-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_7543133-7709053

-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_12-snap.1394-T1
Valid prediction for snap_scaffold_12-snap.1406-T1
Valid prediction for snap_scaffold_12-snap.1401-T1
Valid prediction for Augustus_model.g19537.t1
Valid prediction for snap_scaffold_12-snap.1408-T1
Valid prediction for GlimmerHMM_glimmerT_29607-T1
Valid prediction for CodingQuarry_transcript_10299-T1
Couldn't classify 72820, 73164
Sorry, prediction pasa_asmbl_8602.p1 fails validation.
(GCT)	 GA	72820-73164	AC	GAA
Valid prediction for GlimmerHMM_glimmerT_29586-T1
Valid prediction for Augustus_model.g19549.t1
Valid prediction for CodingQuarry_transcript_10303-T1
Valid prediction for HiQ_model.g19534.t1
Valid prediction for snap_scaffold_12-snap.1395-T1
Valid prediction for Augustus_model.g19547.t1
Valid prediction for Augustus_model.g19550.t1
Valid prediction for GlimmerHMM_glimmerT_29594-T1
Valid prediction for pasa_asmbl_7771.p1
Valid prediction for snap_scaffold_12-snap.1399-T1
Valid prediction for snap_scaffold_12-snap.1416-T1
Valid prediction for GlimmerHMM_glimmerT_29605-T1
Valid prediction for snap_scaffold_12-snap.1393-T1
Valid prediction for GlimmerHMM_glimmerT_29598-T1
Valid prediction for GlimmerHMM_glimmerT_29608-T1
Valid prediction for GlimmerHMM_glimmerT_29597-T1
Valid prediction for snap_scaffold_12-snap.1391-T1
Valid prediction for snap_scaffold_12-snap.1396-T1
Valid prediction for Augustus_model.g19532.t1
Valid prediction for Augustus_model.g19546.t1
Valid prediction for GlimmerHMM_glimmerT_29585-T1
Valid prediction for Augustus_model.g19544.t1
Valid prediction for HiQ_model.g19540.t1
Valid prediction for Augustus_model.g19530.t1
Valid prediction for snap_scaffold_12-snap.1411-T1
Valid prediction for pasa_asmbl_7783.p1
Valid prediction for GlimmerHMM_glimmerT_29591-T1
Valid prediction for GlimmerHMM_glimmerT_29600-T1
Valid prediction for GlimmerHMM_glimmerT_29604-T1
Valid prediction for CodingQuarry_transcript_10295-T1
Valid prediction for CodingQuarry_transcript_10302-T1
Valid prediction for snap_scaffold_12-snap.1413-T1
Valid prediction for CodingQuarry_transcript_10294-T1
Valid prediction for Augustus_model.g19541.t1
Valid prediction for snap_scaffold_12-snap.1405-T1
Valid prediction for Augustus_model.g19528.t1
Couldn't classify 132422, 132556
Couldn't classify 133983, 134359
Sorry, prediction pasa_asmbl_7789.p1 fails validation.
(CAT)	 GT	132422-132556	GT	ACG
(GGC)	 AG	133418-133453	GT	CAG
(ACT)	 AG	133547-133651	GT	ATG
(GAG)	 AG	133765-133882	GT	AGG
(ACT)	 AG	133983-134359	GG	GGG
-recovered pasa_asmbl_7789.p1, internal, 133418, 133453
-recovered pasa_asmbl_7789.p1, internal, 133547, 133651
-recovered pasa_asmbl_7789.p1, internal, 133765, 133882
Valid prediction for GlimmerHMM_glimmerT_29601-T1
Valid prediction for snap_scaffold_12-snap.1422-T1
Valid prediction for GlimmerHMM_glimmerT_29609-T1
Valid prediction for snap_scaffold_12-snap.1417-T1
Couldn't classify 55207, 55312
Sorry, prediction pasa_asmbl_7769.p1 fails validation.
(GGG)	 CC	55207-55312	GT	AGG
(TCT)	 AG	55730-55906	GT	CGG
(GTA)	 AG	56007-56100	GT	AGG
(TCC)	 AG	56335-56408	GT	GGG
(GGT)	 AG	56634-56783	GT	TGG
(GCT)	 AG	56977-57279	GT	TGG
(GAT)	 AG	57392-57765	CA	GAC
-recovered pasa_asmbl_7769.p1, terminal, 57392, 57765
-recovered pasa_asmbl_7769.p1, internal, 55730, 55906
-recovered pasa_asmbl_7769.p1, internal, 56007, 56100
-recovered pasa_asmbl_7769.p1, internal, 56335, 56408
-recovered pasa_asmbl_7769.p1, internal, 56634, 56783
-recovered pasa_asmbl_7769.p1, internal, 56977, 57279
Couldn't classify 109182, 109542
Couldn't classify 112394, 112479
Sorry, prediction pasa_asmbl_7780.p2 fails validation.
(GTT)	 CA	109182-109542	GT	TGG
(TGG)	 AG	112394-112479	GA	AAG
Valid prediction for HiQ_model.g19531.t1
Valid prediction for GlimmerHMM_glimmerT_29593-T1
Valid prediction for pasa_asmbl_7773.p1
Valid prediction for snap_scaffold_12-snap.1412-T1
Valid prediction for CodingQuarry_transcript_10304-T1
Couldn't classify 54889, 54946
Sorry, prediction pasa_asmbl_7768.p1 fails validation.
(ATG)	 CA	53778-53939	GT	TGG
(GAG)	 AG	54295-54427	GT	AGG
(ATA)	 AG	54555-54711	GT	AGG
(GCT)	 AG	54889-54946	TT	TGT
-recovered pasa_asmbl_7768.p1, initial, 53778, 53939
add_exon() Sorry, pasa_asmbl_7768.p1 54295-54427-terminal-3 is invalid.
-recovered pasa_asmbl_7768.p1, terminal, 54295, 54427
-recovered pasa_asmbl_7768.p1, internal, 54295, 54427
-recovered pasa_asmbl_7768.p1, internal, 54555, 54711
Valid prediction for Augustus_model.g19535.t1
Valid prediction for snap_scaffold_12-snap.1400-T1
Valid prediction for snap_scaffold_12-snap.1410-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g19539.t1
Valid prediction for CodingQuarry_transcript_10306-T1
Valid prediction for Augustus_model.g19542.t1
Valid prediction for pasa_asmbl_7776.p1
Valid prediction for CodingQuarry_transcript_10296-T1
Valid prediction for snap_scaffold_12-snap.1403-T1
Valid prediction for snap_scaffold_12-snap.1419-T1
Valid prediction for GlimmerHMM_glimmerT_29589-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_29592-T1
Valid prediction for snap_scaffold_12-snap.1418-T1
Valid prediction for HiQ_model.g19536.t1
Valid prediction for snap_scaffold_12-snap.1407-T1
Valid prediction for snap_scaffold_12-snap.1397-T1
Valid prediction for GlimmerHMM_glimmerT_29588-T1
Valid prediction for GlimmerHMM_glimmerT_29590-T1
Valid prediction for pasa_asmbl_8599.p1
Valid prediction for CodingQuarry_transcript_10293-T1
Valid prediction for Augustus_model.g19527.t1
Valid prediction for snap_scaffold_12-snap.1404-T1
Valid prediction for snap_scaffold_12-snap.1402-T1
Valid prediction for CodingQuarry_transcript_10297-T1
Valid prediction for GlimmerHMM_glimmerT_29599-T1
Valid prediction for Augustus_model.g19545.t1
Valid prediction for pasa_asmbl_8614.p1
Valid prediction for snap_scaffold_12-snap.1390-T1
Valid prediction for snap_scaffold_12-snap.1392-T1
Valid prediction for snap_scaffold_12-snap.1409-T1
Valid prediction for GlimmerHMM_glimmerT_29584-T1
Valid prediction for snap_scaffold_12-snap.1414-T1
Valid prediction for HiQ_model.g19538.t1
Valid prediction for GlimmerHMM_glimmerT_29603-T1
Valid prediction for CodingQuarry_transcript_10298-T1
Valid prediction for Augustus_model.g19543.t1
Valid prediction for CodingQuarry_transcript_10301-T1
Valid prediction for snap_scaffold_12-snap.1415-T1
Valid prediction for GlimmerHMM_glimmerT_29596-T1
Valid prediction for HiQ_model.g19529.t1
Valid prediction for Augustus_model.g19533.t1
Valid prediction for Augustus_model.g19548.t1
Valid prediction for snap_scaffold_12-snap.1420-T1
Valid prediction for GlimmerHMM_glimmerT_29602-T1
Valid prediction for pasa_asmbl_8610.p1
Valid prediction for snap_scaffold_12-snap.1398-T1
Valid prediction for CodingQuarry_transcript_10300-T1
Valid prediction for snap_scaffold_12-snap.1421-T1
Valid prediction for Augustus_model.g19526.t1
Valid prediction for GlimmerHMM_glimmerT_29587-T1
Valid prediction for GlimmerHMM_glimmerT_29606-T1
Valid prediction for GlimmerHMM_glimmerT_29595-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7385, rend_intergenic: 2009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14710, rend_intergenic: 8267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34494, rend_intergenic: 16976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68750, rend_intergenic: 64077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72022, rend_intergenic: 69284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99246, rend_intergenic: 92805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142756, rend_intergenic: 137099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151534, rend_intergenic: 146236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161331, rend_intergenic: 155534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 165921
-exon list size: 373


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.7    
6.9    
7.2    
7.5    
7.7    
8.0    
8.3    
8.5    
8.8    
9.1    
9.3    
9.6    
9.9    
10.1    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.3    
13.6    
13.9    
14.1    
14.4    
14.7    
14.9    
15.2    
15.5    
15.7    
16.0    
16.3    
16.5    
16.8    
17.1    
17.3    
17.6    
17.9    
18.1    
18.4    
18.7    
18.9    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.1    
21.3    
21.6    
21.9    
22.1    
22.4    
22.7    
22.9    
23.2    
23.5    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.1    
26.4    
26.7    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.1    
30.4    
30.7    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
34.9    
35.2    
35.5    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.7    
38.9    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.1    
41.3    
41.6    
41.9    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.7    
44.0    
44.3    
44.5    
44.8    
45.1    
45.3    
45.6    
45.9    
46.1    
46.4    
46.7    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.3    
53.6    
53.9    
54.1    
54.4    
54.7    
54.9    
55.2    
55.5    
55.7    
56.0    
56.3    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.1    
58.4    
58.7    
58.9    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.1    
61.3    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.5    
63.7    
64.0    
64.3    
64.5    
64.8    
65.1    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.3    
68.5    
68.8    
69.1    
69.3    
69.6    
69.9    
70.1    
70.4    
70.7    
70.9    
71.2    
71.5    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.1    
77.3    
77.6    
77.9    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.1    
81.3    
81.6    
81.9    
82.1    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.5    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.7    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
90.9    
91.2    
91.5    
91.7    
92.0    
92.3    
92.5    
92.8    
93.1    
93.3    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 7385, rend_intergenic: 2009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14710, rend_intergenic: 8267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34494, rend_intergenic: 16976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68750, rend_intergenic: 64077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72022, rend_intergenic: 69284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99246, rend_intergenic: 92805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142756, rend_intergenic: 137099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151534, rend_intergenic: 146236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161331, rend_intergenic: 155534  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