-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_16941166-17131609

-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_5-snap.3153-T1
Valid prediction for CodingQuarry_transcript_52425-T1
Couldn't classify 68820, 68945
Sorry, prediction pasa_asmbl_46127.p1 fails validation.
(AAG)	 GG	68820-68945	GT	CTG
(TTG)	 AG	69037-69207	GT	AGG
(CGG)	 AG	69515-69707	GT	AGG
(TGA)	 AG	70181-70413	CC	GAC
-recovered pasa_asmbl_46127.p1, terminal, 70181, 70413
-recovered pasa_asmbl_46127.p1, internal, 69037, 69207
-recovered pasa_asmbl_46127.p1, internal, 69515, 69707
Valid prediction for GlimmerHMM_glimmerT_13459-T1
Couldn't classify 83363, 83509
Couldn't classify 87612, 87619
Sorry, prediction pasa_asmbl_46130.p1 fails validation.
(GGT)	 GA	83363-83509	GT	AGG
(GGT)	 AG	83640-83810	GT	AGG
(ATC)	 AG	83944-84013	GT	AGG
(GTC)	 AG	85813-85886	GT	AGG
(AGA)	 AG	86960-87046	GT	AGG
(TGT)	 AG	87199-87259	GT	AGG
(AAG)	 AG	87365-87523	GT	CAG
(CGT)	 AG	87612-87619	CT	TCC
-recovered pasa_asmbl_46130.p1, internal, 83640, 83810
-recovered pasa_asmbl_46130.p1, internal, 83944, 84013
-recovered pasa_asmbl_46130.p1, internal, 85813, 85886
-recovered pasa_asmbl_46130.p1, internal, 86960, 87046
-recovered pasa_asmbl_46130.p1, internal, 87199, 87259
-recovered pasa_asmbl_46130.p1, internal, 87365, 87523
Valid prediction for snap_scaffold_5-snap.3161-T1
Valid prediction for snap_scaffold_5-snap.3145-T1
Valid prediction for GlimmerHMM_glimmerT_13443-T1
Valid prediction for snap_scaffold_5-snap.3139-T1
Valid prediction for snap_scaffold_5-snap.3141-T1
Valid prediction for GlimmerHMM_glimmerT_13441-T1
Valid prediction for pasa_asmbl_46135.p1
Valid prediction for snap_scaffold_5-snap.3148-T1
Valid prediction for GlimmerHMM_glimmerT_13458-T1
Valid prediction for GlimmerHMM_glimmerT_13451-T1
Valid prediction for Augustus_model.g8942.t1
Valid prediction for snap_scaffold_5-snap.3172-T1
Valid prediction for snap_scaffold_5-snap.3149-T1
Valid prediction for Augustus_model.g8938.t1
Valid prediction for Augustus_model.g8949.t1
Valid prediction for GlimmerHMM_glimmerT_13457-T1
Valid prediction for GlimmerHMM_glimmerT_13448-T1
Couldn't classify 95551, 95599
Sorry, prediction pasa_asmbl_46133.p1 fails validation.
(GTC)	 AT	95551-95599	GC	ATG
(GGA)	 AG	95977-96107	GT	TGG
(GCC)	 AG	96283-96419	GT	AGG
(GGG)	 AG	96576-96780	GT	GGG
(GAG)	 AG	97029-97073	CA	GAC
-recovered pasa_asmbl_46133.p1, terminal, 97029, 97073
-recovered pasa_asmbl_46133.p1, internal, 95977, 96107
-recovered pasa_asmbl_46133.p1, internal, 96283, 96419
-recovered pasa_asmbl_46133.p1, internal, 96576, 96780
Valid prediction for snap_scaffold_5-snap.3155-T1
Valid prediction for HiQ_model.g8947.t1
Valid prediction for Augustus_model.g8946.t1
Valid prediction for HiQ_model.g8944.t1
Valid prediction for GlimmerHMM_glimmerT_13442-T1
Valid prediction for GlimmerHMM_glimmerT_13452-T1
Valid prediction for snap_scaffold_5-snap.3138-T1
Valid prediction for snap_scaffold_5-snap.3162-T1
Valid prediction for GlimmerHMM_glimmerT_13446-T1
Valid prediction for Augustus_model.g8948.t1
Valid prediction for snap_scaffold_5-snap.3166-T1
Valid prediction for snap_scaffold_5-snap.3167-T1
Valid prediction for GlimmerHMM_glimmerT_13460-T1
Valid prediction for pasa_asmbl_46128.p1
Valid prediction for snap_scaffold_5-snap.3150-T1
Valid prediction for pasa_asmbl_46124.p1
Valid prediction for snap_scaffold_5-snap.3165-T1
Valid prediction for GlimmerHMM_glimmerT_13463-T1
Valid prediction for GlimmerHMM_glimmerT_13444-T1
Valid prediction for Augustus_model.g8950.t1
Couldn't classify 65955, 66029
Sorry, prediction pasa_asmbl_46367.p2 fails validation.
(ATG)	 CT	63906-63946	GT	TGG
(TTC)	 AG	64343-64394	GT	GGG
(AAA)	 AG	64506-64541	GT	AGG
(GAT)	 AG	65703-65765	GT	AGG
(GAG)	 AG	65955-66029	CC	CCC
-recovered pasa_asmbl_46367.p2, initial, 63906, 63946
-recovered pasa_asmbl_46367.p2, internal, 64343, 64394
-recovered pasa_asmbl_46367.p2, internal, 64506, 64541
-recovered pasa_asmbl_46367.p2, internal, 65703, 65765
Valid prediction for HiQ_model.g8941.t1
Couldn't classify 135997, 136110
Sorry, prediction pasa_asmbl_46136.p1 fails validation.
(GGT)	 CA	135997-136110	GT	ATG
(GCC)	 AG	137245-137458	GT	AGG
(AGA)	 AG	137723-137833	GT	AGG
(ATC)	 AG	137966-138059	GT	AGG
(GTT)	 AG	138345-138483	GT	AGG
(GTG)	 AG	138657-138854	AG	AAA
add_exon() Sorry, pasa_asmbl_46136.p1 137245-137458-terminal-3 is invalid.
-recovered pasa_asmbl_46136.p1, terminal, 137245, 137458
-recovered pasa_asmbl_46136.p1, terminal, 138657, 138854
-recovered pasa_asmbl_46136.p1, internal, 137245, 137458
-recovered pasa_asmbl_46136.p1, internal, 137723, 137833
-recovered pasa_asmbl_46136.p1, internal, 137966, 138059
-recovered pasa_asmbl_46136.p1, internal, 138345, 138483
Valid prediction for GlimmerHMM_glimmerT_13450-T1
Valid prediction for snap_scaffold_5-snap.3159-T1
Valid prediction for snap_scaffold_5-snap.3142-T1
Valid prediction for GlimmerHMM_glimmerT_13447-T1
Valid prediction for GlimmerHMM_glimmerT_13453-T1
Valid prediction for snap_scaffold_5-snap.3143-T1
Valid prediction for GlimmerHMM_glimmerT_13462-T1
Valid prediction for GlimmerHMM_glimmerT_13445-T1
Valid prediction for Augustus_model.g8940.t1
Valid prediction for Augustus_model.g8943.t1
Valid prediction for snap_scaffold_5-snap.3137-T1
Valid prediction for GlimmerHMM_glimmerT_13454-T1
Valid prediction for HiQ_model.g8945.t1
Couldn't classify 61676, 61996
Sorry, prediction pasa_asmbl_46125.p1 fails validation.
(ACA)	 GT	61676-61996	CC	GAC
Valid prediction for GlimmerHMM_glimmerT_13449-T1
Valid prediction for CodingQuarry_transcript_52427-T1
Couldn't classify 87752, 87772
Sorry, prediction pasa_asmbl_46478.p1 fails validation.
(CTG)	 TC	87752-87772	GT	TGG
(GAG)	 AG	88455-88552	GT	CGG
(GGA)	 AG	89026-89113	GT	AGG
(ACT)	 AG	89426-89633	GT	TGG
(TGG)	 AG	89723-89826	GT	AGG
(CAG)	 AG	89904-89988	GT	TCG
(CTG)	 AG	90388-90479	GT	AGG
(TAC)	 AG	90762-90956	GT	AGG
(ATA)	 AG	91237-91452	GT	AGG
(GGG)	 AG	91560-91622	GT	AGG
(CGC)	 AG	91823-92026	GT	AGG
(CAA)	 AG	92347-92391	GT	AGG
(CGG)	 AG	92577-92656	GT	GTG
(TGA)	 AG	93054-93144	CC	GAC
-recovered pasa_asmbl_46478.p1, terminal, 93054, 93144
-recovered pasa_asmbl_46478.p1, internal, 88455, 88552
-recovered pasa_asmbl_46478.p1, internal, 89026, 89113
-recovered pasa_asmbl_46478.p1, internal, 89426, 89633
-recovered pasa_asmbl_46478.p1, internal, 89723, 89826
-recovered pasa_asmbl_46478.p1, internal, 89904, 89988
-recovered pasa_asmbl_46478.p1, internal, 90388, 90479
-recovered pasa_asmbl_46478.p1, internal, 90762, 90956
-recovered pasa_asmbl_46478.p1, internal, 91237, 91452
-recovered pasa_asmbl_46478.p1, internal, 91560, 91622
-recovered pasa_asmbl_46478.p1, internal, 91823, 92026
-recovered pasa_asmbl_46478.p1, internal, 92347, 92391
-recovered pasa_asmbl_46478.p1, internal, 92577, 92656
Valid prediction for snap_scaffold_5-snap.3169-T1
Valid prediction for snap_scaffold_5-snap.3152-T1
Valid prediction for snap_scaffold_5-snap.3147-T1
Valid prediction for CodingQuarry_transcript_52428-T1
Valid prediction for CodingQuarry_transcript_52426-T1
Valid prediction for Augustus_model.g8939.t1
Valid prediction for Augustus_model.g8952.t1
Valid prediction for GlimmerHMM_glimmerT_13464-T1
Valid prediction for Augustus_model.g8951.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 GlimmerHMM_glimmerT_13455-T1
Valid prediction for snap_scaffold_5-snap.3157-T1
Valid prediction for snap_scaffold_5-snap.3151-T1
Valid prediction for snap_scaffold_5-snap.3135-T1
Valid prediction for snap_scaffold_5-snap.3156-T1
Valid prediction for snap_scaffold_5-snap.3171-T1
Valid prediction for snap_scaffold_5-snap.3140-T1
Valid prediction for snap_scaffold_5-snap.3168-T1
Valid prediction for Augustus_model.g8953.t1
Valid prediction for snap_scaffold_5-snap.3136-T1
Valid prediction for snap_scaffold_5-snap.3146-T1
Valid prediction for GlimmerHMM_glimmerT_13465-T1
Valid prediction for snap_scaffold_5-snap.3144-T1
Valid prediction for snap_scaffold_5-snap.3158-T1
Valid prediction for snap_scaffold_5-snap.3154-T1
Valid prediction for snap_scaffold_5-snap.3134-T1
Valid prediction for snap_scaffold_5-snap.3163-T1
Valid prediction for GlimmerHMM_glimmerT_13461-T1
Valid prediction for GlimmerHMM_glimmerT_13440-T1
Valid prediction for GlimmerHMM_glimmerT_13456-T1
Valid prediction for Augustus_model.g8937.t1
Valid prediction for GlimmerHMM_glimmerT_13439-T1
Valid prediction for snap_scaffold_5-snap.3170-T1
Valid prediction for snap_scaffold_5-snap.3160-T1
Valid prediction for snap_scaffold_5-snap.3164-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16183, rend_intergenic: 8899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32552, rend_intergenic: 26493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40547, rend_intergenic: 32645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62464, rend_intergenic: 59217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70413, rend_intergenic: 68787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76556, rend_intergenic: 72260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93144, rend_intergenic: 82862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120271, rend_intergenic: 108697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137508, rend_intergenic: 137241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140391, rend_intergenic: 137725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154780, rend_intergenic: 153841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173598, rend_intergenic: 168186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190444
-exon list size: 420


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.7    
1.9    
2.1    
2.4    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.0    
4.3    
4.5    
4.7    
5.0    
5.2    
5.5    
5.7    
5.9    
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6.4    
6.6    
6.9    
7.1    
7.3    
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8.1    
8.3    
8.5    
8.8    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.4    
10.7    
10.9    
11.1    
11.4    
11.6    
11.8    
12.1    
12.3    
12.6    
12.8    
13.0    
13.3    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
14.9    
15.2    
15.4    
15.6    
15.9    
16.1    
16.4    
16.6    
16.8    
17.1    
17.3    
17.5    
17.8    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.3    
22.5    
22.7    
23.0    
23.2    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.3    
31.5    
31.8    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.4    
34.6    
34.8    
35.1    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.2    
42.4    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.7    
51.9    
52.1    
52.4    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.9    
57.1    
57.3    
57.6    
57.8    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
64.9    
65.2    
65.4    
65.6    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.3    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
73.9    
74.2    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
77.7    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.2    
82.5    
82.7    
82.9    
83.2    
83.4    
83.6    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.2    
92.4    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 16183, rend_intergenic: 8899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32552, rend_intergenic: 26493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40547, rend_intergenic: 32645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62464, rend_intergenic: 59217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70413, rend_intergenic: 68787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76556, rend_intergenic: 72260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93144, rend_intergenic: 82862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120271, rend_intergenic: 108697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137508, rend_intergenic: 137241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140391, rend_intergenic: 137725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154780, rend_intergenic: 153841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173598, rend_intergenic: 168186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support