-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_19271722-19446192

-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_3-snap.3807-T1
Valid prediction for snap_scaffold_3-snap.3815-T1
Valid prediction for Augustus_model.g5579.t1
Valid prediction for snap_scaffold_3-snap.3810-T1
Valid prediction for GlimmerHMM_glimmerT_8488-T1
Valid prediction for snap_scaffold_3-snap.3816-T1
Valid prediction for GlimmerHMM_glimmerT_8484-T1
Valid prediction for GlimmerHMM_glimmerT_8498-T1
Valid prediction for Augustus_model.g5572.t1
Valid prediction for GlimmerHMM_glimmerT_8487-T1
Valid prediction for GlimmerHMM_glimmerT_8503-T1
Valid prediction for snap_scaffold_3-snap.3824-T1
Valid prediction for snap_scaffold_3-snap.3813-T1
Valid prediction for Augustus_model.g5577.t1
Valid prediction for snap_scaffold_3-snap.3831-T1
Valid prediction for snap_scaffold_3-snap.3830-T1
Valid prediction for Augustus_model.g5576.t1
Valid prediction for snap_scaffold_3-snap.3819-T1
Valid prediction for snap_scaffold_3-snap.3821-T1
Valid prediction for GlimmerHMM_glimmerT_8482-T1
Valid prediction for GlimmerHMM_glimmerT_8502-T1
Valid prediction for snap_scaffold_3-snap.3822-T1
Valid prediction for snap_scaffold_3-snap.3804-T1
Valid prediction for snap_scaffold_3-snap.3806-T1
Valid prediction for snap_scaffold_3-snap.3826-T1
Valid prediction for GlimmerHMM_glimmerT_8493-T1
Valid prediction for snap_scaffold_3-snap.3805-T1
Valid prediction for GlimmerHMM_glimmerT_8492-T1
Valid prediction for GlimmerHMM_glimmerT_8494-T1
Valid prediction for snap_scaffold_3-snap.3814-T1
Valid prediction for GlimmerHMM_glimmerT_8500-T1
Valid prediction for GlimmerHMM_glimmerT_8479-T1
Valid prediction for GlimmerHMM_glimmerT_8496-T1
Valid prediction for Augustus_model.g5570.t1
Valid prediction for snap_scaffold_3-snap.3799-T1
Valid prediction for snap_scaffold_3-snap.3802-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 HiQ_model.g5574.t1
Valid prediction for snap_scaffold_3-snap.3832-T1
Valid prediction for snap_scaffold_3-snap.3818-T1
Valid prediction for snap_scaffold_3-snap.3829-T1
Valid prediction for pasa_asmbl_39647.p1
Valid prediction for GlimmerHMM_glimmerT_8495-T1
Valid prediction for GlimmerHMM_glimmerT_8481-T1
Valid prediction for HiQ_model.g5575.t1
Valid prediction for GlimmerHMM_glimmerT_8485-T1
Valid prediction for GlimmerHMM_glimmerT_8483-T1
Valid prediction for GlimmerHMM_glimmerT_8497-T1
Valid prediction for GlimmerHMM_glimmerT_8490-T1
Couldn't classify 47265, 47422
Sorry, prediction pasa_asmbl_39646.p1 fails validation.
(ATG)	 CC	45011-45060	GT	GAG
(AGA)	 AG	45547-45664	GT	AGG
(TTT)	 AG	45764-45922	GT	GTG
(CAT)	 AG	46061-46175	GT	CGG
(GTG)	 AG	46591-46800	GT	AGG
(GTC)	 AG	47265-47422	TT	TGT
-recovered pasa_asmbl_39646.p1, initial, 45011, 45060
-recovered pasa_asmbl_39646.p1, internal, 45547, 45664
-recovered pasa_asmbl_39646.p1, internal, 45764, 45922
-recovered pasa_asmbl_39646.p1, internal, 46061, 46175
-recovered pasa_asmbl_39646.p1, internal, 46591, 46800
Valid prediction for snap_scaffold_3-snap.3800-T1
Valid prediction for snap_scaffold_3-snap.3812-T1
Valid prediction for snap_scaffold_3-snap.3798-T1
Valid prediction for CodingQuarry_transcript_46484-T1
Valid prediction for GlimmerHMM_glimmerT_8478-T1
Valid prediction for snap_scaffold_3-snap.3825-T1
Couldn't classify 144894, 144938
Couldn't classify 151200, 151364
Sorry, prediction pasa_asmbl_39643.p1 fails validation.
(GGT)	 GG	144894-144938	GT	AGG
(TGG)	 AG	145171-145344	GT	AGG
(TTT)	 AG	145908-146058	GT	AGG
(GGA)	 AG	148441-148633	GT	AGG
(GTA)	 AG	149087-149171	GT	AGG
(GAT)	 AG	149331-149448	GT	AGG
(CCG)	 AG	149565-149696	GT	AGG
(GGT)	 AG	150588-150661	GT	AGG
(CCA)	 AG	151200-151364	AC	CCA
add_exon() Sorry, pasa_asmbl_39643.p1 145908-146058-terminal-3 is invalid.
-recovered pasa_asmbl_39643.p1, terminal, 145908, 146058
-recovered pasa_asmbl_39643.p1, internal, 145171, 145344
-recovered pasa_asmbl_39643.p1, internal, 145908, 146058
-recovered pasa_asmbl_39643.p1, internal, 148441, 148633
-recovered pasa_asmbl_39643.p1, internal, 149087, 149171
-recovered pasa_asmbl_39643.p1, internal, 149331, 149448
-recovered pasa_asmbl_39643.p1, internal, 149565, 149696
-recovered pasa_asmbl_39643.p1, internal, 150588, 150661
Valid prediction for snap_scaffold_3-snap.3823-T1
Valid prediction for snap_scaffold_3-snap.3817-T1
Valid prediction for snap_scaffold_3-snap.3803-T1
Couldn't classify 49863, 50080
Sorry, prediction pasa_asmbl_39796.p1 fails validation.
(ATG)	 CC	48328-48377	GT	GAG
(AGA)	 AG	48862-48979	GT	AGG
(TTT)	 AG	49079-49237	GT	GTG
(CAT)	 AG	49376-49490	GT	CGG
(GTG)	 AG	49863-50080	AT	ACA
-recovered pasa_asmbl_39796.p1, initial, 48328, 48377
-recovered pasa_asmbl_39796.p1, internal, 48862, 48979
-recovered pasa_asmbl_39796.p1, internal, 49079, 49237
-recovered pasa_asmbl_39796.p1, internal, 49376, 49490
Valid prediction for snap_scaffold_3-snap.3833-T1
Valid prediction for GlimmerHMM_glimmerT_8491-T1
Valid prediction for HiQ_model.g5568.t1
Couldn't classify 144735, 144779
Sorry, prediction pasa_asmbl_39645.p1 fails validation.
(ATG)	 CG	141991-142106	GT	AGG
(AAA)	 AG	142290-142407	GT	AGG
(ATA)	 AG	144735-144779	CT	GGC
-recovered pasa_asmbl_39645.p1, initial, 141991, 142106
-recovered pasa_asmbl_39645.p1, internal, 142290, 142407
Valid prediction for CodingQuarry_transcript_46487-T1
Valid prediction for snap_scaffold_3-snap.3808-T1
Valid prediction for snap_scaffold_3-snap.3811-T1
Valid prediction for CodingQuarry_transcript_46486-T1
Valid prediction for Augustus_model.g5569.t1
Valid prediction for GlimmerHMM_glimmerT_8486-T1
Valid prediction for HiQ_model.g5567.t1
Valid prediction for GlimmerHMM_glimmerT_8501-T1
Valid prediction for snap_scaffold_3-snap.3828-T1
Valid prediction for GlimmerHMM_glimmerT_8489-T1
Valid prediction for Augustus_model.g5578.t1
Valid prediction for snap_scaffold_3-snap.3827-T1
Valid prediction for CodingQuarry_transcript_46485-T1
Valid prediction for GlimmerHMM_glimmerT_8480-T1
Valid prediction for GlimmerHMM_glimmerT_8477-T1
Valid prediction for snap_scaffold_3-snap.3820-T1
Valid prediction for Augustus_model.g5573.t1
Valid prediction for pasa_asmbl_39641.p1
Valid prediction for snap_scaffold_3-snap.3809-T1
Valid prediction for Augustus_model.g5571.t1
Valid prediction for GlimmerHMM_glimmerT_8499-T1
Valid prediction for snap_scaffold_3-snap.3801-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12201, rend_intergenic: 10105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15780, rend_intergenic: 12858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35135, rend_intergenic: 23024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55686, rend_intergenic: 37476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66451, rend_intergenic: 56619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70189, rend_intergenic: 68654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81905, rend_intergenic: 72172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86796, rend_intergenic: 82566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120237, rend_intergenic: 99066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121710, rend_intergenic: 120385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126144, rend_intergenic: 123265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128360, rend_intergenic: 126901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142209, rend_intergenic: 140558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152824, rend_intergenic: 145317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164166, rend_intergenic: 154010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171914, rend_intergenic: 164721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 164932, rend_intergenic: 164929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174471
-exon list size: 325


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 12201, rend_intergenic: 10105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15780, rend_intergenic: 12858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35135, rend_intergenic: 23024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55686, rend_intergenic: 37476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66451, rend_intergenic: 56619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70189, rend_intergenic: 68654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81905, rend_intergenic: 72172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86796, rend_intergenic: 82566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120237, rend_intergenic: 99066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121710, rend_intergenic: 120385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126144, rend_intergenic: 123265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128360, rend_intergenic: 126901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142209, rend_intergenic: 140558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152824, rend_intergenic: 145317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164166, rend_intergenic: 154010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171914, rend_intergenic: 164721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 164932, rend_intergenic: 164929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 19705
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15738
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12176
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support