
Valid prediction for GlimmerHMM_glimmerT_17602-T1
Valid prediction for snap_scaffold_7-snap.1438-T1
Valid prediction for HiQ_model.g11781.t1
Valid prediction for snap_scaffold_7-snap.1405-T1
Valid prediction for snap_scaffold_7-snap.1425-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_17585-T1
Valid prediction for HiQ_model.g11783.t1
Valid prediction for snap_scaffold_7-snap.1424-T1
Valid prediction for snap_scaffold_7-snap.1428-T1
Valid prediction for Augustus_model.g11775.t1
Valid prediction for GlimmerHMM_glimmerT_17590-T1
Valid prediction for CodingQuarry_transcript_57540-T1
Valid prediction for snap_scaffold_7-snap.1398-T1
Valid prediction for snap_scaffold_7-snap.1414-T1
Valid prediction for Augustus_model.g11786.t1
Valid prediction for snap_scaffold_7-snap.1417-T1
Valid prediction for Augustus_model.g11787.t1
Valid prediction for snap_scaffold_7-snap.1415-T1
Valid prediction for GlimmerHMM_glimmerT_17609-T1
Valid prediction for GlimmerHMM_glimmerT_17607-T1
Valid prediction for GlimmerHMM_glimmerT_17591-T1
Valid prediction for snap_scaffold_7-snap.1441-T1
Valid prediction for snap_scaffold_7-snap.1406-T1
Valid prediction for GlimmerHMM_glimmerT_17608-T1
Valid prediction for GlimmerHMM_glimmerT_17598-T1
Valid prediction for Augustus_model.g11789.t1
Valid prediction for GlimmerHMM_glimmerT_17606-T1
Valid prediction for snap_scaffold_7-snap.1437-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.1410-T1
Valid prediction for snap_scaffold_7-snap.1423-T1
Valid prediction for GlimmerHMM_glimmerT_17586-T1
Valid prediction for Augustus_model.g11784.t1
Valid prediction for snap_scaffold_7-snap.1433-T1
Valid prediction for Augustus_model.g11803.t1
Valid prediction for snap_scaffold_7-snap.1416-T1
Valid prediction for Augustus_model.g11774.t1
Valid prediction for pasa_asmbl_50936.p1
Valid prediction for snap_scaffold_7-snap.1399-T1
Valid prediction for snap_scaffold_7-snap.1418-T1
Valid prediction for snap_scaffold_7-snap.1432-T1
Valid prediction for snap_scaffold_7-snap.1427-T1
Valid prediction for GlimmerHMM_glimmerT_17599-T1
Valid prediction for GlimmerHMM_glimmerT_17583-T1
Valid prediction for Augustus_model.g11802.t1
Valid prediction for snap_scaffold_7-snap.1392-T1
Valid prediction for snap_scaffold_7-snap.1422-T1
Valid prediction for GlimmerHMM_glimmerT_17595-T1
Valid prediction for snap_scaffold_7-snap.1411-T1
Valid prediction for GlimmerHMM_glimmerT_17593-T1
Valid prediction for snap_scaffold_7-snap.1442-T1
Valid prediction for Augustus_model.g11793.t1
Valid prediction for GlimmerHMM_glimmerT_17594-T1
Valid prediction for Augustus_model.g11792.t1
Valid prediction for Augustus_model.g11777.t1
Valid prediction for snap_scaffold_7-snap.1408-T1
Valid prediction for snap_scaffold_7-snap.1394-T1
Valid prediction for snap_scaffold_7-snap.1409-T1
Valid prediction for snap_scaffold_7-snap.1397-T1
Valid prediction for snap_scaffold_7-snap.1407-T1
Valid prediction for Augustus_model.g11788.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 94314, rend_intergenic: 89394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249359, rend_intergenic: 239290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258727, rend_intergenic: 250190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 289958, rend_intergenic: 283193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 307153, rend_intergenic: 304802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 319579
-exon list size: 519


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.6    
3.8    
4.0    
4.2    
4.4    
4.6    
4.8    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.2    
13.4    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
15.0    
15.2    
15.4    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.7    
17.9    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.2    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 94314, rend_intergenic: 89394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249359, rend_intergenic: 239290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258727, rend_intergenic: 250190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 289958, rend_intergenic: 283193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 307153, rend_intergenic: 304802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support