-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_5504488-5791649

-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_2-snap.1281-T1
Valid prediction for snap_scaffold_2-snap.1259-T1
Valid prediction for snap_scaffold_2-snap.1277-T1
Valid prediction for snap_scaffold_2-snap.1258-T1
Valid prediction for GlimmerHMM_glimmerT_3851-T1
Valid prediction for snap_scaffold_2-snap.1245-T1
Valid prediction for snap_scaffold_2-snap.1280-T1
Valid prediction for snap_scaffold_2-snap.1264-T1
Valid prediction for snap_scaffold_2-snap.1271-T1
Valid prediction for snap_scaffold_2-snap.1256-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1269-T1
Valid prediction for snap_scaffold_2-snap.1251-T1
Valid prediction for GlimmerHMM_glimmerT_3841-T1
Valid prediction for Augustus_model.g2565.t1
Valid prediction for snap_scaffold_2-snap.1276-T1
Valid prediction for GlimmerHMM_glimmerT_3855-T1
Couldn't classify 216629, 216731
Sorry, prediction pasa_asmbl_24439.p1 fails validation.
(CGC)	 CA	216629-216731	GT	AGG
(TGA)	 AG	218446-218535	GT	AGG
(AAG)	 AG	219097-219167	GT	AGG
(GTA)	 AG	219287-219389	GT	TGG
(AGA)	 AG	219586-219726	GT	CTG
(CTA)	 AG	220085-220200	GT	AGG
(AAA)	 AG	220320-220378	GT	GAG
(GAT)	 AG	220480-220499	GT	TGG
(ACA)	 AG	220592-220653	GT	AGG
(TCG)	 AG	220730-220798	GT	AGG
(TTT)	 AG	221041-221142	GT	AGG
(GTC)	 AG	221238-221310	GT	AGG
(ACG)	 AG	221628-221704	GC	AAG
add_exon() Sorry, pasa_asmbl_24439.p1 218446-218535-terminal-1 is invalid.
-recovered pasa_asmbl_24439.p1, terminal, 218446, 218535
-recovered pasa_asmbl_24439.p1, terminal, 221628, 221704
-recovered pasa_asmbl_24439.p1, internal, 218446, 218535
-recovered pasa_asmbl_24439.p1, internal, 219097, 219167
-recovered pasa_asmbl_24439.p1, internal, 219287, 219389
-recovered pasa_asmbl_24439.p1, internal, 219586, 219726
-recovered pasa_asmbl_24439.p1, internal, 220085, 220200
-recovered pasa_asmbl_24439.p1, internal, 220320, 220378
-recovered pasa_asmbl_24439.p1, internal, 220480, 220499
-recovered pasa_asmbl_24439.p1, internal, 220592, 220653
-recovered pasa_asmbl_24439.p1, internal, 220730, 220798
-recovered pasa_asmbl_24439.p1, internal, 221041, 221142
-recovered pasa_asmbl_24439.p1, internal, 221238, 221310
-recovered pasa_asmbl_24439.p1, internal, 221628, 221704
Couldn't classify 15069, 15135
Sorry, prediction pasa_asmbl_24428.p1 fails validation.
(ATG)	 CT	12175-12304	GT	AGG
(TGA)	 AG	12452-12530	GT	AGG
(TGA)	 AG	15069-15135	GA	GCG
-recovered pasa_asmbl_24428.p1, initial, 12175, 12304
-recovered pasa_asmbl_24428.p1, internal, 12452, 12530
Valid prediction for snap_scaffold_2-snap.1257-T1
Valid prediction for snap_scaffold_2-snap.1262-T1
Valid prediction for GlimmerHMM_glimmerT_3847-T1
Valid prediction for GlimmerHMM_glimmerT_3846-T1
Valid prediction for CodingQuarry_transcript_28561-T1
Valid prediction for HiQ_model.g2578.t1
Valid prediction for Augustus_model.g2570.t1
Valid prediction for Augustus_model.g2576.t1
Valid prediction for snap_scaffold_2-snap.1247-T1
Valid prediction for CodingQuarry_transcript_28563-T1
Couldn't classify 209649, 209677
Couldn't classify 211012, 211051
Sorry, prediction pasa_asmbl_24432.p1 fails validation.
(TAT)	 AC	209649-209677	GT	AGG
(GGT)	 AG	209906-209974	GT	AGG
(TGT)	 AG	210083-210209	GC	AGG
(GTT)	 AG	210290-210355	GT	AAG
(TTC)	 AG	210440-210499	GT	AGG
(GGA)	 AG	210592-210681	GT	AGG
(GGA)	 AG	210786-210892	GT	AGG
(TGC)	 AG	211012-211051	CC	AAC
-recovered pasa_asmbl_24432.p1, internal, 209906, 209974
-recovered pasa_asmbl_24432.p1, internal, 210083, 210209
-recovered pasa_asmbl_24432.p1, internal, 210290, 210355
-recovered pasa_asmbl_24432.p1, internal, 210440, 210499
-recovered pasa_asmbl_24432.p1, internal, 210592, 210681
-recovered pasa_asmbl_24432.p1, internal, 210786, 210892
Valid prediction for snap_scaffold_2-snap.1282-T1
Valid prediction for GlimmerHMM_glimmerT_3852-T1
Valid prediction for Augustus_model.g2571.t1
Valid prediction for Augustus_model.g2572.t1
Valid prediction for snap_scaffold_2-snap.1268-T1
Valid prediction for snap_scaffold_2-snap.1283-T1
Couldn't classify 6069, 6107
Couldn't classify 7602, 7723
Sorry, prediction pasa_asmbl_24427.p1 fails validation.
(CAT)	 GT	6069-6107	GT	AGG
(CCA)	 AG	6402-6627	GT	CCG
(TGC)	 AG	6906-7021	GT	AGG
(TTG)	 AG	7229-7433	GT	AGG
(TTC)	 AG	7602-7723	GG	CAG
-recovered pasa_asmbl_24427.p1, internal, 6402, 6627
-recovered pasa_asmbl_24427.p1, internal, 6906, 7021
-recovered pasa_asmbl_24427.p1, internal, 7229, 7433
Valid prediction for CodingQuarry_transcript_28562-T1
Valid prediction for snap_scaffold_2-snap.1252-T1
Valid prediction for snap_scaffold_2-snap.1253-T1
Valid prediction for snap_scaffold_2-snap.1275-T1
Couldn't classify 208439, 208498
Couldn't classify 209318, 209383
Sorry, prediction pasa_asmbl_25376.p1 fails validation.
(CAT)	 AA	208439-208498	GT	CGG
(TGC)	 AG	208621-208706	GT	GAG
(CCC)	 AG	208823-208957	GT	AGG
(TGA)	 AG	209037-209133	GT	CAG
(AAC)	 AG	209318-209383	GG	CAG
add_exon() Sorry, pasa_asmbl_25376.p1 208621-208706-terminal-2 is invalid.
-recovered pasa_asmbl_25376.p1, terminal, 208621, 208706
-recovered pasa_asmbl_25376.p1, internal, 208621, 208706
-recovered pasa_asmbl_25376.p1, internal, 208823, 208957
-recovered pasa_asmbl_25376.p1, internal, 209037, 209133
Valid prediction for GlimmerHMM_glimmerT_3842-T1
Valid prediction for GlimmerHMM_glimmerT_3837-T1
Valid prediction for snap_scaffold_2-snap.1284-T1
Valid prediction for Augustus_model.g2566.t1
Valid prediction for Augustus_model.g2568.t1
Valid prediction for GlimmerHMM_glimmerT_3850-T1
Valid prediction for HiQ_model.g2577.t1
Valid prediction for GlimmerHMM_glimmerT_3856-T1
Valid prediction for GlimmerHMM_glimmerT_3839-T1
Valid prediction for pasa_asmbl_24433.p1
Valid prediction for Augustus_model.g2567.t1
Couldn't classify 224054, 224083
Sorry, prediction pasa_asmbl_24440.p1 fails validation.
(CAA)	 TG	224054-224083	GT	GGG
(GTC)	 AG	224613-224715	GT	GGG
(CCA)	 AG	224822-224962	GT	ACG
(TCA)	 AG	225485-225600	GT	AGG
(GTC)	 AG	225790-225845	GT	AGG
(TGA)	 AG	225936-225967	GT	CAG
(GAG)	 AG	226062-226123	GT	AGG
(GCC)	 AG	226403-226471	GT	AGG
(TTT)	 AG	226631-226732	GT	TGG
(CTT)	 AG	226953-227025	GT	AGG
(ACA)	 AG	228165-228238	GC	GAG
-recovered pasa_asmbl_24440.p1, terminal, 228165, 228238
-recovered pasa_asmbl_24440.p1, internal, 224613, 224715
-recovered pasa_asmbl_24440.p1, internal, 224822, 224962
-recovered pasa_asmbl_24440.p1, internal, 225485, 225600
-recovered pasa_asmbl_24440.p1, internal, 225790, 225845
-recovered pasa_asmbl_24440.p1, internal, 225936, 225967
-recovered pasa_asmbl_24440.p1, internal, 226062, 226123
-recovered pasa_asmbl_24440.p1, internal, 226403, 226471
-recovered pasa_asmbl_24440.p1, internal, 226631, 226732
-recovered pasa_asmbl_24440.p1, internal, 226953, 227025
-recovered pasa_asmbl_24440.p1, internal, 228165, 228238
Valid prediction for snap_scaffold_2-snap.1270-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.g2569.t1
Valid prediction for snap_scaffold_2-snap.1246-T1
Valid prediction for snap_scaffold_2-snap.1265-T1
Couldn't classify 78953, 78981
Couldn't classify 82933, 83070
Sorry, prediction pasa_asmbl_23159.p1 fails validation.
(GCA)	 CG	78953-78981	GT	AGG
(GTC)	 AG	79734-79781	GT	TGG
(TAG)	 AG	80203-80383	GT	AGG
(CAC)	 AG	80490-80632	GT	AGG
(AGA)	 AG	80876-80972	GT	AGG
(GTC)	 AG	81142-81223	GT	AGG
(ACG)	 AG	81473-81558	GT	AGG
(GTG)	 AG	81643-81791	GT	AAG
(ACT)	 AG	81952-82198	GT	AGG
(TCG)	 AG	82402-82527	GT	AGG
(GGT)	 AG	82618-82770	GT	AGG
(GTG)	 AG	82933-83070	TA	GAT
-recovered pasa_asmbl_23159.p1, internal, 79734, 79781
-recovered pasa_asmbl_23159.p1, internal, 80203, 80383
-recovered pasa_asmbl_23159.p1, internal, 80490, 80632
-recovered pasa_asmbl_23159.p1, internal, 80876, 80972
-recovered pasa_asmbl_23159.p1, internal, 81142, 81223
-recovered pasa_asmbl_23159.p1, internal, 81473, 81558
-recovered pasa_asmbl_23159.p1, internal, 81643, 81791
-recovered pasa_asmbl_23159.p1, internal, 81952, 82198
-recovered pasa_asmbl_23159.p1, internal, 82402, 82527
-recovered pasa_asmbl_23159.p1, internal, 82618, 82770
Valid prediction for HiQ_model.g2574.t1
Valid prediction for snap_scaffold_2-snap.1274-T1
Valid prediction for snap_scaffold_2-snap.1266-T1
Valid prediction for GlimmerHMM_glimmerT_3843-T1
Valid prediction for CodingQuarry_transcript_28560-T1
Valid prediction for snap_scaffold_2-snap.1278-T1
Valid prediction for snap_scaffold_2-snap.1272-T1
Valid prediction for Augustus_model.g2573.t1
Valid prediction for snap_scaffold_2-snap.1260-T1
Valid prediction for snap_scaffold_2-snap.1254-T1
Valid prediction for snap_scaffold_2-snap.1248-T1
Valid prediction for snap_scaffold_2-snap.1279-T1
Valid prediction for snap_scaffold_2-snap.1267-T1
Valid prediction for snap_scaffold_2-snap.1249-T1
Valid prediction for Augustus_model.g2579.t1
Valid prediction for snap_scaffold_2-snap.1250-T1
Valid prediction for HiQ_model.g2575.t1
Valid prediction for GlimmerHMM_glimmerT_3840-T1
Valid prediction for GlimmerHMM_glimmerT_3836-T1
Valid prediction for GlimmerHMM_glimmerT_3838-T1
Valid prediction for GlimmerHMM_glimmerT_3849-T1
Valid prediction for CodingQuarry_transcript_28559-T1
Valid prediction for snap_scaffold_2-snap.1263-T1
Valid prediction for pasa_asmbl_23154.p1
Valid prediction for GlimmerHMM_glimmerT_3844-T1
Valid prediction for GlimmerHMM_glimmerT_3853-T1
Valid prediction for snap_scaffold_2-snap.1261-T1
Valid prediction for snap_scaffold_2-snap.1255-T1
Valid prediction for Augustus_model.g2580.t1
Valid prediction for snap_scaffold_2-snap.1273-T1
Valid prediction for GlimmerHMM_glimmerT_3848-T1
Couldn't classify 55906, 56343
Sorry, prediction pasa_asmbl_23161.p1 fails validation.
(TCT)	 GT	55906-56343	CC	AGC
Valid prediction for GlimmerHMM_glimmerT_3854-T1
Valid prediction for snap_scaffold_2-snap.1285-T1
Valid prediction for GlimmerHMM_glimmerT_3845-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 41600, rend_intergenic: 34878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61556, rend_intergenic: 53715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91647, rend_intergenic: 86213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96729, rend_intergenic: 95025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131821, rend_intergenic: 130317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143075, rend_intergenic: 136154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 287162
-exon list size: 352


building trellis

0.3    
0.6    
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1.1    
1.4    
1.7    
2.0    
2.3    
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3.7    
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11.6    
11.9    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.5    
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16.1    
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16.7    
16.9    
17.2    
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17.8    
18.1    
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18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.0    
22.3    
22.6    
22.9    
23.2    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
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27.1    
27.4    
27.7    
28.0    
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28.5    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
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31.1    
31.4    
31.6    
31.9    
32.2    
32.5    
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33.1    
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33.6    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.1    
38.4    
38.7    
39.0    
39.3    
39.5    
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40.1    
40.4    
40.7    
41.0    
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41.5    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
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44.1    
44.4    
44.6    
44.9    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.6    
61.9    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.9    
73.2    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.8    
77.1    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.6    
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95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 41600, rend_intergenic: 34878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61556, rend_intergenic: 53715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91647, rend_intergenic: 86213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96729, rend_intergenic: 95025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131821, rend_intergenic: 130317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143075, rend_intergenic: 136154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12174
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support