-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_9762961-9933813

-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 GlimmerHMM_glimmerT_40878-T1
Valid prediction for GlimmerHMM_glimmerT_40874-T1
Valid prediction for snap_scaffold_17-snap.1938-T1
Valid prediction for GlimmerHMM_glimmerT_40873-T1
Valid prediction for GlimmerHMM_glimmerT_40891-T1
Valid prediction for snap_scaffold_17-snap.1942-T1
Valid prediction for snap_scaffold_17-snap.1931-T1
Valid prediction for HiQ_model.g27293.t1
Valid prediction for snap_scaffold_17-snap.1936-T1
Valid prediction for snap_scaffold_17-snap.1956-T1
Valid prediction for snap_scaffold_17-snap.1950-T1
Valid prediction for snap_scaffold_17-snap.1947-T1
Couldn't classify 149929, 150396
Sorry, prediction pasa_asmbl_19127.p1 fails validation.
(GCA)	 AC	149929-150396	GT	AAG
(TCT)	 AG	150747-150896	GT	AGG
(ACT)	 AG	151451-151622	GT	AGG
(ATC)	 AG	152083-152211	GT	GCG
(TGA)	 AG	152371-152516	GT	CGG
(GAG)	 AG	152594-152677	GT	AGG
(GGA)	 AG	153251-153298	TA	AGT
-recovered pasa_asmbl_19127.p1, terminal, 153251, 153298
-recovered pasa_asmbl_19127.p1, internal, 150747, 150896
-recovered pasa_asmbl_19127.p1, internal, 151451, 151622
-recovered pasa_asmbl_19127.p1, internal, 152083, 152211
-recovered pasa_asmbl_19127.p1, internal, 152371, 152516
-recovered pasa_asmbl_19127.p1, internal, 152594, 152677
Valid prediction for snap_scaffold_17-snap.1949-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.1940-T1
Valid prediction for snap_scaffold_17-snap.1941-T1
Valid prediction for snap_scaffold_17-snap.1967-T1
Valid prediction for Augustus_model.g27278.t1
Valid prediction for snap_scaffold_17-snap.1933-T1
Valid prediction for snap_scaffold_17-snap.1968-T1
Valid prediction for GlimmerHMM_glimmerT_40885-T1
Valid prediction for Augustus_model.g27294.t1
Valid prediction for snap_scaffold_17-snap.1952-T1
Valid prediction for Augustus_model.g27283.t1
Valid prediction for snap_scaffold_17-snap.1963-T1
Valid prediction for snap_scaffold_17-snap.1945-T1
Valid prediction for Augustus_model.g27282.t1
Valid prediction for GlimmerHMM_glimmerT_40876-T1
Valid prediction for GlimmerHMM_glimmerT_40890-T1
Valid prediction for snap_scaffold_17-snap.1965-T1
Valid prediction for snap_scaffold_17-snap.1935-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 CodingQuarry_transcript_22144-T1
Valid prediction for Augustus_model.g27279.t1
Valid prediction for CodingQuarry_transcript_22143-T1
Valid prediction for pasa_asmbl_18206.p1
Valid prediction for Augustus_model.g27289.t1
Valid prediction for GlimmerHMM_glimmerT_40877-T1
Valid prediction for GlimmerHMM_glimmerT_40882-T1
Valid prediction for GlimmerHMM_glimmerT_40880-T1
Valid prediction for snap_scaffold_17-snap.1966-T1
Valid prediction for snap_scaffold_17-snap.1951-T1
Valid prediction for snap_scaffold_17-snap.1961-T1
Valid prediction for Augustus_model.g27290.t1
Valid prediction for GlimmerHMM_glimmerT_40884-T1
Valid prediction for snap_scaffold_17-snap.1964-T1
Valid prediction for snap_scaffold_17-snap.1939-T1
Valid prediction for snap_scaffold_17-snap.1934-T1
Valid prediction for CodingQuarry_transcript_22140-T1
Couldn't classify 91919, 92299
Sorry, prediction pasa_asmbl_18204.p1 fails validation.
(TTT)	 TT	91919-92299	GC	GAG
Couldn't classify 51390, 51447
Couldn't classify 53705, 53806
Sorry, prediction pasa_asmbl_18218.p1 fails validation.
(AAG)	 TC	51390-51447	GT	GGG
(ACT)	 AG	52245-52310	GT	TAG
(GTG)	 AG	52402-52476	GT	AGG
(AAA)	 AG	52577-52645	GT	CGG
(GTC)	 AG	53352-53485	GT	TGG
(AGT)	 AG	53705-53806	AA	AGA
-recovered pasa_asmbl_18218.p1, internal, 52245, 52310
-recovered pasa_asmbl_18218.p1, internal, 52402, 52476
-recovered pasa_asmbl_18218.p1, internal, 52577, 52645
-recovered pasa_asmbl_18218.p1, internal, 53352, 53485
Valid prediction for snap_scaffold_17-snap.1954-T1
Valid prediction for GlimmerHMM_glimmerT_40872-T1
Couldn't classify 23741, 23907
Sorry, prediction pasa_asmbl_18219.p1 fails validation.
(ATC)	 CC	23741-23907	GT	AGG
(CCA)	 AG	24131-24276	GT	TGG
(GAA)	 AG	24446-24635	GT	AGG
(CTA)	 AG	25028-25173	GT	AGG
(GTA)	 AG	25443-25632	GT	ACG
(GTA)	 AG	26009-26154	GT	TGG
(ATG)	 AG	26346-26509	GT	AGG
(TTC)	 AG	26664-26843	GG	GAG
add_exon() Sorry, pasa_asmbl_18219.p1 26346-26509-initial-1 is invalid.
-recovered pasa_asmbl_18219.p1, initial, 26346, 26509
-recovered pasa_asmbl_18219.p1, terminal, 26664, 26843
-recovered pasa_asmbl_18219.p1, internal, 24131, 24276
-recovered pasa_asmbl_18219.p1, internal, 24446, 24635
-recovered pasa_asmbl_18219.p1, internal, 25028, 25173
-recovered pasa_asmbl_18219.p1, internal, 25443, 25632
-recovered pasa_asmbl_18219.p1, internal, 26009, 26154
-recovered pasa_asmbl_18219.p1, internal, 26346, 26509
Valid prediction for CodingQuarry_transcript_22145-T1
Valid prediction for GlimmerHMM_glimmerT_40888-T1
Valid prediction for CodingQuarry_transcript_22138-T1
Valid prediction for Augustus_model.g27281.t1
Couldn't classify 64899, 65012
Sorry, prediction pasa_asmbl_18213.p2 fails validation.
(CAC)	 AT	64899-65012	GT	AGG
(GTG)	 AG	65137-65194	GT	GGG
(CAC)	 AG	65289-65585	GT	CGG
(GTC)	 AG	65675-65967	AA	GAA
-recovered pasa_asmbl_18213.p2, terminal, 65675, 65967
-recovered pasa_asmbl_18213.p2, internal, 65137, 65194
-recovered pasa_asmbl_18213.p2, internal, 65289, 65585
Valid prediction for GlimmerHMM_glimmerT_40879-T1
Valid prediction for GlimmerHMM_glimmerT_40886-T1
Valid prediction for GlimmerHMM_glimmerT_40889-T1
Valid prediction for snap_scaffold_17-snap.1960-T1
Valid prediction for snap_scaffold_17-snap.1937-T1
Valid prediction for GlimmerHMM_glimmerT_40875-T1
Valid prediction for pasa_asmbl_18466.p1
Valid prediction for GlimmerHMM_glimmerT_40883-T1
Valid prediction for pasa_asmbl_18207.p1
Valid prediction for Augustus_model.g27291.t1
Valid prediction for CodingQuarry_transcript_22142-T1
Valid prediction for snap_scaffold_17-snap.1948-T1
Valid prediction for snap_scaffold_17-snap.1957-T1
Valid prediction for pasa_asmbl_18210.p1
Valid prediction for Augustus_model.g27292.t1
Valid prediction for snap_scaffold_17-snap.1932-T1
Valid prediction for snap_scaffold_17-snap.1955-T1
Valid prediction for GlimmerHMM_glimmerT_40881-T1
Valid prediction for snap_scaffold_17-snap.1958-T1
Valid prediction for Augustus_model.g27288.t1
Valid prediction for snap_scaffold_17-snap.1969-T1
Valid prediction for snap_scaffold_17-snap.1959-T1
Valid prediction for HiQ_model.g27286.t1
Valid prediction for Augustus_model.g27295.t1
Valid prediction for snap_scaffold_17-snap.1953-T1
Valid prediction for HiQ_model.g27284.t1
Valid prediction for Augustus_model.g27285.t1
Valid prediction for GlimmerHMM_glimmerT_40887-T1
Valid prediction for snap_scaffold_17-snap.1946-T1
Valid prediction for snap_scaffold_17-snap.1943-T1
Valid prediction for CodingQuarry_transcript_22139-T1
Valid prediction for snap_scaffold_17-snap.1962-T1
Valid prediction for HiQ_model.g27287.t1
Valid prediction for snap_scaffold_17-snap.1944-T1
Valid prediction for Augustus_model.g27280.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12284, rend_intergenic: 8529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16988, rend_intergenic: 15226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22510, rend_intergenic: 17836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24680, rend_intergenic: 22570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37707, rend_intergenic: 27170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48294, rend_intergenic: 39237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66793, rend_intergenic: 64695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73572, rend_intergenic: 66986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74758, rend_intergenic: 73681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79572, rend_intergenic: 76211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97054, rend_intergenic: 94239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153298, rend_intergenic: 150123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155100, rend_intergenic: 153962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158528, rend_intergenic: 157539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166488, rend_intergenic: 158571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170853
-exon list size: 380


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.7    
5.0    
5.2    
5.5    
5.8    
6.0    
6.3    
6.5    
6.8    
7.1    
7.3    
7.6    
7.9    
8.1    
8.4    
8.6    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.5    
11.8    
12.0    
12.3    
12.6    
12.8    
13.1    
13.4    
13.6    
13.9    
14.1    
14.4    
14.7    
14.9    
15.2    
15.4    
15.7    
16.0    
16.2    
16.5    
16.8    
17.0    
17.3    
17.5    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
21.5    
21.7    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.6    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
27.0    
27.2    
27.5    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.4    
31.7    
31.9    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.9    
47.1    
47.4    
47.6    
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    
52.4    
52.6    
52.9    
53.1    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.1    
64.4    
64.7    
64.9    
65.2    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.1    
68.3    
68.6    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.4    
70.7    
70.9    
71.2    
71.5    
71.7    
72.0    
72.3    
72.5    
72.8    
73.0    
73.3    
73.6    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.4    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.3    
78.5    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.7    
94.0    
94.2    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 12284, rend_intergenic: 8529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16988, rend_intergenic: 15226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22510, rend_intergenic: 17836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24680, rend_intergenic: 22570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37707, rend_intergenic: 27170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48294, rend_intergenic: 39237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66793, rend_intergenic: 64695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73572, rend_intergenic: 66986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74758, rend_intergenic: 73681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79572, rend_intergenic: 76211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97054, rend_intergenic: 94239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153298, rend_intergenic: 150123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155100, rend_intergenic: 153962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158528, rend_intergenic: 157539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166488, rend_intergenic: 158571  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