-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_4867114-5086396

-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_14593-T1
Valid prediction for GlimmerHMM_glimmerT_14598-T1
Valid prediction for snap_scaffold_6-snap.1174-T1
Valid prediction for pasa_asmbl_46913.p1
Valid prediction for snap_scaffold_6-snap.1190-T1
Valid prediction for GlimmerHMM_glimmerT_14590-T1
Couldn't classify 184845, 185091
Sorry, prediction pasa_asmbl_46915.p1 fails validation.
(CTA)	 GA	184845-185091	GT	GGG
(GCA)	 AG	185213-185347	GT	AGG
(GTA)	 AG	185649-185935	AG	AAA
-recovered pasa_asmbl_46915.p1, terminal, 185649, 185935
-recovered pasa_asmbl_46915.p1, internal, 185213, 185347
Valid prediction for Augustus_model.g9655.t1
Valid prediction for snap_scaffold_6-snap.1150-T1
Valid prediction for snap_scaffold_6-snap.1161-T1
Valid prediction for snap_scaffold_6-snap.1175-T1
Valid prediction for Augustus_model.g9673.t1
Valid prediction for Augustus_model.g9661.t1
Valid prediction for snap_scaffold_6-snap.1167-T1
Valid prediction for snap_scaffold_6-snap.1163-T1
Valid prediction for HiQ_model.g9670.t1
Valid prediction for snap_scaffold_6-snap.1180-T1
Valid prediction for snap_scaffold_6-snap.1153-T1
Valid prediction for GlimmerHMM_glimmerT_14600-T1
Valid prediction for HiQ_model.g9669.t1
Valid prediction for Augustus_model.g9658.t1
Valid prediction for GlimmerHMM_glimmerT_14596-T1
Valid prediction for snap_scaffold_6-snap.1173-T1
Valid prediction for CodingQuarry_transcript_55032-T1
Valid prediction for snap_scaffold_6-snap.1185-T1
Valid prediction for snap_scaffold_6-snap.1172-T1
Valid prediction for GlimmerHMM_glimmerT_14585-T1
Valid prediction for CodingQuarry_transcript_55034-T1
Valid prediction for GlimmerHMM_glimmerT_14594-T1
Valid prediction for GlimmerHMM_glimmerT_14580-T1
Valid prediction for snap_scaffold_6-snap.1184-T1
Valid prediction for GlimmerHMM_glimmerT_14592-T1
Valid prediction for GlimmerHMM_glimmerT_14584-T1
Couldn't classify 127462, 127611
Sorry, prediction pasa_asmbl_46900.p1 fails validation.
(ATG)	 CC	121114-121230	GT	ATG
(TTG)	 AG	121640-121718	GT	GAG
(GGT)	 AG	121936-122033	GT	AGG
(GCT)	 AG	122141-122269	GT	AGG
(ATG)	 AG	122739-122821	GT	GGG
(GTT)	 AG	123658-123784	GT	CTG
(GGT)	 AG	123880-123962	GT	GGG
(ATT)	 AG	124084-124177	GT	TGG
(GTG)	 AG	126070-126282	GT	CGG
(GAG)	 AG	127462-127611	GG	CAG
-recovered pasa_asmbl_46900.p1, initial, 121114, 121230
-recovered pasa_asmbl_46900.p1, initial, 122739, 122821
add_exon() Sorry, pasa_asmbl_46900.p1 121640-121718-terminal-3 is invalid.
-recovered pasa_asmbl_46900.p1, terminal, 121640, 121718
-recovered pasa_asmbl_46900.p1, internal, 121640, 121718
-recovered pasa_asmbl_46900.p1, internal, 121936, 122033
-recovered pasa_asmbl_46900.p1, internal, 122141, 122269
-recovered pasa_asmbl_46900.p1, internal, 122739, 122821
-recovered pasa_asmbl_46900.p1, internal, 123658, 123784
-recovered pasa_asmbl_46900.p1, internal, 123880, 123962
-recovered pasa_asmbl_46900.p1, internal, 124084, 124177
-recovered pasa_asmbl_46900.p1, internal, 126070, 126282
Valid prediction for GlimmerHMM_glimmerT_14599-T1
Valid prediction for snap_scaffold_6-snap.1155-T1
Valid prediction for HiQ_model.g9663.t1
Valid prediction for pasa_asmbl_46904.p1
Valid prediction for Augustus_model.g9668.t1
Valid prediction for snap_scaffold_6-snap.1182-T1
Valid prediction for snap_scaffold_6-snap.1169-T1
Valid prediction for snap_scaffold_6-snap.1147-T1
Valid prediction for GlimmerHMM_glimmerT_14602-T1
Valid prediction for snap_scaffold_6-snap.1164-T1
Valid prediction for Augustus_model.g9666.t1
Valid prediction for snap_scaffold_6-snap.1187-T1
Valid prediction for snap_scaffold_6-snap.1157-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 snap_scaffold_6-snap.1148-T1
Valid prediction for GlimmerHMM_glimmerT_14587-T1
Valid prediction for CodingQuarry_transcript_55035-T1
Valid prediction for snap_scaffold_6-snap.1152-T1
Valid prediction for GlimmerHMM_glimmerT_14591-T1
Valid prediction for Augustus_model.g9656.t1
Valid prediction for pasa_asmbl_48395.p1
Valid prediction for Augustus_model.g9665.t1
Valid prediction for GlimmerHMM_glimmerT_14601-T1
Valid prediction for Augustus_model.g9660.t1
Couldn't classify 72534, 72677
Sorry, prediction pasa_asmbl_48381.p1 fails validation.
(GCT)	 GT	72534-72677	GT	AGG
(CCC)	 AG	73622-73748	GT	TGG
(CTC)	 AG	73864-73912	GT	TGG
(GAG)	 AG	74208-74387	GT	AGG
(GAA)	 AG	75174-75459	GC	GAG
-recovered pasa_asmbl_48381.p1, terminal, 75174, 75459
-recovered pasa_asmbl_48381.p1, internal, 73622, 73748
-recovered pasa_asmbl_48381.p1, internal, 73864, 73912
-recovered pasa_asmbl_48381.p1, internal, 74208, 74387
-recovered pasa_asmbl_48381.p1, internal, 75174, 75459
Valid prediction for pasa_asmbl_48390.p1
Valid prediction for GlimmerHMM_glimmerT_14603-T1
Valid prediction for Augustus_model.g9662.t1
Valid prediction for GlimmerHMM_glimmerT_14586-T1
Valid prediction for HiQ_model.g9671.t1
Valid prediction for GlimmerHMM_glimmerT_14575-T1
Valid prediction for snap_scaffold_6-snap.1162-T1
Valid prediction for GlimmerHMM_glimmerT_14582-T1
Couldn't classify 69096, 69096
Sorry, prediction CodingQuarry_transcript_55033-T1 fails validation.
(ATG)	 GC	68081-68193	GT	TGG
(ACA)	 AG	69096-69096	CA	GAC
-recovered CodingQuarry_transcript_55033-T1, initial, 68081, 68193
Valid prediction for Augustus_model.g9674.t1
Valid prediction for snap_scaffold_6-snap.1168-T1
Valid prediction for HiQ_model.g9659.t1
Valid prediction for snap_scaffold_6-snap.1156-T1
Valid prediction for snap_scaffold_6-snap.1176-T1
Couldn't classify 2420, 2532
Couldn't classify 2755, 2810
Sorry, prediction CodingQuarry_transcript_55038-T1 fails validation.
(ATG)	 GC	2420-2532	AT	GAA
(TGA)	 AC	2755-2810	GT	ATG
(CCC)	 AG	3090-3277	AG	AAA
-recovered CodingQuarry_transcript_55038-T1, terminal, 3090, 3277
Valid prediction for snap_scaffold_6-snap.1159-T1
Valid prediction for Augustus_model.g9667.t1
Valid prediction for snap_scaffold_6-snap.1188-T1
Valid prediction for snap_scaffold_6-snap.1166-T1
Valid prediction for Augustus_model.g9654.t1
Valid prediction for snap_scaffold_6-snap.1179-T1
Valid prediction for CodingQuarry_transcript_55028-T1
Valid prediction for GlimmerHMM_glimmerT_14589-T1
Valid prediction for Augustus_model.g9664.t1
Valid prediction for CodingQuarry_transcript_55030-T1
Valid prediction for GlimmerHMM_glimmerT_14583-T1
Valid prediction for snap_scaffold_6-snap.1160-T1
Valid prediction for snap_scaffold_6-snap.1186-T1
Valid prediction for GlimmerHMM_glimmerT_14577-T1
Couldn't classify 100843, 101343
Sorry, prediction pasa_asmbl_48379.p2 fails validation.
(ATG)	 CC	100843-101343	AG	TGA
Valid prediction for GlimmerHMM_glimmerT_14576-T1
Valid prediction for CodingQuarry_transcript_55027-T1
Valid prediction for snap_scaffold_6-snap.1191-T1
Valid prediction for CodingQuarry_transcript_55036-T1
Valid prediction for snap_scaffold_6-snap.1151-T1
Valid prediction for GlimmerHMM_glimmerT_14595-T1
Valid prediction for snap_scaffold_6-snap.1183-T1
Valid prediction for Augustus_model.g9657.t1
Valid prediction for snap_scaffold_6-snap.1171-T1
Valid prediction for Augustus_model.g9652.t1
Valid prediction for Augustus_model.g9653.t1
Valid prediction for snap_scaffold_6-snap.1189-T1
Couldn't classify 1564, 1743
Couldn't classify 2397, 2532
Couldn't classify 2755, 2810
Sorry, prediction pasa_asmbl_48398.p1 fails validation.
(GCC)	 GG	1564-1743	GT	TGG
(GAC)	 AG	2139-2229	GT	CGG
(TTG)	 AG	2397-2532	AT	GAA
(TGA)	 AC	2755-2810	GT	ATG
(CCC)	 AG	3090-3277	AG	AAA
-recovered pasa_asmbl_48398.p1, terminal, 3090, 3277
-recovered pasa_asmbl_48398.p1, internal, 2139, 2229
Valid prediction for CodingQuarry_transcript_55037-T1
Valid prediction for snap_scaffold_6-snap.1181-T1
Valid prediction for pasa_asmbl_48372.p1
Valid prediction for snap_scaffold_6-snap.1154-T1
Valid prediction for snap_scaffold_6-snap.1178-T1
Valid prediction for snap_scaffold_6-snap.1177-T1
Valid prediction for GlimmerHMM_glimmerT_14579-T1
Valid prediction for GlimmerHMM_glimmerT_14581-T1
Valid prediction for GlimmerHMM_glimmerT_14597-T1
Valid prediction for GlimmerHMM_glimmerT_14578-T1
Valid prediction for CodingQuarry_transcript_55029-T1
Valid prediction for snap_scaffold_6-snap.1158-T1
Valid prediction for snap_scaffold_6-snap.1165-T1
Valid prediction for snap_scaffold_6-snap.1149-T1
Valid prediction for Augustus_model.g9672.t1
Valid prediction for pasa_asmbl_48369.p1
Valid prediction for snap_scaffold_6-snap.1170-T1
Valid prediction for GlimmerHMM_glimmerT_14588-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14601, rend_intergenic: 10965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29950, rend_intergenic: 28123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32898, rend_intergenic: 30163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34011, rend_intergenic: 33336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36826, rend_intergenic: 35719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43839, rend_intergenic: 36952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59642, rend_intergenic: 56515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70004, rend_intergenic: 62116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99793, rend_intergenic: 93667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108027, rend_intergenic: 105736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177243, rend_intergenic: 175093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200669, rend_intergenic: 186323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 219283
-exon list size: 419


building trellis

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18.1    
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18.8    
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19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.1    
21.4    
21.6    
21.9    
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22.3    
22.6    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.0    
28.3    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
29.9    
30.2    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.2    
43.5    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.1    
45.4    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
48.0    
48.2    
48.5    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.5    
51.8    
52.0    
52.3    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.6    
54.9    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
56.5    
56.8    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
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62.9    
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63.9    
64.1    
64.4    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
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67.9    
68.2    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.8    
70.1    
70.3    
70.5    
70.8    
71.0    
71.3    
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72.0    
72.2    
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73.2    
73.4    
73.6    
73.9    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.4    
77.7    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.2    
82.4    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.9    
88.1    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.5    
94.8    
95.0    
95.2    
95.5    
95.7    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 14601, rend_intergenic: 10965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29950, rend_intergenic: 28123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32898, rend_intergenic: 30163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34011, rend_intergenic: 33336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36826, rend_intergenic: 35719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43839, rend_intergenic: 36952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59642, rend_intergenic: 56515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70004, rend_intergenic: 62116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99793, rend_intergenic: 93667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108027, rend_intergenic: 105736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177243, rend_intergenic: 175093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200669, rend_intergenic: 186323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support