-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_9092124-9303597

-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_18-snap.1946-T1
Valid prediction for snap_scaffold_18-snap.1959-T1
Valid prediction for GlimmerHMM_glimmerT_42870-T1
Valid prediction for CodingQuarry_transcript_23866-T1
Valid prediction for snap_scaffold_18-snap.1942-T1
Valid prediction for GlimmerHMM_glimmerT_42881-T1
Valid prediction for snap_scaffold_18-snap.1940-T1
Valid prediction for snap_scaffold_18-snap.1925-T1
Valid prediction for CodingQuarry_transcript_23868-T1
Valid prediction for CodingQuarry_transcript_23867-T1
Valid prediction for GlimmerHMM_glimmerT_42884-T1
Valid prediction for pasa_asmbl_20875.p1
Valid prediction for GlimmerHMM_glimmerT_42886-T1
Valid prediction for GlimmerHMM_glimmerT_42889-T1
Valid prediction for GlimmerHMM_glimmerT_42873-T1
Valid prediction for snap_scaffold_18-snap.1929-T1
Valid prediction for snap_scaffold_18-snap.1958-T1
Valid prediction for GlimmerHMM_glimmerT_42892-T1
Valid prediction for snap_scaffold_18-snap.1931-T1
Valid prediction for snap_scaffold_18-snap.1941-T1
Valid prediction for snap_scaffold_18-snap.1928-T1
Valid prediction for snap_scaffold_18-snap.1936-T1
Valid prediction for Augustus_model.g28593.t1
Valid prediction for Augustus_model.g28598.t1
Valid prediction for Augustus_model.g28587.t1
Valid prediction for snap_scaffold_18-snap.1947-T1
Valid prediction for snap_scaffold_18-snap.1926-T1
Valid prediction for HiQ_model.g28592.t1
Valid prediction for snap_scaffold_18-snap.1945-T1
Valid prediction for GlimmerHMM_glimmerT_42875-T1
Valid prediction for Augustus_model.g28597.t1
Valid prediction for snap_scaffold_18-snap.1961-T1
Valid prediction for snap_scaffold_18-snap.1956-T1
Valid prediction for snap_scaffold_18-snap.1922-T1
Valid prediction for snap_scaffold_18-snap.1962-T1
Valid prediction for snap_scaffold_18-snap.1933-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.1923-T1
Valid prediction for snap_scaffold_18-snap.1953-T1
Valid prediction for pasa_asmbl_20881.p1
Valid prediction for snap_scaffold_18-snap.1954-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_42879-T1
Valid prediction for snap_scaffold_18-snap.1937-T1
Valid prediction for snap_scaffold_18-snap.1932-T1
Valid prediction for GlimmerHMM_glimmerT_42883-T1
Valid prediction for GlimmerHMM_glimmerT_42872-T1
Valid prediction for GlimmerHMM_glimmerT_42874-T1
Valid prediction for Augustus_model.g28595.t1
Valid prediction for GlimmerHMM_glimmerT_42867-T1
Valid prediction for snap_scaffold_18-snap.1951-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_18-snap.1950-T1
Valid prediction for GlimmerHMM_glimmerT_42891-T1
Valid prediction for snap_scaffold_18-snap.1938-T1
Valid prediction for snap_scaffold_18-snap.1957-T1
Valid prediction for Augustus_model.g28599.t1
Valid prediction for Augustus_model.g28588.t1
Valid prediction for GlimmerHMM_glimmerT_42878-T1
Valid prediction for GlimmerHMM_glimmerT_42887-T1
Couldn't classify 184492, 184536
Sorry, prediction pasa_asmbl_20055.p1 fails validation.
(TCG)	 CA	184492-184536	GT	TGG
(AAG)	 AG	185103-185251	GT	GAG
(GCA)	 AG	187217-187301	GT	TGG
(ATG)	 AG	190299-190454	GA	GAG
add_exon() Sorry, pasa_asmbl_20055.p1 185103-185251-terminal-2 is invalid.
-recovered pasa_asmbl_20055.p1, terminal, 185103, 185251
-recovered pasa_asmbl_20055.p1, terminal, 190299, 190454
-recovered pasa_asmbl_20055.p1, internal, 185103, 185251
-recovered pasa_asmbl_20055.p1, internal, 187217, 187301
Valid prediction for snap_scaffold_18-snap.1924-T1
Valid prediction for snap_scaffold_18-snap.1939-T1
Valid prediction for snap_scaffold_18-snap.1960-T1
Valid prediction for Augustus_model.g28586.t1
Valid prediction for GlimmerHMM_glimmerT_42888-T1
Couldn't classify 111373, 111516
Sorry, prediction pasa_asmbl_20057.p1 fails validation.
(ATG)	 CT	110636-110950	GT	AGG
(GTG)	 AG	111373-111516	AT	GCA
-recovered pasa_asmbl_20057.p1, initial, 110636, 110950
Valid prediction for snap_scaffold_18-snap.1952-T1
Valid prediction for GlimmerHMM_glimmerT_42871-T1
Valid prediction for pasa_asmbl_20059.p1
Valid prediction for snap_scaffold_18-snap.1943-T1
Valid prediction for snap_scaffold_18-snap.1948-T1
Valid prediction for GlimmerHMM_glimmerT_42877-T1
Valid prediction for Augustus_model.g28589.t1
Valid prediction for GlimmerHMM_glimmerT_42869-T1
Valid prediction for Augustus_model.g28600.t1
Valid prediction for snap_scaffold_18-snap.1963-T1
Valid prediction for GlimmerHMM_glimmerT_42882-T1
Valid prediction for Augustus_model.g28594.t1
Valid prediction for snap_scaffold_18-snap.1944-T1
Valid prediction for Augustus_model.g28591.t1
Valid prediction for CodingQuarry_transcript_23870-T1
Valid prediction for GlimmerHMM_glimmerT_42893-T1
Valid prediction for CodingQuarry_transcript_23869-T1
Valid prediction for snap_scaffold_18-snap.1934-T1
Valid prediction for snap_scaffold_18-snap.1955-T1
Couldn't classify 116550, 117026
Sorry, prediction pasa_asmbl_20056.p1 fails validation.
(ATC)	 TC	116550-117026	AC	AGA
Valid prediction for GlimmerHMM_glimmerT_42885-T1
Valid prediction for GlimmerHMM_glimmerT_42880-T1
Valid prediction for GlimmerHMM_glimmerT_42890-T1
Valid prediction for snap_scaffold_18-snap.1930-T1
Valid prediction for Augustus_model.g28590.t1
Valid prediction for Augustus_model.g28596.t1
Valid prediction for snap_scaffold_18-snap.1949-T1
Valid prediction for CodingQuarry_transcript_23871-T1
Valid prediction for snap_scaffold_18-snap.1927-T1
Valid prediction for GlimmerHMM_glimmerT_42868-T1
Valid prediction for snap_scaffold_18-snap.1935-T1
Valid prediction for GlimmerHMM_glimmerT_42876-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15487, rend_intergenic: 12051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31405, rend_intergenic: 16147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51529, rend_intergenic: 34796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67744, rend_intergenic: 51921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84227, rend_intergenic: 75790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85805, rend_intergenic: 84449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98158, rend_intergenic: 85823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118560, rend_intergenic: 109588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163111, rend_intergenic: 145793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168717, rend_intergenic: 164029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193791, rend_intergenic: 187611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202102, rend_intergenic: 201828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211474
-exon list size: 376


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.6    
2.9    
3.2    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.0    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.5    
9.8    
10.1    
10.3    
10.6    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.4    
12.7    
13.0    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.8    
15.1    
15.3    
15.6    
15.9    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.2    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
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    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
45.0    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.8    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.0    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
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    
69.0    
69.3    
69.6    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.8    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 15487, rend_intergenic: 12051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31405, rend_intergenic: 16147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51529, rend_intergenic: 34796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67744, rend_intergenic: 51921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84227, rend_intergenic: 75790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85805, rend_intergenic: 84449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98158, rend_intergenic: 85823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118560, rend_intergenic: 109588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163111, rend_intergenic: 145793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168717, rend_intergenic: 164029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193791, rend_intergenic: 187611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202102, rend_intergenic: 201828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support