-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_9912467-10147589

-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_30619-T1
Valid prediction for pasa_asmbl_26929.p1
Couldn't classify 135739, 136096
Sorry, prediction pasa_asmbl_26921.p1 fails validation.
(AGG)	 CA	135739-136096	GT	AGG
(TTG)	 AG	136298-136425	GT	AAG
-recovered pasa_asmbl_26921.p1, terminal, 136298, 136425
-recovered pasa_asmbl_26921.p1, internal, 136298, 136425
Valid prediction for GlimmerHMM_glimmerT_46693-T1
Valid prediction for GlimmerHMM_glimmerT_46674-T1
Valid prediction for GlimmerHMM_glimmerT_46699-T1
Valid prediction for snap_scaffold_20-snap.2176-T1
Valid prediction for Augustus_model.g31030.t1
Valid prediction for GlimmerHMM_glimmerT_46698-T1
Valid prediction for CodingQuarry_transcript_30626-T1
Valid prediction for GlimmerHMM_glimmerT_46686-T1
Valid prediction for Augustus_model.g31027.t1
Valid prediction for CodingQuarry_transcript_30620-T1
Valid prediction for pasa_asmbl_26936.p1
Valid prediction for snap_scaffold_20-snap.2173-T1
Valid prediction for GlimmerHMM_glimmerT_46682-T1
Valid prediction for CodingQuarry_transcript_30631-T1
Valid prediction for GlimmerHMM_glimmerT_46692-T1
Valid prediction for HiQ_model.g31014.t1
Valid prediction for Augustus_model.g31015.t1
Couldn't classify 36054, 36150
Sorry, prediction pasa_asmbl_26912.p1 fails validation.
(ATG)	 CC	30094-31776	GT	CGG
(GCG)	 AG	32236-32396	GT	AAG
(GGG)	 AG	32605-32731	GT	TTG
(TTG)	 AG	33004-33060	GT	TGG
(GGC)	 AG	33497-33619	GT	AGG
(CAG)	 AG	33954-34017	GT	TGG
(GAG)	 AG	35447-35570	GT	AGG
(AAA)	 AG	36054-36150	CA	TCC
-recovered pasa_asmbl_26912.p1, initial, 30094, 31776
-recovered pasa_asmbl_26912.p1, internal, 32236, 32396
-recovered pasa_asmbl_26912.p1, internal, 32605, 32731
-recovered pasa_asmbl_26912.p1, internal, 33004, 33060
-recovered pasa_asmbl_26912.p1, internal, 33497, 33619
-recovered pasa_asmbl_26912.p1, internal, 33954, 34017
-recovered pasa_asmbl_26912.p1, internal, 35447, 35570
Valid prediction for CodingQuarry_transcript_30625-T1
Valid prediction for pasa_asmbl_26916.p1
Valid prediction for snap_scaffold_20-snap.2151-T1
Valid prediction for CodingQuarry_transcript_30634-T1
Valid prediction for snap_scaffold_20-snap.2157-T1
Valid prediction for Augustus_model.g31020.t1
Valid prediction for GlimmerHMM_glimmerT_46684-T1
Valid prediction for snap_scaffold_20-snap.2152-T1
Valid prediction for CodingQuarry_transcript_30623-T1
Valid prediction for GlimmerHMM_glimmerT_46680-T1
Valid prediction for HiQ_model.g31025.t1
Valid prediction for GlimmerHMM_glimmerT_46695-T1
Valid prediction for snap_scaffold_20-snap.2166-T1
Valid prediction for snap_scaffold_20-snap.2172-T1
Valid prediction for snap_scaffold_20-snap.2180-T1
Valid prediction for Augustus_model.g31007.t1
Valid prediction for HiQ_model.g31011.t1
Valid prediction for GlimmerHMM_glimmerT_46668-T1
Valid prediction for pasa_asmbl_26926.p1
Couldn't classify 194109, 194537
Sorry, prediction pasa_asmbl_26928.p1 fails validation.
(CAG)	 CC	194109-194537	AG	TAA
Valid prediction for snap_scaffold_20-snap.2162-T1
Valid prediction for CodingQuarry_transcript_30630-T1
Valid prediction for snap_scaffold_20-snap.2169-T1
Valid prediction for GlimmerHMM_glimmerT_46703-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_46688-T1
Valid prediction for snap_scaffold_20-snap.2156-T1
Valid prediction for snap_scaffold_20-snap.2153-T1
Valid prediction for snap_scaffold_20-snap.2177-T1
Valid prediction for pasa_asmbl_26933.p1
Valid prediction for Augustus_model.g31006.t1
Valid prediction for CodingQuarry_transcript_30629-T1
Valid prediction for snap_scaffold_20-snap.2179-T1
Valid prediction for GlimmerHMM_glimmerT_46696-T1
Valid prediction for Augustus_model.g31023.t1
Valid prediction for snap_scaffold_20-snap.2174-T1
Valid prediction for HiQ_model.g31019.t1
Valid prediction for CodingQuarry_transcript_30624-T1
Valid prediction for GlimmerHMM_glimmerT_46679-T1
Couldn't classify 195644, 195766
Sorry, prediction pasa_asmbl_26930.p1 fails validation.
(CAG)	 AG	195644-195766	GT	AGG
(CTC)	 AG	195917-196006	GT	AGG
(CTG)	 AG	196136-196219	GT	AGG
(AGG)	 AG	196359-196520	GC	GAG
-recovered pasa_asmbl_26930.p1, terminal, 196359, 196520
-recovered pasa_asmbl_26930.p1, internal, 195644, 195766
-recovered pasa_asmbl_26930.p1, internal, 195917, 196006
-recovered pasa_asmbl_26930.p1, internal, 196136, 196219
-recovered pasa_asmbl_26930.p1, internal, 196359, 196520
Valid prediction for GlimmerHMM_glimmerT_46681-T1
Valid prediction for GlimmerHMM_glimmerT_46669-T1
Valid prediction for CodingQuarry_transcript_30633-T1
Couldn't classify 183571, 183755
Sorry, prediction pasa_asmbl_26923.p1 fails validation.
(ATG)	 CA	180112-180158	GT	CGG
(GGA)	 AG	180739-180808	GT	AGG
(GTT)	 AG	182423-182539	GT	CAG
(GAA)	 AG	182842-182939	GT	AGG
(TTA)	 AG	183217-183326	GT	GGG
(ACC)	 AG	183571-183755	GA	CAG
-recovered pasa_asmbl_26923.p1, initial, 180112, 180158
-recovered pasa_asmbl_26923.p1, internal, 180739, 180808
-recovered pasa_asmbl_26923.p1, internal, 182423, 182539
-recovered pasa_asmbl_26923.p1, internal, 182842, 182939
-recovered pasa_asmbl_26923.p1, internal, 183217, 183326
Valid prediction for snap_scaffold_20-snap.2165-T1
Valid prediction for GlimmerHMM_glimmerT_46673-T1
Valid prediction for GlimmerHMM_glimmerT_46687-T1
Couldn't classify 221100, 221190
Sorry, prediction pasa_asmbl_26938.p1 fails validation.
(TTG)	 GG	221100-221190	GT	TGG
(AGG)	 AG	221397-221643	GT	CAG
(AGC)	 AG	221799-221868	GT	AGG
(GAG)	 AG	222324-222410	GT	AGG
(ATC)	 AG	222715-222848	GT	AGG
(ACT)	 AG	223010-223070	CA	AAC
-recovered pasa_asmbl_26938.p1, terminal, 223010, 223070
-recovered pasa_asmbl_26938.p1, internal, 221397, 221643
-recovered pasa_asmbl_26938.p1, internal, 221799, 221868
-recovered pasa_asmbl_26938.p1, internal, 222324, 222410
-recovered pasa_asmbl_26938.p1, internal, 222715, 222848
Valid prediction for GlimmerHMM_glimmerT_46702-T1
Valid prediction for snap_scaffold_20-snap.2182-T1
Valid prediction for snap_scaffold_20-snap.2161-T1
Valid prediction for GlimmerHMM_glimmerT_46691-T1
Valid prediction for Augustus_model.g31016.t1
Valid prediction for Augustus_model.g31009.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_20-snap.2158-T1
Valid prediction for snap_scaffold_20-snap.2178-T1
Valid prediction for pasa_asmbl_26081.p1
Valid prediction for GlimmerHMM_glimmerT_46671-T1
Valid prediction for Augustus_model.g31008.t1
Valid prediction for Augustus_model.g31021.t1
Valid prediction for GlimmerHMM_glimmerT_46700-T1
Valid prediction for snap_scaffold_20-snap.2154-T1
Valid prediction for snap_scaffold_20-snap.2167-T1
Valid prediction for GlimmerHMM_glimmerT_46683-T1
Valid prediction for GlimmerHMM_glimmerT_46685-T1
Valid prediction for snap_scaffold_20-snap.2159-T1
Valid prediction for GlimmerHMM_glimmerT_46664-T1
Valid prediction for Augustus_model.g31005.t1
Valid prediction for Augustus_model.g31029.t1
Valid prediction for GlimmerHMM_glimmerT_46697-T1
Valid prediction for pasa_asmbl_26080.p1
Valid prediction for GlimmerHMM_glimmerT_46672-T1
Valid prediction for CodingQuarry_transcript_30622-T1
Valid prediction for HiQ_model.g31010.t1
Couldn't classify 230012, 230214
Sorry, prediction pasa_asmbl_26061.p1 fails validation.
(ATG)	 AC	229589-229733	GT	AGG
(GTG)	 AG	230012-230214	AA	CCA
-recovered pasa_asmbl_26061.p1, initial, 229589, 229733
Valid prediction for GlimmerHMM_glimmerT_46689-T1
Valid prediction for HiQ_model.g31022.t1
Couldn't classify 159788, 159964
Sorry, prediction pasa_asmbl_26072.p1 fails validation.
(CTG)	 CC	159788-159964	GT	AGG
(CCC)	 AG	160106-160780	GG	GAG
-recovered pasa_asmbl_26072.p1, terminal, 160106, 160780
Couldn't classify 24381, 24918
Sorry, prediction pasa_asmbl_26086.p1 fails validation.
(ATG)	 AG	23387-23535	GT	AGG
(GAA)	 AG	23718-23808	GT	AGG
(TAT)	 AG	23949-24067	GT	AAG
(GTA)	 AG	24381-24918	GA	CCG
-recovered pasa_asmbl_26086.p1, initial, 23387, 23535
-recovered pasa_asmbl_26086.p1, internal, 23387, 23535
-recovered pasa_asmbl_26086.p1, internal, 23718, 23808
-recovered pasa_asmbl_26086.p1, internal, 23949, 24067
Valid prediction for HiQ_model.g31017.t1
Valid prediction for Augustus_model.g31018.t1
Couldn't classify 233475, 233509
Couldn't classify 234102, 234290
Sorry, prediction pasa_asmbl_26331.p2 fails validation.
(CAT)	 CT	233475-233509	GT	AAG
(GCT)	 AG	233819-233915	GT	AGG
(GCA)	 AG	234102-234290	TC	AGT
-recovered pasa_asmbl_26331.p2, internal, 233819, 233915
Valid prediction for HiQ_model.g31012.t1
Valid prediction for snap_scaffold_20-snap.2168-T1
Valid prediction for snap_scaffold_20-snap.2164-T1
Valid prediction for GlimmerHMM_glimmerT_46666-T1
Valid prediction for pasa_asmbl_26068.p1
Valid prediction for GlimmerHMM_glimmerT_46667-T1
Valid prediction for GlimmerHMM_glimmerT_46701-T1
Valid prediction for GlimmerHMM_glimmerT_46677-T1
Valid prediction for snap_scaffold_20-snap.2175-T1
Valid prediction for GlimmerHMM_glimmerT_46670-T1
Valid prediction for Augustus_model.g31004.t1
Valid prediction for CodingQuarry_transcript_30628-T1
Valid prediction for GlimmerHMM_glimmerT_46676-T1
Valid prediction for pasa_asmbl_26076.p1
Valid prediction for HiQ_model.g31026.t1
Valid prediction for snap_scaffold_20-snap.2163-T1
Couldn't classify 153294, 153422
Couldn't classify 154127, 154176
Sorry, prediction pasa_asmbl_26073.p1 fails validation.
(TCG)	 AC	153294-153422	GT	AGG
(GTG)	 AG	153728-153896	GT	AGG
(GAT)	 AG	154127-154176	GA	ATG
-recovered pasa_asmbl_26073.p1, internal, 153728, 153896
Valid prediction for snap_scaffold_20-snap.2181-T1
Valid prediction for GlimmerHMM_glimmerT_46694-T1
Valid prediction for snap_scaffold_20-snap.2171-T1
Valid prediction for Augustus_model.g31013.t1
Valid prediction for snap_scaffold_20-snap.2150-T1
Valid prediction for GlimmerHMM_glimmerT_46665-T1
Valid prediction for Augustus_model.g31024.t1
Valid prediction for snap_scaffold_20-snap.2160-T1
Valid prediction for GlimmerHMM_glimmerT_46678-T1
Valid prediction for snap_scaffold_20-snap.2155-T1
Valid prediction for CodingQuarry_transcript_30632-T1
Valid prediction for GlimmerHMM_glimmerT_46690-T1
Valid prediction for Augustus_model.g31028.t1
Valid prediction for GlimmerHMM_glimmerT_46675-T1
Valid prediction for snap_scaffold_20-snap.2170-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 84637, rend_intergenic: 84025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 235123
-exon list size: 383


building trellis

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3.4    
3.6    
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15.3    
15.6    
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17.1    
17.4    
17.7    
17.9    
18.2    
18.4    
18.7    
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19.2    
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20.3    
20.5    
20.8    
21.0    
21.3    
21.6    
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22.1    
22.3    
22.6    
22.9    
23.1    
23.4    
23.6    
23.9    
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24.4    
24.7    
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25.5    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.5    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
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    
34.5    
34.8    
35.1    
35.3    
35.6    
35.8    
36.1    
36.4    
36.6    
36.9    
37.1    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.8    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.8    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.9    
63.1    
63.4    
63.6    
63.9    
64.2    
64.4    
64.7    
64.9    
65.2    
65.5    
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    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.5    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.4    
76.6    
76.9    
77.1    
77.4    
77.7    
77.9    
78.2    
78.4    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.8    
87.0    
87.3    
87.5    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.5    
92.7    
93.0    
93.2    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.4    
96.6    
96.9    
97.1    
97.4    
97.7    
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: 84637, rend_intergenic: 84025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support