-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_12260175-12421608

-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 CodingQuarry_transcript_25842-T1
Valid prediction for snap_scaffold_19-snap.2408-T1
Valid prediction for snap_scaffold_19-snap.2407-T1
Valid prediction for snap_scaffold_19-snap.2410-T1
Valid prediction for snap_scaffold_19-snap.2397-T1
Valid prediction for snap_scaffold_19-snap.2425-T1
Couldn't classify 66757, 66824
Couldn't classify 73587, 74025
Sorry, prediction pasa_asmbl_21782.p1 fails validation.
(GTG)	 AA	66757-66824	GT	GAG
(TCT)	 AG	67007-67076	GT	TGG
(GAC)	 AG	67214-67320	GT	CGG
(ACG)	 AG	67883-67913	GT	ACG
(GTT)	 AG	68007-68120	GT	AGG
(GCT)	 AG	68364-68535	GT	GGG
(GTT)	 AG	68989-69172	GT	AGG
(GCC)	 AG	72010-72039	GT	TGG
(GAG)	 AG	72782-72899	GT	ATG
(GAT)	 AG	73181-73302	GT	AGG
(GGA)	 AG	73587-74025	TC	AGT
-recovered pasa_asmbl_21782.p1, internal, 67007, 67076
-recovered pasa_asmbl_21782.p1, internal, 67214, 67320
-recovered pasa_asmbl_21782.p1, internal, 67883, 67913
-recovered pasa_asmbl_21782.p1, internal, 68007, 68120
-recovered pasa_asmbl_21782.p1, internal, 68364, 68535
-recovered pasa_asmbl_21782.p1, internal, 68989, 69172
-recovered pasa_asmbl_21782.p1, internal, 72010, 72039
-recovered pasa_asmbl_21782.p1, internal, 72782, 72899
-recovered pasa_asmbl_21782.p1, internal, 73181, 73302
Valid prediction for snap_scaffold_19-snap.2405-T1
Valid prediction for GlimmerHMM_glimmerT_45048-T1
Couldn't classify 75287, 75337
Sorry, prediction pasa_asmbl_21786.p1 fails validation.
(ATG)	 GC	74212-74436	GT	AGG
(GTA)	 AG	74784-75068	GT	AGG
(CCT)	 AG	75287-75337	CC	GAC
-recovered pasa_asmbl_21786.p1, initial, 74212, 74436
-recovered pasa_asmbl_21786.p1, internal, 74784, 75068
Valid prediction for GlimmerHMM_glimmerT_45059-T1
Valid prediction for snap_scaffold_19-snap.2417-T1
Valid prediction for HiQ_model.g29897.t1
Valid prediction for pasa_asmbl_21776.p1
Valid prediction for HiQ_model.g29902.t1
Valid prediction for CodingQuarry_transcript_25847-T1
Valid prediction for snap_scaffold_19-snap.2424-T1
Valid prediction for HiQ_model.g29896.t1
Valid prediction for snap_scaffold_19-snap.2398-T1
Valid prediction for snap_scaffold_19-snap.2421-T1
Valid prediction for GlimmerHMM_glimmerT_45064-T1
Couldn't classify 76505, 76601
Couldn't classify 79389, 79569
Sorry, prediction pasa_asmbl_21790.p1 fails validation.
(GTG)	 AG	76505-76601	GT	CGG
(ACT)	 AG	76750-76907	GT	AGG
(GAG)	 AG	77074-77137	GT	AGG
(GGT)	 AG	77648-77683	GT	TGG
(GGG)	 AG	77897-77922	GT	ACG
(CTG)	 AG	78005-78112	GT	AGG
(GAG)	 AG	78208-78494	GT	TGG
(GAC)	 AG	78958-79013	GT	AGG
(GAA)	 AG	79109-79298	GT	AGG
(ATC)	 AG	79389-79569	AC	CCA
-recovered pasa_asmbl_21790.p1, internal, 76505, 76601
-recovered pasa_asmbl_21790.p1, internal, 76750, 76907
-recovered pasa_asmbl_21790.p1, internal, 77074, 77137
-recovered pasa_asmbl_21790.p1, internal, 77648, 77683
-recovered pasa_asmbl_21790.p1, internal, 77897, 77922
-recovered pasa_asmbl_21790.p1, internal, 78005, 78112
-recovered pasa_asmbl_21790.p1, internal, 78208, 78494
-recovered pasa_asmbl_21790.p1, internal, 78958, 79013
-recovered pasa_asmbl_21790.p1, internal, 79109, 79298
Valid prediction for GlimmerHMM_glimmerT_45065-T1
Valid prediction for snap_scaffold_19-snap.2416-T1
Valid prediction for GlimmerHMM_glimmerT_45061-T1
Valid prediction for Augustus_model.g29899.t1
Valid prediction for GlimmerHMM_glimmerT_45057-T1
Valid prediction for Augustus_model.g29898.t1
Valid prediction for pasa_asmbl_21796.p1
Valid prediction for pasa_asmbl_21795.p1
Valid prediction for GlimmerHMM_glimmerT_45062-T1
Valid prediction for snap_scaffold_19-snap.2418-T1
Valid prediction for CodingQuarry_transcript_25845-T1
Valid prediction for GlimmerHMM_glimmerT_45055-T1
Valid prediction for GlimmerHMM_glimmerT_45058-T1
Valid prediction for Augustus_model.g29895.t1
Valid prediction for CodingQuarry_transcript_25843-T1
Valid prediction for pasa_asmbl_21781.p1

-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 snap_scaffold_19-snap.2409-T1
Valid prediction for GlimmerHMM_glimmerT_45056-T1
Valid prediction for Augustus_model.g29889.t1
Valid prediction for GlimmerHMM_glimmerT_45060-T1
Valid prediction for snap_scaffold_19-snap.2422-T1
Valid prediction for GlimmerHMM_glimmerT_45046-T1
Couldn't classify 20814, 21203
Sorry, prediction pasa_asmbl_22478.p1 fails validation.
(CTG)	 CG	20814-21203	GT	AAG
(GTG)	 AG	21459-21593	GT	AGG
(GGA)	 AG	22365-22445	GT	CTG
(GCC)	 AG	22574-22630	GT	AGG
(AGC)	 AG	22820-22895	GT	AGG
(GCC)	 AG	23909-24051	GT	AGG
(GGA)	 AG	24180-24197	GT	AGG
(GGA)	 AG	24504-24710	GT	CAG
(GGT)	 AG	24880-24906	GT	CAG
(GGC)	 AG	25076-25138	GT	AGG
(GGA)	 AG	25409-25492	GT	CTG
(ACA)	 AG	25676-25726	GT	GGG
(GGT)	 AG	25818-25952	GT	CAG
(GGT)	 AG	26470-26523	GT	AGG
(GGC)	 AG	26636-26680	GT	AGG
(CAA)	 AG	27351-27434	GT	AGG
(GGT)	 AG	28521-28652	GT	GTG
(CAC)	 AG	28790-28855	GT	AGG
(GGT)	 AG	28939-28965	GT	CGG
(GGC)	 AG	29059-29157	GT	GGG
(GGC)	 AG	29284-29319	GT	TGG
(GGT)	 AG	29542-29628	GT	ATG
(CAC)	 AG	29703-29735	GT	AGG
(GCT)	 AG	29842-29877	GT	CAG
(GGG)	 AG	30131-30190	GT	AGG
(GGC)	 AG	30424-30501	GT	GGG
(GGA)	 AG	30608-30643	GT	CTG
(GGT)	 AG	30854-30907	GT	CAG
(GGT)	 AG	31208-31279	GT	CAG
(GGT)	 AG	31442-31501	GT	GGG
(AGG)	 AG	31866-31896	GT	AGG
(CCT)	 AG	32093-32146	GT	AGG
(GAC)	 AG	32266-32300	GT	AGG
(AAC)	 AG	32657-32773	GT	CGG
(GGC)	 AG	32875-33031	GT	GAG
(CCA)	 AG	33202-33266	GT	GGG
(GTG)	 AG	33340-33468	GT	AGG
(CTT)	 AG	33686-33718	GT	AGG
(GGT)	 AG	33950-34420	GT	CAG
(CTT)	 AG	34534-34731	GT	AGG
(GAC)	 AG	34895-35004	GT	TGG
(GCC)	 AG	35751-35967	GC	AGG
-recovered pasa_asmbl_22478.p1, terminal, 35751, 35967
-recovered pasa_asmbl_22478.p1, internal, 21459, 21593
-recovered pasa_asmbl_22478.p1, internal, 22365, 22445
-recovered pasa_asmbl_22478.p1, internal, 22574, 22630
-recovered pasa_asmbl_22478.p1, internal, 22820, 22895
-recovered pasa_asmbl_22478.p1, internal, 23909, 24051
-recovered pasa_asmbl_22478.p1, internal, 24180, 24197
-recovered pasa_asmbl_22478.p1, internal, 24504, 24710
-recovered pasa_asmbl_22478.p1, internal, 24880, 24906
-recovered pasa_asmbl_22478.p1, internal, 25076, 25138
-recovered pasa_asmbl_22478.p1, internal, 25409, 25492
-recovered pasa_asmbl_22478.p1, internal, 25676, 25726
-recovered pasa_asmbl_22478.p1, internal, 25818, 25952
-recovered pasa_asmbl_22478.p1, internal, 26470, 26523
-recovered pasa_asmbl_22478.p1, internal, 26636, 26680
-recovered pasa_asmbl_22478.p1, internal, 27351, 27434
-recovered pasa_asmbl_22478.p1, internal, 28521, 28652
-recovered pasa_asmbl_22478.p1, internal, 28790, 28855
-recovered pasa_asmbl_22478.p1, internal, 28939, 28965
-recovered pasa_asmbl_22478.p1, internal, 29059, 29157
-recovered pasa_asmbl_22478.p1, internal, 29284, 29319
-recovered pasa_asmbl_22478.p1, internal, 29542, 29628
-recovered pasa_asmbl_22478.p1, internal, 29703, 29735
-recovered pasa_asmbl_22478.p1, internal, 29842, 29877
-recovered pasa_asmbl_22478.p1, internal, 30131, 30190
-recovered pasa_asmbl_22478.p1, internal, 30424, 30501
-recovered pasa_asmbl_22478.p1, internal, 30608, 30643
-recovered pasa_asmbl_22478.p1, internal, 30854, 30907
-recovered pasa_asmbl_22478.p1, internal, 31208, 31279
-recovered pasa_asmbl_22478.p1, internal, 31442, 31501
-recovered pasa_asmbl_22478.p1, internal, 31866, 31896
-recovered pasa_asmbl_22478.p1, internal, 32093, 32146
-recovered pasa_asmbl_22478.p1, internal, 32266, 32300
-recovered pasa_asmbl_22478.p1, internal, 32657, 32773
-recovered pasa_asmbl_22478.p1, internal, 32875, 33031
-recovered pasa_asmbl_22478.p1, internal, 33202, 33266
-recovered pasa_asmbl_22478.p1, internal, 33340, 33468
-recovered pasa_asmbl_22478.p1, internal, 33686, 33718
-recovered pasa_asmbl_22478.p1, internal, 33950, 34420
-recovered pasa_asmbl_22478.p1, internal, 34534, 34731
-recovered pasa_asmbl_22478.p1, internal, 34895, 35004
-recovered pasa_asmbl_22478.p1, internal, 35751, 35967
Valid prediction for GlimmerHMM_glimmerT_45063-T1
Valid prediction for snap_scaffold_19-snap.2419-T1
Valid prediction for GlimmerHMM_glimmerT_45054-T1
Valid prediction for Augustus_model.g29904.t1
Valid prediction for Augustus_model.g29894.t1
Valid prediction for GlimmerHMM_glimmerT_45049-T1
Valid prediction for snap_scaffold_19-snap.2423-T1
Valid prediction for GlimmerHMM_glimmerT_45050-T1
Valid prediction for HiQ_model.g29903.t1
Valid prediction for Augustus_model.g29901.t1
Valid prediction for GlimmerHMM_glimmerT_45067-T1
Valid prediction for CodingQuarry_transcript_25840-T1
Valid prediction for snap_scaffold_19-snap.2415-T1
Valid prediction for GlimmerHMM_glimmerT_45047-T1
Valid prediction for snap_scaffold_19-snap.2414-T1
Valid prediction for Augustus_model.g29892.t1
Valid prediction for snap_scaffold_19-snap.2402-T1
Valid prediction for pasa_asmbl_22475.p1
Valid prediction for Augustus_model.g29905.t1
Valid prediction for snap_scaffold_19-snap.2406-T1
Valid prediction for Augustus_model.g29900.t1
Valid prediction for GlimmerHMM_glimmerT_45051-T1
Valid prediction for snap_scaffold_19-snap.2412-T1
Valid prediction for snap_scaffold_19-snap.2399-T1
Valid prediction for GlimmerHMM_glimmerT_45066-T1
Valid prediction for snap_scaffold_19-snap.2420-T1
Valid prediction for Augustus_model.g29893.t1
Valid prediction for snap_scaffold_19-snap.2400-T1
Valid prediction for Augustus_model.g29891.t1
Valid prediction for GlimmerHMM_glimmerT_45052-T1
Valid prediction for snap_scaffold_19-snap.2401-T1
Valid prediction for Augustus_model.g29890.t1
Valid prediction for snap_scaffold_19-snap.2413-T1
Valid prediction for snap_scaffold_19-snap.2403-T1
Valid prediction for GlimmerHMM_glimmerT_45053-T1
Valid prediction for snap_scaffold_19-snap.2404-T1
Valid prediction for snap_scaffold_19-snap.2411-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7789, rend_intergenic: 7055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59898, rend_intergenic: 55259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63727, rend_intergenic: 62297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152047, rend_intergenic: 150339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161434
-exon list size: 362


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.5    
2.7    
3.0    
3.3    
3.6    
3.8    
4.1    
4.4    
4.7    
4.9    
5.2    
5.5    
5.8    
6.0    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.1    
9.3    
9.6    
9.9    
10.2    
10.4    
10.7    
11.0    
11.3    
11.5    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.5    
13.7    
14.0    
14.3    
14.6    
14.8    
15.1    
15.4    
15.7    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.9    
18.1    
18.4    
18.7    
19.0    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.4    
23.6    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.0    
31.3    
31.6    
31.9    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.2    
35.4    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.7    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
45.1    
45.3    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.5    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.5    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.7    
54.9    
55.2    
55.5    
55.8    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.1    
59.3    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.3    
61.5    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.5    
63.7    
64.0    
64.3    
64.6    
64.8    
65.1    
65.4    
65.7    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.1    
68.4    
68.7    
69.0    
69.2    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.4    
76.6    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.0    
81.3    
81.6    
81.9    
82.1    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.3    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.5    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.5    
88.7    
89.0    
89.3    
89.6    
89.8    
90.1    
90.4    
90.7    
90.9    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.1    
95.3    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 7789, rend_intergenic: 7055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59898, rend_intergenic: 55259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63727, rend_intergenic: 62297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152047, rend_intergenic: 150339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support