-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_3343050-3490019

-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_26-snap.686-T1
Couldn't classify 87479, 87616
Sorry, prediction pasa_asmbl_34778.p1 fails validation.
(GTC)	 CT	87479-87616	GT	ATG
(GAT)	 AG	87759-87908	GT	TCG
(GCA)	 AG	88009-88074	GT	AGG
(ATT)	 AG	88307-88738	GT	AGG
(ACG)	 AG	89060-89350	GT	CAG
(GGA)	 AG	89484-89648	TC	AAT
-recovered pasa_asmbl_34778.p1, terminal, 89484, 89648
-recovered pasa_asmbl_34778.p1, internal, 87759, 87908
-recovered pasa_asmbl_34778.p1, internal, 88009, 88074
-recovered pasa_asmbl_34778.p1, internal, 88307, 88738
-recovered pasa_asmbl_34778.p1, internal, 89060, 89350
Valid prediction for snap_scaffold_26-snap.689-T1
Couldn't classify 82787, 82865
Sorry, prediction pasa_asmbl_34776.p1 fails validation.
(GGG)	 GG	82787-82865	GT	TGG
(GAT)	 AG	82972-83142	GT	TGG
(GTT)	 AG	83316-83461	GT	TGG
(GAT)	 AG	83739-83897	CT	GAC
-recovered pasa_asmbl_34776.p1, terminal, 83739, 83897
-recovered pasa_asmbl_34776.p1, internal, 82972, 83142
-recovered pasa_asmbl_34776.p1, internal, 83316, 83461
Valid prediction for GlimmerHMM_glimmerT_55343-T1
Valid prediction for snap_scaffold_26-snap.698-T1
Valid prediction for snap_scaffold_26-snap.713-T1
Valid prediction for Augustus_model.g36647.t1
Valid prediction for GlimmerHMM_glimmerT_55331-T1
Valid prediction for GlimmerHMM_glimmerT_55335-T1
Valid prediction for Augustus_model.g36658.t1
Valid prediction for snap_scaffold_26-snap.708-T1
Valid prediction for pasa_asmbl_34771.p1
Valid prediction for HiQ_model.g36657.t1
Valid prediction for snap_scaffold_26-snap.684-T1
Valid prediction for GlimmerHMM_glimmerT_55349-T1
Valid prediction for Augustus_model.g36646.t1
Valid prediction for CodingQuarry_transcript_40278-T1
Valid prediction for GlimmerHMM_glimmerT_55351-T1
Valid prediction for snap_scaffold_26-snap.704-T1
Valid prediction for snap_scaffold_26-snap.695-T1
Valid prediction for Augustus_model.g36661.t1
Valid prediction for snap_scaffold_26-snap.690-T1
Valid prediction for snap_scaffold_26-snap.682-T1
Valid prediction for GlimmerHMM_glimmerT_55350-T1
Valid prediction for snap_scaffold_26-snap.706-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.711-T1
Valid prediction for snap_scaffold_26-snap.701-T1
Valid prediction for snap_scaffold_26-snap.685-T1
Valid prediction for Augustus_model.g36649.t1
Valid prediction for GlimmerHMM_glimmerT_55347-T1
Valid prediction for GlimmerHMM_glimmerT_55346-T1
Valid prediction for Augustus_model.g36652.t1
Valid prediction for Augustus_model.g36660.t1
Valid prediction for GlimmerHMM_glimmerT_55348-T1
Valid prediction for Augustus_model.g36655.t1
Couldn't classify 17108, 17197
Sorry, prediction pasa_asmbl_34773.p1 fails validation.
(GGT)	 AG	17108-17197	GT	CGG
(TTT)	 AG	17334-17417	GT	CTG
(GTC)	 AG	17573-17628	GT	TGG
(TCG)	 AG	17712-17758	GT	TGG
(ACG)	 AG	17951-18026	GT	AAG
(CAC)	 AG	18129-18162	GT	AGG
(TGT)	 AG	18329-18403	GT	AGG
(TGG)	 AG	18537-18624	GT	AGG
(ACG)	 AG	18839-18939	AC	AGA
-recovered pasa_asmbl_34773.p1, terminal, 18839, 18939
-recovered pasa_asmbl_34773.p1, internal, 17108, 17197
-recovered pasa_asmbl_34773.p1, internal, 17334, 17417
-recovered pasa_asmbl_34773.p1, internal, 17573, 17628
-recovered pasa_asmbl_34773.p1, internal, 17712, 17758
-recovered pasa_asmbl_34773.p1, internal, 17951, 18026
-recovered pasa_asmbl_34773.p1, internal, 18129, 18162
-recovered pasa_asmbl_34773.p1, internal, 18329, 18403
-recovered pasa_asmbl_34773.p1, internal, 18537, 18624
Valid prediction for CodingQuarry_transcript_40277-T1
Valid prediction for snap_scaffold_26-snap.710-T1
Valid prediction for GlimmerHMM_glimmerT_55332-T1
Valid prediction for snap_scaffold_26-snap.691-T1
Valid prediction for snap_scaffold_26-snap.702-T1
Valid prediction for Augustus_model.g36659.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 Augustus_model.g36645.t1
Valid prediction for snap_scaffold_26-snap.683-T1
Valid prediction for snap_scaffold_26-snap.703-T1
Valid prediction for GlimmerHMM_glimmerT_55344-T1
Valid prediction for GlimmerHMM_glimmerT_55338-T1
Valid prediction for GlimmerHMM_glimmerT_55345-T1
Valid prediction for Augustus_model.g36654.t1
Valid prediction for snap_scaffold_26-snap.692-T1
Valid prediction for snap_scaffold_26-snap.687-T1
Valid prediction for snap_scaffold_26-snap.693-T1
Valid prediction for Augustus_model.g36653.t1
Valid prediction for GlimmerHMM_glimmerT_55330-T1
Valid prediction for snap_scaffold_26-snap.700-T1
Valid prediction for snap_scaffold_26-snap.712-T1
Valid prediction for snap_scaffold_26-snap.707-T1
Valid prediction for snap_scaffold_26-snap.697-T1
Valid prediction for snap_scaffold_26-snap.688-T1
Valid prediction for GlimmerHMM_glimmerT_55340-T1
Valid prediction for GlimmerHMM_glimmerT_55334-T1
Valid prediction for Augustus_model.g36651.t1
Valid prediction for GlimmerHMM_glimmerT_55337-T1
Valid prediction for Augustus_model.g36656.t1
Valid prediction for snap_scaffold_26-snap.709-T1
Couldn't classify 137303, 137391
Couldn't classify 140103, 141606
Sorry, prediction pasa_asmbl_35488.p1 fails validation.
(TAC)	 TT	137303-137391	GT	GGG
(CGG)	 AG	137611-137823	GT	AAG
(GTT)	 AG	137957-138044	GT	AGG
(GTG)	 AG	138302-138423	GC	AGG
(GAT)	 AG	138784-138889	GT	CTG
(CTG)	 AG	139556-139627	GT	AGG
(GTT)	 AG	139888-139997	GT	CGG
(GGT)	 AG	140103-141606	GC	ATG
-recovered pasa_asmbl_35488.p1, internal, 137611, 137823
-recovered pasa_asmbl_35488.p1, internal, 137957, 138044
-recovered pasa_asmbl_35488.p1, internal, 138302, 138423
-recovered pasa_asmbl_35488.p1, internal, 138784, 138889
-recovered pasa_asmbl_35488.p1, internal, 139556, 139627
-recovered pasa_asmbl_35488.p1, internal, 139888, 139997
-recovered pasa_asmbl_35488.p1, internal, 140103, 141606
Couldn't classify 136388, 136719
Couldn't classify 136813, 136867
Sorry, prediction pasa_asmbl_35864.p1 fails validation.
(GAC)	 GT	136388-136719	GT	AAG
(GAC)	 AG	136813-136867	GC	GTG
-recovered pasa_asmbl_35864.p1, internal, 136813, 136867
Valid prediction for GlimmerHMM_glimmerT_55336-T1
Valid prediction for snap_scaffold_26-snap.694-T1
Valid prediction for GlimmerHMM_glimmerT_55342-T1
Valid prediction for GlimmerHMM_glimmerT_55333-T1
Valid prediction for snap_scaffold_26-snap.705-T1
Couldn't classify 141661, 142142
Sorry, prediction pasa_asmbl_35486.p1 fails validation.
(GCA)	 CT	141661-142142	GT	CAG
(GAG)	 AG	142615-142708	GT	TGG
(GGC)	 AG	143247-143372	GA	GAG
-recovered pasa_asmbl_35486.p1, terminal, 143247, 143372
-recovered pasa_asmbl_35486.p1, internal, 142615, 142708
Valid prediction for Augustus_model.g36648.t1
Valid prediction for Augustus_model.g36650.t1
Valid prediction for GlimmerHMM_glimmerT_55339-T1
Valid prediction for snap_scaffold_26-snap.699-T1
Valid prediction for snap_scaffold_26-snap.696-T1
Valid prediction for GlimmerHMM_glimmerT_55341-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 18939, rend_intergenic: 18936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5290, rend_intergenic: 3599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11969, rend_intergenic: 5458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19762, rend_intergenic: 16482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28055, rend_intergenic: 20844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40332, rend_intergenic: 32993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41901, rend_intergenic: 40437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46844, rend_intergenic: 42598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56169, rend_intergenic: 53287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61328, rend_intergenic: 56379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79270, rend_intergenic: 62568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109406, rend_intergenic: 96247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113443, rend_intergenic: 110411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143861, rend_intergenic: 126236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 146970
-exon list size: 387


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.1    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.9    
4.1    
4.4    
4.6    
4.9    
5.1    
5.4    
5.7    
5.9    
6.2    
6.4    
6.7    
6.9    
7.2    
7.5    
7.7    
8.0    
8.2    
8.5    
8.7    
9.0    
9.3    
9.5    
9.8    
10.0    
10.3    
10.5    
10.8    
11.1    
11.3    
11.6    
11.8    
12.1    
12.3    
12.6    
12.9    
13.1    
13.4    
13.6    
13.9    
14.1    
14.4    
14.7    
14.9    
15.2    
15.4    
15.7    
15.9    
16.2    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.4    
23.7    
23.9    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.8    
28.0    
28.3    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.8    
37.0    
37.3    
37.5    
37.8    
38.0    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
44.0    
44.2    
44.5    
44.7    
45.0    
45.2    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.8    
55.0    
55.3    
55.5    
55.8    
56.0    
56.3    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
62.0    
62.2    
62.5    
62.7    
63.0    
63.2    
63.5    
63.8    
64.0    
64.3    
64.5    
64.8    
65.0    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.2    
69.4    
69.7    
69.9    
70.2    
70.4    
70.7    
71.0    
71.2    
71.5    
71.7    
72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.3    
76.6    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 19 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 18939, rend_intergenic: 18936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5290, rend_intergenic: 3599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11969, rend_intergenic: 5458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19762, rend_intergenic: 16482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28055, rend_intergenic: 20844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40332, rend_intergenic: 32993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41901, rend_intergenic: 40437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46844, rend_intergenic: 42598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56169, rend_intergenic: 53287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61328, rend_intergenic: 56379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79270, rend_intergenic: 62568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109406, rend_intergenic: 96247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113443, rend_intergenic: 110411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143861, rend_intergenic: 126236  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