-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_10966435-11265691

-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_10-snap.2163-T1
Valid prediction for GlimmerHMM_glimmerT_25416-T1
Valid prediction for snap_scaffold_10-snap.2176-T1
Valid prediction for GlimmerHMM_glimmerT_25410-T1
Valid prediction for Augustus_model.g16894.t1
Valid prediction for pasa_asmbl_3446.p1
Valid prediction for GlimmerHMM_glimmerT_25417-T1
Couldn't classify 146263, 146336
Sorry, prediction pasa_asmbl_3450.p1 fails validation.
(ATG)	 AG	141024-141095	GT	AGG
(ATG)	 AG	141517-141618	GT	AGG
(GCA)	 AG	142818-142928	GT	CTG
(ATG)	 AG	143140-143244	GT	ATG
(ACG)	 AG	143661-143790	GT	ACG
(GTC)	 AG	143907-144013	GT	TTG
(GGC)	 AG	144119-144213	GT	CGG
(GCC)	 AG	145166-145247	GT	CAG
(ATT)	 AG	145509-145551	GT	AAG
(TCG)	 AG	145776-145844	GT	AGG
(GTA)	 AG	146263-146336	GG	TTG
-recovered pasa_asmbl_3450.p1, initial, 141024, 141095
-recovered pasa_asmbl_3450.p1, initial, 141517, 141618
-recovered pasa_asmbl_3450.p1, initial, 143140, 143244
-recovered pasa_asmbl_3450.p1, internal, 141024, 141095
-recovered pasa_asmbl_3450.p1, internal, 141517, 141618
-recovered pasa_asmbl_3450.p1, internal, 142818, 142928
-recovered pasa_asmbl_3450.p1, internal, 143140, 143244
-recovered pasa_asmbl_3450.p1, internal, 143661, 143790
-recovered pasa_asmbl_3450.p1, internal, 143907, 144013
-recovered pasa_asmbl_3450.p1, internal, 144119, 144213
-recovered pasa_asmbl_3450.p1, internal, 145166, 145247
-recovered pasa_asmbl_3450.p1, internal, 145509, 145551
-recovered pasa_asmbl_3450.p1, internal, 145776, 145844
Valid prediction for CodingQuarry_transcript_5567-T1
Valid prediction for snap_scaffold_10-snap.2187-T1
Valid prediction for snap_scaffold_10-snap.2160-T1
Valid prediction for GlimmerHMM_glimmerT_25425-T1
Valid prediction for Augustus_model.g16902.t1
Valid prediction for GlimmerHMM_glimmerT_25424-T1
Valid prediction for GlimmerHMM_glimmerT_25419-T1
Valid prediction for HiQ_model.g16904.t1
Valid prediction for HiQ_model.g16899.t1
Couldn't classify 157609, 157770
Sorry, prediction pasa_asmbl_3454.p2 fails validation.
(AGC)	 AC	157609-157770	GT	AGG
(ATC)	 AG	159607-159742	GT	CGG
(TGT)	 AG	161546-161715	GC	GAG
-recovered pasa_asmbl_3454.p2, terminal, 161546, 161715
-recovered pasa_asmbl_3454.p2, internal, 159607, 159742
-recovered pasa_asmbl_3454.p2, internal, 161546, 161715
Valid prediction for GlimmerHMM_glimmerT_25404-T1
Valid prediction for GlimmerHMM_glimmerT_25429-T1
Valid prediction for Augustus_model.g16910.t1
Valid prediction for snap_scaffold_10-snap.2173-T1
Valid prediction for GlimmerHMM_glimmerT_25411-T1
Valid prediction for snap_scaffold_10-snap.2186-T1
Valid prediction for GlimmerHMM_glimmerT_25414-T1
Valid prediction for Augustus_model.g16901.t1
Valid prediction for snap_scaffold_10-snap.2169-T1
Valid prediction for GlimmerHMM_glimmerT_25428-T1
Valid prediction for snap_scaffold_10-snap.2168-T1
Valid prediction for Augustus_model.g16897.t1
Valid prediction for CodingQuarry_transcript_5564-T1
Valid prediction for snap_scaffold_10-snap.2167-T1
Valid prediction for snap_scaffold_10-snap.2159-T1
Valid prediction for pasa_asmbl_3444.p1
Valid prediction for snap_scaffold_10-snap.2172-T1
Valid prediction for snap_scaffold_10-snap.2188-T1
Valid prediction for Augustus_model.g16896.t1
Valid prediction for snap_scaffold_10-snap.2181-T1
Valid prediction for HiQ_model.g16898.t1
Valid prediction for GlimmerHMM_glimmerT_25426-T1
Valid prediction for GlimmerHMM_glimmerT_25420-T1
Valid prediction for GlimmerHMM_glimmerT_25406-T1
Valid prediction for GlimmerHMM_glimmerT_25413-T1
Couldn't classify 116483, 116653
Couldn't classify 116763, 117017
Sorry, prediction CodingQuarry_transcript_5566-T1 fails validation.
(ATG)	 GG	114145-114171	GT	GTG
(TGG)	 AG	114605-114810	GT	GAG
(GGT)	 AG	115300-115374	GT	CTG
(AAT)	 AG	115481-115574	GT	TGG
(TTT)	 AG	115728-115840	GT	TGG
(GCA)	 AG	116158-116257	GT	AGG
(GAC)	 AG	116483-116653	GG	TCG
(GAA)	 CG	116763-117017	CT	GAC
-recovered CodingQuarry_transcript_5566-T1, initial, 114145, 114171
-recovered CodingQuarry_transcript_5566-T1, internal, 114605, 114810
-recovered CodingQuarry_transcript_5566-T1, internal, 115300, 115374
-recovered CodingQuarry_transcript_5566-T1, internal, 115481, 115574
-recovered CodingQuarry_transcript_5566-T1, internal, 115728, 115840
-recovered CodingQuarry_transcript_5566-T1, internal, 116158, 116257
Valid prediction for snap_scaffold_10-snap.2162-T1
Valid prediction for GlimmerHMM_glimmerT_25407-T1
Valid prediction for snap_scaffold_10-snap.2156-T1
Valid prediction for snap_scaffold_10-snap.2166-T1
Valid prediction for Augustus_model.g16908.t1
Valid prediction for snap_scaffold_10-snap.2164-T1
Valid prediction for CodingQuarry_transcript_5565-T1
Valid prediction for snap_scaffold_10-snap.2185-T1
Valid prediction for GlimmerHMM_glimmerT_25418-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.g16905.t1
Valid prediction for snap_scaffold_10-snap.2161-T1
Couldn't classify 69325, 70032
Sorry, prediction pasa_asmbl_4773.p1 fails validation.
(ATG)	 GC	69325-70032	CA	GCC
Valid prediction for Augustus_model.g16907.t1
Valid prediction for snap_scaffold_10-snap.2155-T1
Valid prediction for snap_scaffold_10-snap.2153-T1
Couldn't classify 106656, 106746
Sorry, prediction pasa_asmbl_4771.p1 fails validation.
(AGG)	 GG	106656-106746	GT	AGG
(CGC)	 AG	107704-108048	GT	AGG
(GAT)	 AG	109943-110087	GT	GAG
(GGA)	 AG	113070-113200	GT	AGG
(GAT)	 AG	113315-113415	TT	AGT
-recovered pasa_asmbl_4771.p1, terminal, 113315, 113415
-recovered pasa_asmbl_4771.p1, internal, 107704, 108048
-recovered pasa_asmbl_4771.p1, internal, 109943, 110087
-recovered pasa_asmbl_4771.p1, internal, 113070, 113200
Valid prediction for snap_scaffold_10-snap.2180-T1
Valid prediction for Augustus_model.g16895.t1
Valid prediction for snap_scaffold_10-snap.2170-T1
Valid prediction for snap_scaffold_10-snap.2158-T1
Couldn't classify 178531, 178582
Sorry, prediction pasa_asmbl_4767.p1 fails validation.
(ATG)	 CA	173069-173266	GT	GAG
(GAA)	 AG	173463-173611	GT	AGG
(AAT)	 AG	173860-174096	GT	GGG
(AAT)	 AG	174295-174462	GT	CGG
(GGT)	 AG	174552-174654	GT	AGG
(AGT)	 AG	175157-175266	GT	CGG
(GCT)	 AG	175811-176006	GT	AGG
(GAG)	 AG	176391-176574	GT	CAG
(ATG)	 AG	177724-178414	GT	AGG
(ATG)	 AG	178531-178582	GG	ACG
-recovered pasa_asmbl_4767.p1, initial, 173069, 173266
add_exon() Sorry, pasa_asmbl_4767.p1 177724-178414-initial-1 is invalid.
-recovered pasa_asmbl_4767.p1, initial, 177724, 178414
-recovered pasa_asmbl_4767.p1, internal, 173463, 173611
-recovered pasa_asmbl_4767.p1, internal, 173860, 174096
-recovered pasa_asmbl_4767.p1, internal, 174295, 174462
-recovered pasa_asmbl_4767.p1, internal, 174552, 174654
-recovered pasa_asmbl_4767.p1, internal, 175157, 175266
-recovered pasa_asmbl_4767.p1, internal, 175811, 176006
-recovered pasa_asmbl_4767.p1, internal, 176391, 176574
-recovered pasa_asmbl_4767.p1, internal, 177724, 178414
Valid prediction for snap_scaffold_10-snap.2179-T1
Valid prediction for snap_scaffold_10-snap.2182-T1
Valid prediction for Augustus_model.g16909.t1
Valid prediction for GlimmerHMM_glimmerT_25409-T1
Valid prediction for GlimmerHMM_glimmerT_25422-T1
Valid prediction for snap_scaffold_10-snap.2191-T1
Valid prediction for snap_scaffold_10-snap.2190-T1
Valid prediction for snap_scaffold_10-snap.2192-T1
Valid prediction for GlimmerHMM_glimmerT_25421-T1
Valid prediction for GlimmerHMM_glimmerT_25405-T1
Valid prediction for snap_scaffold_10-snap.2178-T1
Valid prediction for HiQ_model.g16900.t1
Valid prediction for GlimmerHMM_glimmerT_25427-T1
Valid prediction for snap_scaffold_10-snap.2175-T1
Valid prediction for snap_scaffold_10-snap.2189-T1
Valid prediction for snap_scaffold_10-snap.2154-T1
Valid prediction for snap_scaffold_10-snap.2165-T1
Couldn't classify 70336, 71160
Sorry, prediction pasa_asmbl_4772.p1 fails validation.
(GGG)	 GG	70336-71160	AG	CAA
Valid prediction for GlimmerHMM_glimmerT_25415-T1
Valid prediction for snap_scaffold_10-snap.2174-T1
Valid prediction for GlimmerHMM_glimmerT_25423-T1
Valid prediction for GlimmerHMM_glimmerT_25408-T1
Couldn't classify 117752, 117910
Sorry, prediction pasa_asmbl_4769.p1 fails validation.
(GTT)	 AA	117752-117910	GT	ATG
(CTG)	 AG	118738-118893	CT	GAC
-recovered pasa_asmbl_4769.p1, terminal, 118738, 118893
Valid prediction for snap_scaffold_10-snap.2193-T1
Valid prediction for GlimmerHMM_glimmerT_25412-T1
Valid prediction for snap_scaffold_10-snap.2177-T1
Valid prediction for snap_scaffold_10-snap.2171-T1
Valid prediction for Augustus_model.g16893.t1
Valid prediction for snap_scaffold_10-snap.2183-T1
Valid prediction for snap_scaffold_10-snap.2184-T1
Valid prediction for Augustus_model.g16903.t1
Valid prediction for snap_scaffold_10-snap.2157-T1
Valid prediction for Augustus_model.g16906.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37582, rend_intergenic: 34293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150562, rend_intergenic: 139405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172385, rend_intergenic: 154858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 295951, rend_intergenic: 271817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 299257
-exon list size: 320


building trellis

0.3    
0.6    
0.9    
1.2    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
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    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
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    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.8    
99.1    
99.4    
99.7    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 37582, rend_intergenic: 34293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150562, rend_intergenic: 139405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172385, rend_intergenic: 154858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 295951, rend_intergenic: 271817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support