-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_6553273-6727923

-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_6-snap.1508-T1
Valid prediction for snap_scaffold_6-snap.1499-T1
Valid prediction for Augustus_model.g9817.t1
Valid prediction for snap_scaffold_6-snap.1497-T1
Valid prediction for Augustus_model.g9809.t1
Valid prediction for GlimmerHMM_glimmerT_14848-T1
Valid prediction for snap_scaffold_6-snap.1527-T1
Valid prediction for GlimmerHMM_glimmerT_14854-T1
Valid prediction for GlimmerHMM_glimmerT_14845-T1
Valid prediction for GlimmerHMM_glimmerT_14844-T1
Valid prediction for snap_scaffold_6-snap.1524-T1
Valid prediction for snap_scaffold_6-snap.1488-T1
Valid prediction for GlimmerHMM_glimmerT_14864-T1
Valid prediction for GlimmerHMM_glimmerT_14835-T1
Valid prediction for GlimmerHMM_glimmerT_14841-T1
Valid prediction for snap_scaffold_6-snap.1481-T1
Valid prediction for snap_scaffold_6-snap.1510-T1
Valid prediction for Augustus_model.g9814.t1
Valid prediction for Augustus_model.g9810.t1
Valid prediction for Augustus_model.g9813.t1
Valid prediction for snap_scaffold_6-snap.1486-T1
Valid prediction for snap_scaffold_6-snap.1483-T1
Valid prediction for snap_scaffold_6-snap.1496-T1
Valid prediction for snap_scaffold_6-snap.1507-T1
Valid prediction for snap_scaffold_6-snap.1491-T1
Valid prediction for snap_scaffold_6-snap.1501-T1
Valid prediction for GlimmerHMM_glimmerT_14842-T1
Couldn't classify 114638, 115309
Sorry, prediction pasa_asmbl_47005.p1 fails validation.
(CAG)	 AA	114638-115309	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_14838-T1
Valid prediction for snap_scaffold_6-snap.1480-T1
Valid prediction for snap_scaffold_6-snap.1512-T1
Valid prediction for Augustus_model.g9811.t1
Valid prediction for snap_scaffold_6-snap.1504-T1
Valid prediction for snap_scaffold_6-snap.1525-T1
Valid prediction for snap_scaffold_6-snap.1514-T1
Valid prediction for GlimmerHMM_glimmerT_14850-T1
Valid prediction for GlimmerHMM_glimmerT_14840-T1
Valid prediction for snap_scaffold_6-snap.1500-T1
Valid prediction for snap_scaffold_6-snap.1506-T1
Valid prediction for GlimmerHMM_glimmerT_14843-T1
Valid prediction for GlimmerHMM_glimmerT_14837-T1
Valid prediction for Augustus_model.g9825.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_6-snap.1487-T1
Valid prediction for snap_scaffold_6-snap.1511-T1
Valid prediction for GlimmerHMM_glimmerT_14853-T1
Valid prediction for Augustus_model.g9815.t1
Couldn't classify 8064, 8217
Couldn't classify 9034, 9275
Sorry, prediction pasa_asmbl_49369.p2 fails validation.
(CTG)	 AC	8064-8217	GT	TGG
(GCT)	 AG	9034-9275	AA	AGA
Valid prediction for snap_scaffold_6-snap.1502-T1
Valid prediction for snap_scaffold_6-snap.1492-T1
Valid prediction for snap_scaffold_6-snap.1526-T1
Valid prediction for Augustus_model.g9816.t1
Valid prediction for GlimmerHMM_glimmerT_14857-T1
Valid prediction for snap_scaffold_6-snap.1520-T1
Valid prediction for GlimmerHMM_glimmerT_14834-T1
Couldn't classify 10623, 10794
Couldn't classify 11287, 11427
Sorry, prediction pasa_asmbl_49448.p1 fails validation.
(AAC)	 CC	10623-10794	GT	AGG
(GCA)	 AG	10940-11121	GT	TGG
(CCA)	 AG	11287-11427	GC	TGG
-recovered pasa_asmbl_49448.p1, internal, 10940, 11121
-recovered pasa_asmbl_49448.p1, internal, 11287, 11427
Valid prediction for snap_scaffold_6-snap.1521-T1
Valid prediction for GlimmerHMM_glimmerT_14859-T1
Couldn't classify 106541, 106623
Couldn't classify 106648, 106844
Sorry, prediction CodingQuarry_transcript_55073-T1 fails validation.
(ATG)	 CG	106320-106336	GT	AGG
(GCG)	 AG	106541-106623	AG	GAA
(GAG)	 GA	106648-106844	AT	AAA
-recovered CodingQuarry_transcript_55073-T1, initial, 106320, 106336
Valid prediction for GlimmerHMM_glimmerT_14862-T1
Valid prediction for GlimmerHMM_glimmerT_14856-T1
Valid prediction for snap_scaffold_6-snap.1484-T1
Valid prediction for snap_scaffold_6-snap.1489-T1
Valid prediction for Augustus_model.g9826.t1
Valid prediction for GlimmerHMM_glimmerT_14858-T1
Valid prediction for GlimmerHMM_glimmerT_14851-T1
Valid prediction for Augustus_model.g9820.t1
Valid prediction for Augustus_model.g9818.t1
Valid prediction for GlimmerHMM_glimmerT_14866-T1
Valid prediction for Augustus_model.g9824.t1
Valid prediction for GlimmerHMM_glimmerT_14833-T1
Valid prediction for Augustus_model.g9821.t1
Valid prediction for snap_scaffold_6-snap.1495-T1
Valid prediction for Augustus_model.g9812.t1
Valid prediction for GlimmerHMM_glimmerT_14846-T1
Valid prediction for snap_scaffold_6-snap.1509-T1
Valid prediction for Augustus_model.g9823.t1
Valid prediction for snap_scaffold_6-snap.1490-T1
Couldn't classify 61732, 61733
Sorry, prediction CodingQuarry_transcript_55074-T1 fails validation.
(ATG)	 CA	61732-61733	GT	ATG
(GGC)	 AG	62286-62429	GT	AGG
(CTC)	 AG	62611-62784	GT	ACG
(GTC)	 AG	62904-63009	GT	AGG
(GAC)	 AG	63089-63242	GT	AGG
(GCC)	 AG	63350-63491	GT	CGG
(GTC)	 AG	63624-63729	AG	AAA
-recovered CodingQuarry_transcript_55074-T1, terminal, 63624, 63729
-recovered CodingQuarry_transcript_55074-T1, internal, 62286, 62429
-recovered CodingQuarry_transcript_55074-T1, internal, 62611, 62784
-recovered CodingQuarry_transcript_55074-T1, internal, 62904, 63009
-recovered CodingQuarry_transcript_55074-T1, internal, 63089, 63242
-recovered CodingQuarry_transcript_55074-T1, internal, 63350, 63491
Valid prediction for GlimmerHMM_glimmerT_14861-T1
Couldn't classify 61732, 61733
Sorry, prediction pasa_asmbl_49326.p1 fails validation.
(ATG)	 CA	61732-61733	GT	ATG
(GGC)	 AG	62286-62429	GT	AGG
(CTC)	 AG	62611-62784	GT	ACG
(GTC)	 AG	62904-63009	GT	AGG
(GAC)	 AG	63089-63242	GT	AGG
(GCC)	 AG	63350-63491	GT	CGG
(GTC)	 AG	63624-63729	AG	AAA
-recovered pasa_asmbl_49326.p1, terminal, 63624, 63729
-recovered pasa_asmbl_49326.p1, internal, 62286, 62429
-recovered pasa_asmbl_49326.p1, internal, 62611, 62784
-recovered pasa_asmbl_49326.p1, internal, 62904, 63009
-recovered pasa_asmbl_49326.p1, internal, 63089, 63242
-recovered pasa_asmbl_49326.p1, internal, 63350, 63491
Valid prediction for Augustus_model.g9822.t1
Valid prediction for snap_scaffold_6-snap.1494-T1
Valid prediction for snap_scaffold_6-snap.1513-T1
Valid prediction for snap_scaffold_6-snap.1505-T1
Valid prediction for GlimmerHMM_glimmerT_14852-T1
Valid prediction for snap_scaffold_6-snap.1522-T1
Valid prediction for GlimmerHMM_glimmerT_14847-T1
Valid prediction for snap_scaffold_6-snap.1493-T1
Valid prediction for snap_scaffold_6-snap.1518-T1
Valid prediction for snap_scaffold_6-snap.1498-T1
Valid prediction for snap_scaffold_6-snap.1519-T1
Valid prediction for snap_scaffold_6-snap.1503-T1
Valid prediction for GlimmerHMM_glimmerT_14865-T1
Valid prediction for GlimmerHMM_glimmerT_14849-T1
Valid prediction for snap_scaffold_6-snap.1482-T1
Valid prediction for GlimmerHMM_glimmerT_14839-T1
Valid prediction for GlimmerHMM_glimmerT_14855-T1
Valid prediction for snap_scaffold_6-snap.1515-T1
Valid prediction for GlimmerHMM_glimmerT_14860-T1
Valid prediction for snap_scaffold_6-snap.1485-T1
Valid prediction for pasa_asmbl_48461.p1
Valid prediction for snap_scaffold_6-snap.1517-T1
Valid prediction for snap_scaffold_6-snap.1523-T1
Valid prediction for GlimmerHMM_glimmerT_14863-T1
Valid prediction for Augustus_model.g9819.t1
Valid prediction for GlimmerHMM_glimmerT_14836-T1
Valid prediction for snap_scaffold_6-snap.1516-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11818, rend_intergenic: 10056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15506, rend_intergenic: 13035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20279, rend_intergenic: 15536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32083, rend_intergenic: 25974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35747, rend_intergenic: 34826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39372, rend_intergenic: 38015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47879, rend_intergenic: 39729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51424, rend_intergenic: 48441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61093, rend_intergenic: 56479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67420, rend_intergenic: 63912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80978, rend_intergenic: 77222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104014, rend_intergenic: 101055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107631, rend_intergenic: 106224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158637, rend_intergenic: 155786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171028, rend_intergenic: 164734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174651
-exon list size: 382


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.9    
3.1    
3.4    
3.6    
3.9    
4.2    
4.4    
4.7    
4.9    
5.2    
5.5    
5.7    
6.0    
6.2    
6.5    
6.8    
7.0    
7.3    
7.6    
7.8    
8.1    
8.3    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.5    
13.8    
14.1    
14.3    
14.6    
14.8    
15.1    
15.4    
15.6    
15.9    
16.1    
16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
18.0    
18.2    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.7    
22.9    
23.2    
23.4    
23.7    
24.0    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.2    
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    
35.2    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.7    
41.9    
42.2    
42.4    
42.7    
43.0    
43.2    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.1    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.9    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.8    
57.0    
57.3    
57.6    
57.8    
58.1    
58.3    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.5    
63.8    
64.1    
64.3    
64.6    
64.8    
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    
68.8    
69.0    
69.3    
69.5    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.8    
82.0    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.6    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.7    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.4    
96.6    
96.9    
97.1    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 11818, rend_intergenic: 10056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15506, rend_intergenic: 13035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20279, rend_intergenic: 15536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32083, rend_intergenic: 25974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35747, rend_intergenic: 34826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39372, rend_intergenic: 38015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47879, rend_intergenic: 39729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51424, rend_intergenic: 48441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61093, rend_intergenic: 56479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67420, rend_intergenic: 63912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80978, rend_intergenic: 77222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104014, rend_intergenic: 101055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107631, rend_intergenic: 106224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158637, rend_intergenic: 155786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171028, rend_intergenic: 164734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support