-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_3649326-3848245

-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 GlimmerHMM_glimmerT_31409-T1
Valid prediction for Augustus_model.g20888.t1
Valid prediction for CodingQuarry_transcript_12969-T1
Valid prediction for snap_scaffold_13-snap.691-T1
Couldn't classify 95216, 95980
Sorry, prediction pasa_asmbl_10740.p1 fails validation.
(TCT)	 CG	95216-95980	AA	GCA
Valid prediction for GlimmerHMM_glimmerT_31417-T1
Valid prediction for snap_scaffold_13-snap.685-T1
Valid prediction for snap_scaffold_13-snap.674-T1
Valid prediction for CodingQuarry_transcript_12971-T1
Valid prediction for GlimmerHMM_glimmerT_31406-T1
Valid prediction for snap_scaffold_13-snap.676-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_31408-T1
Valid prediction for snap_scaffold_13-snap.695-T1
Valid prediction for HiQ_model.g20882.t1
Valid prediction for snap_scaffold_13-snap.684-T1
Valid prediction for Augustus_model.g20878.t1
Valid prediction for snap_scaffold_13-snap.681-T1
Valid prediction for HiQ_model.g20879.t1
Valid prediction for GlimmerHMM_glimmerT_31425-T1
Valid prediction for GlimmerHMM_glimmerT_31415-T1
Valid prediction for CodingQuarry_transcript_12973-T1
Valid prediction for GlimmerHMM_glimmerT_31421-T1
Valid prediction for CodingQuarry_transcript_12966-T1
Valid prediction for snap_scaffold_13-snap.688-T1
Valid prediction for Augustus_model.g20896.t1
Valid prediction for snap_scaffold_13-snap.670-T1
Valid prediction for CodingQuarry_transcript_12972-T1
Valid prediction for Augustus_model.g20876.t1
Valid prediction for snap_scaffold_13-snap.699-T1
Couldn't classify 96448, 96482
Sorry, prediction pasa_asmbl_10744.p1 fails validation.
(GCC)	 AT	96448-96482	GT	AGG
(GTT)	 AG	96679-96748	GT	ATG
(ATC)	 AG	96925-97072	GT	AGG
(GTC)	 AG	97373-97502	GT	AGG
(AAC)	 AG	97677-97772	GT	AGG
(GCT)	 AG	98220-98326	GT	AGG
(GTG)	 AG	98479-98584	GT	AAG
(GTA)	 AG	98755-98843	GT	AGG
(GTG)	 AG	98984-99603	TA	AAT
add_exon() Sorry, pasa_asmbl_10744.p1 96925-97072-terminal-3 is invalid.
-recovered pasa_asmbl_10744.p1, terminal, 96925, 97072
add_exon() Sorry, pasa_asmbl_10744.p1 97677-97772-terminal-1 is invalid.
-recovered pasa_asmbl_10744.p1, terminal, 97677, 97772
-recovered pasa_asmbl_10744.p1, terminal, 98984, 99603
-recovered pasa_asmbl_10744.p1, internal, 96679, 96748
-recovered pasa_asmbl_10744.p1, internal, 96925, 97072
-recovered pasa_asmbl_10744.p1, internal, 97373, 97502
-recovered pasa_asmbl_10744.p1, internal, 97677, 97772
-recovered pasa_asmbl_10744.p1, internal, 98220, 98326
-recovered pasa_asmbl_10744.p1, internal, 98479, 98584
-recovered pasa_asmbl_10744.p1, internal, 98755, 98843
Couldn't classify 124783, 124813
Sorry, prediction pasa_asmbl_10745.p1 fails validation.
(AGT)	 CC	124783-124813	GT	AGG
(GTG)	 AG	124954-125573	TA	AAT
-recovered pasa_asmbl_10745.p1, terminal, 124954, 125573
Valid prediction for GlimmerHMM_glimmerT_31426-T1
Valid prediction for snap_scaffold_13-snap.686-T1
Valid prediction for HiQ_model.g20893.t1
Valid prediction for GlimmerHMM_glimmerT_31423-T1
Valid prediction for GlimmerHMM_glimmerT_31432-T1
Valid prediction for Augustus_model.g20890.t1
Valid prediction for GlimmerHMM_glimmerT_31412-T1
Valid prediction for snap_scaffold_13-snap.671-T1
Valid prediction for snap_scaffold_13-snap.679-T1
Valid prediction for snap_scaffold_13-snap.690-T1
Valid prediction for GlimmerHMM_glimmerT_31413-T1
Valid prediction for Augustus_model.g20886.t1
Valid prediction for pasa_asmbl_10732.p1
Valid prediction for pasa_asmbl_10726.p1
Valid prediction for CodingQuarry_transcript_12964-T1
Valid prediction for CodingQuarry_transcript_12968-T1
Valid prediction for HiQ_model.g20884.t1
Couldn't classify 94859, 95161
Sorry, prediction pasa_asmbl_10739.p1 fails validation.
(ATG)	 CA	94859-95161	CT	CCC
Valid prediction for CodingQuarry_transcript_12965-T1
Valid prediction for GlimmerHMM_glimmerT_31430-T1
Valid prediction for GlimmerHMM_glimmerT_31419-T1
Valid prediction for GlimmerHMM_glimmerT_31411-T1
Valid prediction for GlimmerHMM_glimmerT_31422-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.g20898.t1
Valid prediction for GlimmerHMM_glimmerT_31433-T1
Valid prediction for HiQ_model.g20885.t1
Valid prediction for snap_scaffold_13-snap.701-T1
Valid prediction for HiQ_model.g20897.t1
Valid prediction for HiQ_model.g20902.t1
Valid prediction for CodingQuarry_transcript_12970-T1
Valid prediction for Augustus_model.g20889.t1
Valid prediction for snap_scaffold_13-snap.683-T1
Valid prediction for GlimmerHMM_glimmerT_31428-T1
Valid prediction for HiQ_model.g20887.t1
Couldn't classify 155959, 156120
Sorry, prediction pasa_asmbl_9560.p1 fails validation.
(CAG)	 TT	155959-156120	GT	AGG
(CCA)	 AG	156208-156406	GT	TGG
(GCC)	 AG	156736-156888	GT	AGG
(GTG)	 AG	156998-157119	GT	AGG
(TAT)	 AG	157270-157429	GT	CGG
(GGT)	 AG	157655-157803	GG	GAG
-recovered pasa_asmbl_9560.p1, terminal, 157655, 157803
-recovered pasa_asmbl_9560.p1, internal, 156208, 156406
-recovered pasa_asmbl_9560.p1, internal, 156736, 156888
-recovered pasa_asmbl_9560.p1, internal, 156998, 157119
-recovered pasa_asmbl_9560.p1, internal, 157270, 157429
Valid prediction for GlimmerHMM_glimmerT_31414-T1
Valid prediction for snap_scaffold_13-snap.687-T1
Valid prediction for Augustus_model.g20892.t1
Valid prediction for CodingQuarry_transcript_12975-T1
Couldn't classify 143210, 143927
Couldn't classify 143958, 144088
Sorry, prediction CodingQuarry_transcript_12967-T1 fails validation.
(ATG)	 CA	142919-142921	GT	TGG
(GAC)	 AG	143210-143927	AA	GCA
(CCC)	 GC	143958-144088	AG	GAA
-recovered CodingQuarry_transcript_12967-T1, initial, 142919, 142921
Valid prediction for GlimmerHMM_glimmerT_31416-T1
Couldn't classify 62088, 62145
Sorry, prediction pasa_asmbl_9577.p1 fails validation.
(GAG)	 AG	62088-62145	GT	AGG
(TGT)	 AG	62849-62884	GT	AGG
(GCT)	 AG	63089-63176	GT	AAG
(GTT)	 AG	64482-64643	GT	TGG
(GGA)	 AG	65036-65136	GT	AAG
(TCC)	 AG	65279-65420	GT	AGG
(ATA)	 AG	65503-65539	GA	GAG
-recovered pasa_asmbl_9577.p1, terminal, 65503, 65539
-recovered pasa_asmbl_9577.p1, internal, 62088, 62145
-recovered pasa_asmbl_9577.p1, internal, 62849, 62884
-recovered pasa_asmbl_9577.p1, internal, 63089, 63176
-recovered pasa_asmbl_9577.p1, internal, 64482, 64643
-recovered pasa_asmbl_9577.p1, internal, 65036, 65136
-recovered pasa_asmbl_9577.p1, internal, 65279, 65420
Valid prediction for pasa_asmbl_9588.p1
Valid prediction for snap_scaffold_13-snap.704-T1
Valid prediction for snap_scaffold_13-snap.689-T1
Valid prediction for GlimmerHMM_glimmerT_31420-T1
Valid prediction for GlimmerHMM_glimmerT_31427-T1
Valid prediction for snap_scaffold_13-snap.696-T1
Valid prediction for GlimmerHMM_glimmerT_31437-T1
Valid prediction for pasa_asmbl_9567.p1
Couldn't classify 68639, 68741
Couldn't classify 71810, 71994
Sorry, prediction pasa_asmbl_9574.p1 fails validation.
(TTT)	 AA	68639-68741	GT	TGG
(GTC)	 AG	68991-69185	GT	AGG
(ATA)	 AG	70132-70299	GT	AAG
(AGA)	 AG	70626-70805	GT	TTG
(TCC)	 AG	70878-70913	GT	AAG
(AAC)	 AG	71161-71199	GT	AGG
(AGG)	 AG	71378-71416	GT	ATG
(TGA)	 AG	71537-71698	GT	AGG
(AAC)	 AG	71810-71994	TG	AGT
add_exon() Sorry, pasa_asmbl_9574.p1 68991-69185-terminal-1 is invalid.
-recovered pasa_asmbl_9574.p1, terminal, 68991, 69185
-recovered pasa_asmbl_9574.p1, terminal, 70878, 70913
add_exon() Sorry, pasa_asmbl_9574.p1 71537-71698-terminal-1 is invalid.
-recovered pasa_asmbl_9574.p1, terminal, 71537, 71698
-recovered pasa_asmbl_9574.p1, internal, 68991, 69185
-recovered pasa_asmbl_9574.p1, internal, 70132, 70299
-recovered pasa_asmbl_9574.p1, internal, 70626, 70805
-recovered pasa_asmbl_9574.p1, internal, 70878, 70913
-recovered pasa_asmbl_9574.p1, internal, 71161, 71199
-recovered pasa_asmbl_9574.p1, internal, 71378, 71416
-recovered pasa_asmbl_9574.p1, internal, 71537, 71698
Valid prediction for GlimmerHMM_glimmerT_31431-T1
Valid prediction for snap_scaffold_13-snap.700-T1
Valid prediction for Augustus_model.g20881.t1
Valid prediction for snap_scaffold_13-snap.702-T1
Valid prediction for pasa_asmbl_9562.p1
Valid prediction for snap_scaffold_13-snap.694-T1
Valid prediction for GlimmerHMM_glimmerT_31436-T1
Valid prediction for Augustus_model.g20877.t1
Valid prediction for GlimmerHMM_glimmerT_31435-T1
Valid prediction for Augustus_model.g20880.t1
Valid prediction for snap_scaffold_13-snap.678-T1
Valid prediction for pasa_asmbl_9582.p1
Valid prediction for GlimmerHMM_glimmerT_31434-T1
Valid prediction for snap_scaffold_13-snap.672-T1
Valid prediction for snap_scaffold_13-snap.692-T1
Couldn't classify 106866, 107214
Couldn't classify 109189, 109367
Sorry, prediction pasa_asmbl_9570.p1 fails validation.
(GTT)	 AT	106866-107214	GT	AGG
(AAT)	 AG	107978-108528	GT	CTG
(GCC)	 AG	108696-108861	GT	GTG
(GCA)	 AG	109189-109367	CT	GCC
-recovered pasa_asmbl_9570.p1, internal, 107978, 108528
-recovered pasa_asmbl_9570.p1, internal, 108696, 108861
Valid prediction for GlimmerHMM_glimmerT_31407-T1
Couldn't classify 110582, 110618
Sorry, prediction pasa_asmbl_9569.p1 fails validation.
(ATG)	 AC	109542-110107	GT	AAG
(TGA)	 AG	110197-110238	GT	CTG
(GAT)	 AG	110339-110461	GT	TGG
(GTG)	 AG	110582-110618	TG	CCT
-recovered pasa_asmbl_9569.p1, initial, 109542, 110107
-recovered pasa_asmbl_9569.p1, internal, 110197, 110238
-recovered pasa_asmbl_9569.p1, internal, 110339, 110461
Valid prediction for HiQ_model.g20894.t1
Valid prediction for snap_scaffold_13-snap.682-T1
Couldn't classify 51853, 51995
Couldn't classify 55611, 55675
Sorry, prediction pasa_asmbl_9579.p1 fails validation.
(AGA)	 GA	51853-51995	GT	GGG
(AAC)	 AG	52833-52938	GT	CAG
(ACG)	 AG	53069-53138	GT	CTG
(CTA)	 AG	53239-53301	GT	AGG
(TTA)	 AG	53424-53476	GT	AGG
(GAT)	 AG	53716-53804	GT	AGG
(GTC)	 AG	54280-54493	GT	AGG
(AAC)	 AG	54889-54987	GT	TGG
(GAC)	 AG	55368-55446	GT	GGG
(AAA)	 AG	55611-55675	GT	CGG
-recovered pasa_asmbl_9579.p1, internal, 52833, 52938
-recovered pasa_asmbl_9579.p1, internal, 53069, 53138
-recovered pasa_asmbl_9579.p1, internal, 53239, 53301
-recovered pasa_asmbl_9579.p1, internal, 53424, 53476
-recovered pasa_asmbl_9579.p1, internal, 53716, 53804
-recovered pasa_asmbl_9579.p1, internal, 54280, 54493
-recovered pasa_asmbl_9579.p1, internal, 54889, 54987
-recovered pasa_asmbl_9579.p1, internal, 55368, 55446
-recovered pasa_asmbl_9579.p1, internal, 55611, 55675
Valid prediction for Augustus_model.g20875.t1
Valid prediction for Augustus_model.g20883.t1
Couldn't classify 106240, 106568
Sorry, prediction pasa_asmbl_9571.p1 fails validation.
(ATG)	 CT	105078-105099	GT	TGG
(ACA)	 AG	106240-106568	GA	AGG
-recovered pasa_asmbl_9571.p1, initial, 105078, 105099
Valid prediction for snap_scaffold_13-snap.698-T1
Couldn't classify 154439, 154590
Sorry, prediction pasa_asmbl_10353.p1 fails validation.
(ATG)	 TC	153834-153844	GT	CGG
(TTT)	 AG	153984-154330	GT	AGG
(ATA)	 AG	154439-154590	GT	AGG
-recovered pasa_asmbl_10353.p1, initial, 153834, 153844
-recovered pasa_asmbl_10353.p1, internal, 153984, 154330
-recovered pasa_asmbl_10353.p1, internal, 154439, 154590
Valid prediction for snap_scaffold_13-snap.697-T1
Valid prediction for snap_scaffold_13-snap.677-T1
Valid prediction for Augustus_model.g20891.t1
Valid prediction for snap_scaffold_13-snap.693-T1
Valid prediction for Augustus_model.g20900.t1
Couldn't classify 129935, 131728
Sorry, prediction pasa_asmbl_9566.p1 fails validation.
(ATG)	 AA	129935-131728	TA	GGT
Valid prediction for Augustus_model.g20899.t1
Valid prediction for Augustus_model.g20895.t1
Valid prediction for CodingQuarry_transcript_12974-T1
Valid prediction for snap_scaffold_13-snap.673-T1
Valid prediction for Augustus_model.g20901.t1
Valid prediction for GlimmerHMM_glimmerT_31410-T1
Valid prediction for GlimmerHMM_glimmerT_31418-T1
Valid prediction for snap_scaffold_13-snap.675-T1
Valid prediction for snap_scaffold_13-snap.703-T1
Valid prediction for snap_scaffold_13-snap.680-T1
Valid prediction for snap_scaffold_13-snap.705-T1
Valid prediction for GlimmerHMM_glimmerT_31429-T1
Valid prediction for GlimmerHMM_glimmerT_31424-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16478, rend_intergenic: 12349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60326, rend_intergenic: 58609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198920
-exon list size: 380


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.7    
5.0    
5.2    
5.5    
5.8    
6.0    
6.3    
6.5    
6.8    
7.1    
7.3    
7.6    
7.9    
8.1    
8.4    
8.6    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.5    
11.8    
12.0    
12.3    
12.6    
12.8    
13.1    
13.4    
13.6    
13.9    
14.1    
14.4    
14.7    
14.9    
15.2    
15.4    
15.7    
16.0    
16.2    
16.5    
16.8    
17.0    
17.3    
17.5    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
21.5    
21.7    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.6    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
27.0    
27.2    
27.5    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.4    
31.7    
31.9    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.9    
47.1    
47.4    
47.6    
47.9    
48.2    
48.4    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.6    
51.8    
52.1    
52.4    
52.6    
52.9    
53.1    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.1    
64.4    
64.7    
64.9    
65.2    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.1    
68.3    
68.6    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.4    
70.7    
70.9    
71.2    
71.5    
71.7    
72.0    
72.3    
72.5    
72.8    
73.0    
73.3    
73.6    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.4    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.3    
78.5    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.7    
94.0    
94.2    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 16478, rend_intergenic: 12349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60326, rend_intergenic: 58609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 171815 - 198920
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 171815 - 183317
-exon list size: 1


building trellis

33.3    
66.7    
-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

-building DP trellis

-building trellis in range 183337 - 198920
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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

-building DP trellis

-building trellis in range 184254 - 198920
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

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