-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_5377690-5612865

-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_10-snap.1210-T1
Valid prediction for snap_scaffold_10-snap.1188-T1
Valid prediction for GlimmerHMM_glimmerT_24787-T1
Valid prediction for GlimmerHMM_glimmerT_24773-T1
Valid prediction for snap_scaffold_10-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_24770-T1
Couldn't classify 176827, 176924
Sorry, prediction pasa_asmbl_3188.p1 fails validation.
(AAT)	 AG	176827-176924	GT	AAG
(GTT)	 AG	177104-177202	GT	GGG
(TCC)	 AG	177320-177421	GT	CCG
(GCT)	 AG	177594-177797	GT	GAG
(GTT)	 AG	177998-178125	GT	AGG
(TTC)	 AG	178336-178553	GT	AGG
(GTT)	 AG	178794-178901	GT	AGG
(GTG)	 AG	179051-179165	GT	AGG
(GTG)	 AG	179409-179555	GT	AGG
(ATT)	 AG	179721-179845	GT	AGG
(GAG)	 AG	179934-180028	GT	GGG
(CAA)	 AG	180452-180596	TT	AAT
-recovered pasa_asmbl_3188.p1, terminal, 180452, 180596
-recovered pasa_asmbl_3188.p1, internal, 176827, 176924
-recovered pasa_asmbl_3188.p1, internal, 177104, 177202
-recovered pasa_asmbl_3188.p1, internal, 177320, 177421
-recovered pasa_asmbl_3188.p1, internal, 177594, 177797
-recovered pasa_asmbl_3188.p1, internal, 177998, 178125
-recovered pasa_asmbl_3188.p1, internal, 178336, 178553
-recovered pasa_asmbl_3188.p1, internal, 178794, 178901
-recovered pasa_asmbl_3188.p1, internal, 179051, 179165
-recovered pasa_asmbl_3188.p1, internal, 179409, 179555
-recovered pasa_asmbl_3188.p1, internal, 179721, 179845
-recovered pasa_asmbl_3188.p1, internal, 179934, 180028
Valid prediction for GlimmerHMM_glimmerT_24767-T1
Valid prediction for snap_scaffold_10-snap.1181-T1
Valid prediction for CodingQuarry_transcript_5409-T1
Valid prediction for CodingQuarry_transcript_5408-T1
Valid prediction for snap_scaffold_10-snap.1196-T1
Valid prediction for GlimmerHMM_glimmerT_24783-T1
Valid prediction for snap_scaffold_10-snap.1208-T1
Valid prediction for snap_scaffold_10-snap.1178-T1
Valid prediction for HiQ_model.g16490.t1
Couldn't classify 72230, 72265
Sorry, prediction pasa_asmbl_3170.p2 fails validation.
(CGT)	 AA	72230-72265	GT	CTG
(TTA)	 AG	73383-73483	GT	TGG
(TGC)	 AG	73758-73803	GT	AGG
(AAG)	 AG	74131-74382	AT	AGA
-recovered pasa_asmbl_3170.p2, terminal, 74131, 74382
-recovered pasa_asmbl_3170.p2, internal, 73383, 73483
-recovered pasa_asmbl_3170.p2, internal, 73758, 73803
Valid prediction for HiQ_model.g16486.t1
Valid prediction for snap_scaffold_10-snap.1192-T1
Valid prediction for CodingQuarry_transcript_5407-T1
Valid prediction for Augustus_model.g16479.t1
Couldn't classify 8546, 8613
Couldn't classify 11976, 12034
Sorry, prediction pasa_asmbl_3165.p1 fails validation.
(GAA)	 CA	8546-8613	GT	AGG
(AAA)	 AG	9631-9724	GT	AGG
(GAT)	 AG	9948-10045	GT	TAG
(TTG)	 AG	10152-10292	GT	AGG
(ATA)	 AG	11253-11368	GT	GGG
(GCT)	 AG	11976-12034	GT	CGG
add_exon() Sorry, pasa_asmbl_3165.p1 10152-10292-terminal-1 is invalid.
-recovered pasa_asmbl_3165.p1, terminal, 10152, 10292
-recovered pasa_asmbl_3165.p1, internal, 9631, 9724
-recovered pasa_asmbl_3165.p1, internal, 9948, 10045
-recovered pasa_asmbl_3165.p1, internal, 10152, 10292
-recovered pasa_asmbl_3165.p1, internal, 11253, 11368
-recovered pasa_asmbl_3165.p1, internal, 11976, 12034
Valid prediction for snap_scaffold_10-snap.1200-T1
Valid prediction for snap_scaffold_10-snap.1198-T1
Valid prediction for Augustus_model.g16483.t1
Valid prediction for Augustus_model.g16495.t1
Valid prediction for GlimmerHMM_glimmerT_24785-T1
Valid prediction for pasa_asmbl_3172.p1
Valid prediction for snap_scaffold_10-snap.1207-T1
Valid prediction for GlimmerHMM_glimmerT_24792-T1
Valid prediction for snap_scaffold_10-snap.1187-T1
Valid prediction for HiQ_model.g16493.t1
Valid prediction for CodingQuarry_transcript_5410-T1
Valid prediction for Augustus_model.g16492.t1
Valid prediction for GlimmerHMM_glimmerT_24786-T1
Valid prediction for HiQ_model.g16481.t1
Couldn't classify 165203, 165211
Couldn't classify 172112, 172243
Sorry, prediction pasa_asmbl_3185.p1 fails validation.
(CTC)	 AA	165203-165211	GT	AGG
(GTT)	 AG	165498-165542	GT	AGG
(GTC)	 AG	165823-165900	GT	AGG
(GTT)	 AG	166165-166233	GT	AGG
(GTG)	 AG	166571-166655	GT	AGG
(GAA)	 AG	166947-167068	GT	AAG
(AGC)	 AG	167198-167288	GT	TGG
(AAT)	 AG	167590-167699	GT	AGG
(AGC)	 AG	167898-167927	GT	AGG
(CAG)	 AG	168389-168511	GT	AGG
(GAC)	 AG	168690-168829	GT	CGG
(GCA)	 AG	169112-169156	GT	CGG
(GAT)	 AG	169314-169384	GT	AGG
(TGG)	 AG	169546-169645	GT	AGG
(CAT)	 AG	169873-169960	GT	AGG
(CAA)	 AG	170225-170299	GT	AGG
(ATC)	 AG	171118-171198	GT	AGG
(GAG)	 AG	171671-171766	GT	TGG
(GCA)	 AG	171885-171983	GT	AGG
(GAG)	 AG	172112-172243	GT	AGG
-recovered pasa_asmbl_3185.p1, internal, 165498, 165542
-recovered pasa_asmbl_3185.p1, internal, 165823, 165900
-recovered pasa_asmbl_3185.p1, internal, 166165, 166233
-recovered pasa_asmbl_3185.p1, internal, 166571, 166655
-recovered pasa_asmbl_3185.p1, internal, 166947, 167068
-recovered pasa_asmbl_3185.p1, internal, 167198, 167288
-recovered pasa_asmbl_3185.p1, internal, 167590, 167699
-recovered pasa_asmbl_3185.p1, internal, 167898, 167927
-recovered pasa_asmbl_3185.p1, internal, 168389, 168511
-recovered pasa_asmbl_3185.p1, internal, 168690, 168829
-recovered pasa_asmbl_3185.p1, internal, 169112, 169156
-recovered pasa_asmbl_3185.p1, internal, 169314, 169384
-recovered pasa_asmbl_3185.p1, internal, 169546, 169645
-recovered pasa_asmbl_3185.p1, internal, 169873, 169960
-recovered pasa_asmbl_3185.p1, internal, 170225, 170299
-recovered pasa_asmbl_3185.p1, internal, 171118, 171198
-recovered pasa_asmbl_3185.p1, internal, 171671, 171766
-recovered pasa_asmbl_3185.p1, internal, 171885, 171983
-recovered pasa_asmbl_3185.p1, internal, 172112, 172243
Valid prediction for GlimmerHMM_glimmerT_24790-T1
Valid prediction for CodingQuarry_transcript_5411-T1
Valid prediction for GlimmerHMM_glimmerT_24780-T1
Valid prediction for pasa_asmbl_3182.p1
Valid prediction for GlimmerHMM_glimmerT_24779-T1
Valid prediction for GlimmerHMM_glimmerT_24778-T1
Valid prediction for snap_scaffold_10-snap.1209-T1
Valid prediction for snap_scaffold_10-snap.1184-T1
Valid prediction for HiQ_model.g16488.t1
Valid prediction for GlimmerHMM_glimmerT_24765-T1
Valid prediction for GlimmerHMM_glimmerT_24789-T1
Valid prediction for pasa_asmbl_3181.p1
Valid prediction for snap_scaffold_10-snap.1182-T1
Valid prediction for GlimmerHMM_glimmerT_24776-T1
Valid prediction for snap_scaffold_10-snap.1202-T1
Valid prediction for GlimmerHMM_glimmerT_24782-T1
Valid prediction for snap_scaffold_10-snap.1195-T1
Valid prediction for snap_scaffold_10-snap.1204-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 GlimmerHMM_glimmerT_24771-T1
Valid prediction for pasa_asmbl_4357.p1
Valid prediction for GlimmerHMM_glimmerT_24768-T1
Valid prediction for snap_scaffold_10-snap.1180-T1
Valid prediction for pasa_asmbl_4373.p2
Valid prediction for HiQ_model.g16487.t1
Valid prediction for Augustus_model.g16480.t1
Couldn't classify 120642, 120753
Sorry, prediction pasa_asmbl_4364.p1 fails validation.
(CGT)	 GA	120642-120753	GT	AAG
(CGG)	 AG	120996-121675	TA	AAT
-recovered pasa_asmbl_4364.p1, terminal, 120996, 121675
Valid prediction for GlimmerHMM_glimmerT_24772-T1
Valid prediction for snap_scaffold_10-snap.1193-T1
Valid prediction for snap_scaffold_10-snap.1186-T1
Valid prediction for snap_scaffold_10-snap.1177-T1
Valid prediction for GlimmerHMM_glimmerT_24775-T1
Valid prediction for Augustus_model.g16489.t1
Valid prediction for CodingQuarry_transcript_5413-T1
Valid prediction for GlimmerHMM_glimmerT_24774-T1
Valid prediction for snap_scaffold_10-snap.1179-T1
Valid prediction for snap_scaffold_10-snap.1191-T1
Valid prediction for pasa_asmbl_4374.p1
Valid prediction for snap_scaffold_10-snap.1190-T1
Valid prediction for GlimmerHMM_glimmerT_24764-T1
Valid prediction for snap_scaffold_10-snap.1197-T1
Valid prediction for snap_scaffold_10-snap.1183-T1
Valid prediction for snap_scaffold_10-snap.1194-T1
Valid prediction for GlimmerHMM_glimmerT_24769-T1
Valid prediction for HiQ_model.g16485.t1
Valid prediction for pasa_asmbl_4363.p1
Valid prediction for snap_scaffold_10-snap.1199-T1
Valid prediction for GlimmerHMM_glimmerT_24784-T1
Valid prediction for HiQ_model.g16491.t1
Valid prediction for snap_scaffold_10-snap.1189-T1
Valid prediction for snap_scaffold_10-snap.1201-T1
Valid prediction for GlimmerHMM_glimmerT_24781-T1
Valid prediction for GlimmerHMM_glimmerT_24766-T1
Valid prediction for HiQ_model.g16494.t1
Valid prediction for Augustus_model.g16484.t1
Valid prediction for GlimmerHMM_glimmerT_24777-T1
Valid prediction for GlimmerHMM_glimmerT_24791-T1
Valid prediction for snap_scaffold_10-snap.1203-T1
Valid prediction for CodingQuarry_transcript_5406-T1
Valid prediction for GlimmerHMM_glimmerT_24788-T1
Valid prediction for snap_scaffold_10-snap.1206-T1
Valid prediction for snap_scaffold_10-snap.1205-T1
Valid prediction for CodingQuarry_transcript_5412-T1
Valid prediction for pasa_asmbl_4365.p1
Valid prediction for Augustus_model.g16482.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 77908, rend_intergenic: 75454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173162, rend_intergenic: 168362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 235176
-exon list size: 340


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.8    
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6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
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8.8    
9.1    
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9.6    
9.9    
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10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
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13.7    
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14.6    
14.9    
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16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
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20.8    
21.1    
21.3    
21.6    
21.9    
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22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.7    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.3    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 77908, rend_intergenic: 75454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173162, rend_intergenic: 168362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support