-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_13731915-13952622

-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_1-snap.2374-T1
Valid prediction for snap_scaffold_1-snap.2376-T1
Valid prediction for snap_scaffold_1-snap.2387-T1
Valid prediction for snap_scaffold_1-snap.2370-T1
Valid prediction for GlimmerHMM_glimmerT_1808-T1
Valid prediction for Augustus_model.g1358.t1
Valid prediction for Augustus_model.g1351.t1
Couldn't classify 84922, 85134
Sorry, prediction pasa_asmbl_2316.p1 fails validation.
(CTC)	 CT	84922-85134	GT	AGG
(AAT)	 AG	85262-85415	GT	AGG
(AGA)	 AG	85668-85819	GT	AGG
(GAT)	 AG	86038-86266	GT	GGG
(AGC)	 AG	86390-86499	AC	GAA
-recovered pasa_asmbl_2316.p1, terminal, 86390, 86499
-recovered pasa_asmbl_2316.p1, internal, 85262, 85415
-recovered pasa_asmbl_2316.p1, internal, 85668, 85819
-recovered pasa_asmbl_2316.p1, internal, 86038, 86266
Valid prediction for GlimmerHMM_glimmerT_1827-T1
Valid prediction for GlimmerHMM_glimmerT_1824-T1
Valid prediction for GlimmerHMM_glimmerT_1812-T1
Valid prediction for snap_scaffold_1-snap.2398-T1
Valid prediction for CodingQuarry_transcript_2892-T1
Couldn't classify 18382, 18469
Couldn't classify 21419, 21464
Sorry, prediction pasa_asmbl_2314.p1 fails validation.
(GGC)	 TG	18382-18469	GT	CGG
(GTT)	 AG	18620-18756	GT	TGG
(GAC)	 AG	19821-19926	GT	GGG
(GGC)	 AG	20047-20217	GT	GGG
(GCT)	 AG	20733-20949	GT	AGG
(CCA)	 AG	21419-21464	TA	AGT
-recovered pasa_asmbl_2314.p1, internal, 18620, 18756
-recovered pasa_asmbl_2314.p1, internal, 19821, 19926
-recovered pasa_asmbl_2314.p1, internal, 20047, 20217
-recovered pasa_asmbl_2314.p1, internal, 20733, 20949
Valid prediction for snap_scaffold_1-snap.2385-T1
Valid prediction for GlimmerHMM_glimmerT_1828-T1
Valid prediction for GlimmerHMM_glimmerT_1820-T1
Valid prediction for snap_scaffold_1-snap.2381-T1
Valid prediction for GlimmerHMM_glimmerT_1807-T1
Valid prediction for Augustus_model.g1355.t1
Valid prediction for GlimmerHMM_glimmerT_1834-T1
Valid prediction for Augustus_model.g1353.t1
Valid prediction for pasa_asmbl_2327.p1
Valid prediction for snap_scaffold_1-snap.2392-T1
Valid prediction for GlimmerHMM_glimmerT_1822-T1
Valid prediction for HiQ_model.g1365.t1
Valid prediction for snap_scaffold_1-snap.2391-T1
Valid prediction for snap_scaffold_1-snap.2361-T1
Valid prediction for GlimmerHMM_glimmerT_1805-T1
Valid prediction for pasa_asmbl_2320.p1
Valid prediction for snap_scaffold_1-snap.2383-T1
Valid prediction for snap_scaffold_1-snap.2367-T1
Valid prediction for snap_scaffold_1-snap.2369-T1
Valid prediction for GlimmerHMM_glimmerT_1804-T1
Valid prediction for GlimmerHMM_glimmerT_1802-T1
Valid prediction for Augustus_model.g1366.t1
Valid prediction for snap_scaffold_1-snap.2393-T1
Valid prediction for Augustus_model.g1364.t1
Valid prediction for snap_scaffold_1-snap.2371-T1
Valid prediction for pasa_asmbl_2317.p2
Valid prediction for Augustus_model.g1361.t1
Valid prediction for snap_scaffold_1-snap.2363-T1
Valid prediction for GlimmerHMM_glimmerT_1814-T1
Valid prediction for CodingQuarry_transcript_2895-T1
Valid prediction for snap_scaffold_1-snap.2380-T1
Valid prediction for snap_scaffold_1-snap.2401-T1
Valid prediction for CodingQuarry_transcript_2894-T1
Valid prediction for HiQ_model.g1363.t1
Valid prediction for snap_scaffold_1-snap.2394-T1
Valid prediction for Augustus_model.g1360.t1
Valid prediction for Augustus_model.g1370.t1
Valid prediction for CodingQuarry_transcript_2896-T1
Valid prediction for Augustus_model.g1375.t1
Valid prediction for snap_scaffold_1-snap.2382-T1
Valid prediction for CodingQuarry_transcript_2893-T1
Valid prediction for Augustus_model.g1371.t1
Valid prediction for Augustus_model.g1352.t1
Valid prediction for GlimmerHMM_glimmerT_1799-T1
Valid prediction for GlimmerHMM_glimmerT_1825-T1
Valid prediction for HiQ_model.g1369.t1
Valid prediction for GlimmerHMM_glimmerT_1823-T1
Valid prediction for GlimmerHMM_glimmerT_1810-T1
Valid prediction for snap_scaffold_1-snap.2372-T1
Valid prediction for snap_scaffold_1-snap.2378-T1
Valid prediction for snap_scaffold_1-snap.2397-T1
Valid prediction for snap_scaffold_1-snap.2390-T1
Valid prediction for snap_scaffold_1-snap.2377-T1
Valid prediction for GlimmerHMM_glimmerT_1833-T1
Valid prediction for GlimmerHMM_glimmerT_1800-T1
Valid prediction for Augustus_model.g1373.t1
Valid prediction for Augustus_model.g1357.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_1818-T1
Valid prediction for snap_scaffold_1-snap.2364-T1
Valid prediction for GlimmerHMM_glimmerT_1803-T1
Valid prediction for GlimmerHMM_glimmerT_1830-T1
Valid prediction for pasa_asmbl_865.p1
Valid prediction for snap_scaffold_1-snap.2375-T1
Valid prediction for Augustus_model.g1354.t1
Valid prediction for snap_scaffold_1-snap.2365-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_2898-T1
Valid prediction for snap_scaffold_1-snap.2373-T1
Valid prediction for snap_scaffold_1-snap.2400-T1
Valid prediction for Augustus_model.g1372.t1
Valid prediction for GlimmerHMM_glimmerT_1816-T1
Couldn't classify 89762, 89992
Sorry, prediction pasa_asmbl_850.p1 fails validation.
(CCG)	 CA	89762-89992	GT	ACG
(GAC)	 AG	90339-90827	GC	AGG
-recovered pasa_asmbl_850.p1, terminal, 90339, 90827
-recovered pasa_asmbl_850.p1, internal, 90339, 90827
Valid prediction for snap_scaffold_1-snap.2399-T1
Valid prediction for pasa_asmbl_863.p1
Valid prediction for snap_scaffold_1-snap.2379-T1
Valid prediction for snap_scaffold_1-snap.2368-T1
Valid prediction for snap_scaffold_1-snap.2396-T1
Valid prediction for GlimmerHMM_glimmerT_1801-T1
Valid prediction for pasa_asmbl_846.p1
Valid prediction for snap_scaffold_1-snap.2366-T1
Valid prediction for Augustus_model.g1367.t1
Valid prediction for GlimmerHMM_glimmerT_1813-T1
Valid prediction for snap_scaffold_1-snap.2386-T1
Valid prediction for GlimmerHMM_glimmerT_1811-T1
Valid prediction for CodingQuarry_transcript_2897-T1
Couldn't classify 86741, 86786
Couldn't classify 88472, 88647
Sorry, prediction pasa_asmbl_851.p1 fails validation.
(GGT)	 CA	86741-86786	GT	AGG
(GTG)	 AG	87135-87269	GT	CAG
(AGC)	 AG	87574-87679	GT	CAG
(TTT)	 AG	87792-88019	GT	TGG
(CGA)	 AG	88118-88191	GT	AGG
(AGC)	 AG	88472-88647	GA	AGG
-recovered pasa_asmbl_851.p1, internal, 87135, 87269
-recovered pasa_asmbl_851.p1, internal, 87574, 87679
-recovered pasa_asmbl_851.p1, internal, 87792, 88019
-recovered pasa_asmbl_851.p1, internal, 88118, 88191
Valid prediction for snap_scaffold_1-snap.2388-T1
Valid prediction for HiQ_model.g1362.t1
Valid prediction for snap_scaffold_1-snap.2402-T1
Valid prediction for snap_scaffold_1-snap.2395-T1
Couldn't classify 25233, 25408
Sorry, prediction pasa_asmbl_860.p1 fails validation.
(CAA)	 GT	25233-25408	GT	AGG
(GCG)	 AG	26130-26443	GT	AGG
(TAT)	 AG	26560-26681	GT	AGG
(ATC)	 AG	26802-26946	GC	AGG
(TAG)	 AG	27091-27244	GT	CAG
(GTA)	 AG	27360-27531	GT	AGG
(ATA)	 AG	27908-28003	GT	AGG
(GTT)	 AG	28153-28365	GT	AGG
(CTG)	 AG	28519-28662	GT	AGG
(GTG)	 AG	28776-28922	GT	AGG
(GCT)	 AG	29028-29121	GT	AGG
(CGC)	 AG	29300-29622	GT	AGG
(GTG)	 AG	29761-29883	GT	TGG
(GCT)	 AG	30106-30185	GT	GGG
(GTG)	 AG	30280-30367	AC	AGA
-recovered pasa_asmbl_860.p1, terminal, 30280, 30367
-recovered pasa_asmbl_860.p1, internal, 26130, 26443
-recovered pasa_asmbl_860.p1, internal, 26560, 26681
-recovered pasa_asmbl_860.p1, internal, 26802, 26946
-recovered pasa_asmbl_860.p1, internal, 27091, 27244
-recovered pasa_asmbl_860.p1, internal, 27360, 27531
-recovered pasa_asmbl_860.p1, internal, 27908, 28003
-recovered pasa_asmbl_860.p1, internal, 28153, 28365
-recovered pasa_asmbl_860.p1, internal, 28519, 28662
-recovered pasa_asmbl_860.p1, internal, 28776, 28922
-recovered pasa_asmbl_860.p1, internal, 29028, 29121
-recovered pasa_asmbl_860.p1, internal, 29300, 29622
-recovered pasa_asmbl_860.p1, internal, 29761, 29883
-recovered pasa_asmbl_860.p1, internal, 30106, 30185
Valid prediction for Augustus_model.g1359.t1
Valid prediction for snap_scaffold_1-snap.2384-T1
Valid prediction for GlimmerHMM_glimmerT_1829-T1
Valid prediction for GlimmerHMM_glimmerT_1806-T1
Valid prediction for Augustus_model.g1356.t1
Valid prediction for GlimmerHMM_glimmerT_1809-T1
Valid prediction for snap_scaffold_1-snap.2362-T1
Valid prediction for snap_scaffold_1-snap.2389-T1
Valid prediction for Augustus_model.g1374.t1
Valid prediction for GlimmerHMM_glimmerT_1815-T1
Valid prediction for GlimmerHMM_glimmerT_1831-T1
Valid prediction for GlimmerHMM_glimmerT_1819-T1
Valid prediction for Augustus_model.g1368.t1
Valid prediction for GlimmerHMM_glimmerT_1817-T1
Valid prediction for GlimmerHMM_glimmerT_1821-T1
Valid prediction for snap_scaffold_1-snap.2360-T1
Valid prediction for GlimmerHMM_glimmerT_1826-T1
Valid prediction for GlimmerHMM_glimmerT_1832-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6976, rend_intergenic: 4707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14750, rend_intergenic: 12601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21686, rend_intergenic: 16275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34592, rend_intergenic: 27216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57012, rend_intergenic: 50769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140214, rend_intergenic: 137794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140806, rend_intergenic: 140214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180415, rend_intergenic: 177163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217211, rend_intergenic: 209864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220708
-exon list size: 423


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.9    
2.1    
2.4    
2.6    
2.8    
3.1    
3.3    
3.5    
3.8    
4.0    
4.2    
4.5    
4.7    
4.9    
5.2    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.8    
7.1    
7.3    
7.5    
7.8    
8.0    
8.2    
8.5    
8.7    
8.9    
9.2    
9.4    
9.6    
9.9    
10.1    
10.4    
10.6    
10.8    
11.1    
11.3    
11.5    
11.8    
12.0    
12.2    
12.5    
12.7    
12.9    
13.2    
13.4    
13.6    
13.9    
14.1    
14.4    
14.6    
14.8    
15.1    
15.3    
15.5    
15.8    
16.0    
16.2    
16.5    
16.7    
16.9    
17.2    
17.4    
17.6    
17.9    
18.1    
18.4    
18.6    
18.8    
19.1    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
20.9    
21.2    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.8    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.5    
28.7    
28.9    
29.2    
29.4    
29.6    
29.9    
30.1    
30.4    
30.6    
30.8    
31.1    
31.3    
31.5    
31.8    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.4    
34.6    
34.8    
35.1    
35.3    
35.5    
35.8    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.9    
38.1    
38.4    
38.6    
38.8    
39.1    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.8    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
46.8    
47.1    
47.3    
47.5    
47.8    
48.0    
48.2    
48.5    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.5    
51.8    
52.0    
52.2    
52.5    
52.7    
52.9    
53.2    
53.4    
53.6    
53.9    
54.1    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.2    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.8    
59.1    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
60.9    
61.2    
61.4    
61.6    
61.9    
62.1    
62.4    
62.6    
62.8    
63.1    
63.3    
63.5    
63.8    
64.0    
64.2    
64.5    
64.7    
64.9    
65.2    
65.4    
65.6    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.2    
68.5    
68.7    
68.9    
69.2    
69.4    
69.6    
69.9    
70.1    
70.4    
70.6    
70.8    
71.1    
71.3    
71.5    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.8    
79.1    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
80.9    
81.2    
81.4    
81.6    
81.9    
82.1    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.2    
97.4    
97.6    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 6976, rend_intergenic: 4707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14750, rend_intergenic: 12601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21686, rend_intergenic: 16275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34592, rend_intergenic: 27216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57012, rend_intergenic: 50769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140214, rend_intergenic: 137794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140806, rend_intergenic: 140214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180415, rend_intergenic: 177163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217211, rend_intergenic: 209864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support