-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_2876727-3154453

-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 Augustus_model.g7597.t1
Valid prediction for GlimmerHMM_glimmerT_11628-T1
Valid prediction for snap_scaffold_5-snap.587-T1
Valid prediction for GlimmerHMM_glimmerT_11641-T1
Valid prediction for GlimmerHMM_glimmerT_11642-T1
Valid prediction for snap_scaffold_5-snap.578-T1
Valid prediction for snap_scaffold_5-snap.582-T1
Valid prediction for Augustus_model.g7590.t1
Valid prediction for GlimmerHMM_glimmerT_11631-T1
Valid prediction for snap_scaffold_5-snap.602-T1
Couldn't classify 222958, 223084
Sorry, prediction pasa_asmbl_45211.p2 fails validation.
(CTT)	 CT	222958-223084	GT	TCG
(GTG)	 AG	223417-223578	GT	AGG
(GTT)	 AG	224141-224272	GT	AGG
(TGA)	 AG	225730-225799	GT	AGG
(GAT)	 AG	226229-226253	AA	AGA
-recovered pasa_asmbl_45211.p2, terminal, 226229, 226253
-recovered pasa_asmbl_45211.p2, internal, 223417, 223578
-recovered pasa_asmbl_45211.p2, internal, 224141, 224272
-recovered pasa_asmbl_45211.p2, internal, 225730, 225799
Valid prediction for snap_scaffold_5-snap.586-T1
Valid prediction for GlimmerHMM_glimmerT_11649-T1
Valid prediction for GlimmerHMM_glimmerT_11633-T1
Valid prediction for Augustus_model.g7593.t1
Valid prediction for Augustus_model.g7592.t1
Valid prediction for snap_scaffold_5-snap.569-T1
Valid prediction for GlimmerHMM_glimmerT_11623-T1
Valid prediction for GlimmerHMM_glimmerT_11644-T1
Couldn't classify 211967, 212015
Couldn't classify 216625, 216746
Sorry, prediction pasa_asmbl_45208.p1 fails validation.
(AAG)	 GC	211967-212015	GT	AGG
(CGC)	 AG	212286-212356	GT	AGG
(CCC)	 AG	213554-213776	GT	TGG
(TGC)	 AG	214968-215083	GT	ACG
(GTT)	 AG	216126-216330	GT	AGG
(CTC)	 AG	216625-216746	GG	CCG
-recovered pasa_asmbl_45208.p1, internal, 212286, 212356
-recovered pasa_asmbl_45208.p1, internal, 213554, 213776
-recovered pasa_asmbl_45208.p1, internal, 214968, 215083
-recovered pasa_asmbl_45208.p1, internal, 216126, 216330
Couldn't classify 18280, 18428
Couldn't classify 19995, 20520
Sorry, prediction pasa_asmbl_45201.p1 fails validation.
(AGC)	 CC	18280-18428	GT	AGG
(GCG)	 AG	19995-20520	GG	CCG
Valid prediction for GlimmerHMM_glimmerT_11640-T1
Couldn't classify 109473, 109521
Couldn't classify 110989, 111023
Sorry, prediction pasa_asmbl_46451.p1 fails validation.
(AAG)	 CA	109473-109521	GT	AAG
(TTG)	 AG	109790-109947	GT	AGG
(TCT)	 AG	110304-110499	GT	AGG
(GGG)	 AG	110989-111023	GT	AGG
-recovered pasa_asmbl_46451.p1, internal, 109790, 109947
-recovered pasa_asmbl_46451.p1, internal, 110304, 110499
-recovered pasa_asmbl_46451.p1, internal, 110989, 111023
Valid prediction for snap_scaffold_5-snap.588-T1
Valid prediction for snap_scaffold_5-snap.576-T1
Valid prediction for snap_scaffold_5-snap.567-T1
Couldn't classify 39339, 39875
Sorry, prediction pasa_asmbl_46373.p1 fails validation.
(ATC)	 GC	39339-39875	CA	CCC
Valid prediction for Augustus_model.g7591.t1
Valid prediction for snap_scaffold_5-snap.581-T1
Valid prediction for snap_scaffold_5-snap.603-T1
Valid prediction for Augustus_model.g7595.t1
Valid prediction for GlimmerHMM_glimmerT_11632-T1
Valid prediction for GlimmerHMM_glimmerT_11645-T1
Valid prediction for snap_scaffold_5-snap.605-T1
Valid prediction for GlimmerHMM_glimmerT_11637-T1
Valid prediction for Augustus_model.g7604.t1
Valid prediction for GlimmerHMM_glimmerT_11625-T1
Valid prediction for snap_scaffold_5-snap.563-T1
Couldn't classify 37789, 38106
Sorry, prediction pasa_asmbl_45203.p2 fails validation.
(TTC)	 CA	37789-38106	TC	CCT
Couldn't classify 207602, 207677
Couldn't classify 209155, 209287
Sorry, prediction pasa_asmbl_45207.p1 fails validation.
(GTC)	 AC	207602-207677	GT	TGG
(ATG)	 AG	208037-208177	GT	GAG
(ACA)	 AG	208661-208772	GT	TGG
(GAG)	 AG	209155-209287	GG	AGG
add_exon() Sorry, pasa_asmbl_45207.p1 208037-208177-initial-1 is invalid.
-recovered pasa_asmbl_45207.p1, initial, 208037, 208177
add_exon() Sorry, pasa_asmbl_45207.p1 208037-208177-terminal-1 is invalid.
-recovered pasa_asmbl_45207.p1, terminal, 208037, 208177
-recovered pasa_asmbl_45207.p1, internal, 208037, 208177
-recovered pasa_asmbl_45207.p1, internal, 208661, 208772
Valid prediction for GlimmerHMM_glimmerT_11646-T1
Valid prediction for Augustus_model.g7603.t1
Valid prediction for snap_scaffold_5-snap.601-T1
Valid prediction for snap_scaffold_5-snap.566-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 pasa_asmbl_43906.p1
Valid prediction for snap_scaffold_5-snap.607-T1
Valid prediction for Augustus_model.g7594.t1
Valid prediction for snap_scaffold_5-snap.596-T1
Valid prediction for GlimmerHMM_glimmerT_11647-T1
Valid prediction for GlimmerHMM_glimmerT_11639-T1
Valid prediction for snap_scaffold_5-snap.595-T1
Valid prediction for snap_scaffold_5-snap.575-T1
Valid prediction for GlimmerHMM_glimmerT_11629-T1
Valid prediction for snap_scaffold_5-snap.585-T1
Couldn't classify 216702, 216775
Couldn't classify 217820, 218318
Sorry, prediction pasa_asmbl_43903.p1 fails validation.
(CGC)	 AC	216702-216775	GT	AGG
(GAG)	 AG	217820-218318	GA	TGG
Valid prediction for GlimmerHMM_glimmerT_11624-T1
Valid prediction for GlimmerHMM_glimmerT_11643-T1
Valid prediction for snap_scaffold_5-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_11630-T1
Valid prediction for GlimmerHMM_glimmerT_11626-T1
Valid prediction for snap_scaffold_5-snap.564-T1
Valid prediction for Augustus_model.g7599.t1
Valid prediction for snap_scaffold_5-snap.589-T1
Valid prediction for GlimmerHMM_glimmerT_11634-T1
Valid prediction for Augustus_model.g7602.t1
Valid prediction for HiQ_model.g7600.t1
Valid prediction for CodingQuarry_transcript_51999-T1
Valid prediction for snap_scaffold_5-snap.580-T1
Valid prediction for GlimmerHMM_glimmerT_11636-T1
Valid prediction for Augustus_model.g7598.t1
Valid prediction for snap_scaffold_5-snap.599-T1
Valid prediction for CodingQuarry_transcript_52000-T1
Valid prediction for snap_scaffold_5-snap.600-T1
Valid prediction for snap_scaffold_5-snap.598-T1
Valid prediction for snap_scaffold_5-snap.568-T1
Valid prediction for snap_scaffold_5-snap.590-T1
Valid prediction for snap_scaffold_5-snap.604-T1
Valid prediction for snap_scaffold_5-snap.597-T1
Valid prediction for GlimmerHMM_glimmerT_11627-T1
Valid prediction for GlimmerHMM_glimmerT_11638-T1
Valid prediction for snap_scaffold_5-snap.592-T1
Valid prediction for snap_scaffold_5-snap.594-T1
Valid prediction for snap_scaffold_5-snap.579-T1
Valid prediction for pasa_asmbl_43907.p1
Valid prediction for GlimmerHMM_glimmerT_11635-T1
Valid prediction for snap_scaffold_5-snap.572-T1
Valid prediction for snap_scaffold_5-snap.565-T1
Valid prediction for snap_scaffold_5-snap.606-T1
Valid prediction for snap_scaffold_5-snap.577-T1
Valid prediction for snap_scaffold_5-snap.571-T1
Valid prediction for HiQ_model.g7601.t1
Valid prediction for Augustus_model.g7596.t1
Valid prediction for snap_scaffold_5-snap.591-T1
Valid prediction for GlimmerHMM_glimmerT_11648-T1
Valid prediction for snap_scaffold_5-snap.584-T1
Valid prediction for snap_scaffold_5-snap.593-T1
Valid prediction for snap_scaffold_5-snap.570-T1
Valid prediction for snap_scaffold_5-snap.574-T1
Valid prediction for snap_scaffold_5-snap.573-T1
Sorry, intron length (9) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12058, rend_intergenic: 5504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15289, rend_intergenic: 12113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23305, rend_intergenic: 20742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23795, rend_intergenic: 23321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40395, rend_intergenic: 24796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72352, rend_intergenic: 67434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75520, rend_intergenic: 72543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94715, rend_intergenic: 88304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218791, rend_intergenic: 214964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229055, rend_intergenic: 221412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 277727
-exon list size: 411


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
1.9    
2.2    
2.4    
2.7    
2.9    
3.1    
3.4    
3.6    
3.9    
4.1    
4.4    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
6.1    
6.3    
6.5    
6.8    
7.0    
7.3    
7.5    
7.7    
8.0    
8.2    
8.5    
8.7    
9.0    
9.2    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
10.9    
11.1    
11.4    
11.6    
11.9    
12.1    
12.3    
12.6    
12.8    
13.1    
13.3    
13.6    
13.8    
14.0    
14.3    
14.5    
14.8    
15.0    
15.3    
15.5    
15.7    
16.0    
16.2    
16.5    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.2    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.8    
36.1    
36.3    
36.6    
36.8    
37.0    
37.3    
37.5    
37.8    
38.0    
38.3    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.7    
62.0    
62.2    
62.5    
62.7    
63.0    
63.2    
63.4    
63.7    
63.9    
64.2    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.8    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.3    
84.5    
84.7    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.4    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.7    
93.0    
93.2    
93.5    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 12058, rend_intergenic: 5504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15289, rend_intergenic: 12113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23305, rend_intergenic: 20742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23795, rend_intergenic: 23321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40395, rend_intergenic: 24796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72352, rend_intergenic: 67434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75520, rend_intergenic: 72543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94715, rend_intergenic: 88304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218791, rend_intergenic: 214964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229055, rend_intergenic: 221412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support