-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_3512826-3686096

-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_13-snap.660-T1
Valid prediction for HiQ_model.g21465.t1
Valid prediction for GlimmerHMM_glimmerT_32098-T1
Valid prediction for GlimmerHMM_glimmerT_32100-T1
Valid prediction for snap_scaffold_13-snap.656-T1
Valid prediction for GeneMark_model.54991_t
Valid prediction for GeneMark_model.55000_t
Valid prediction for snap_scaffold_13-snap.655-T1
Valid prediction for GlimmerHMM_glimmerT_32094-T1
Valid prediction for HiQ_model.g21463.t1
Valid prediction for snap_scaffold_13-snap.654-T1
Valid prediction for GeneMark_model.55003_t
Valid prediction for snap_scaffold_13-snap.673-T1
Valid prediction for snap_scaffold_13-snap.650-T1
Couldn't classify 117902, 117933
Sorry, prediction pasa_asmbl_10702.p1 fails validation.
(CGT)	 AG	117902-117933	GT	AAG
(GTC)	 AG	118378-118549	GT	AGG
(GTC)	 AG	118689-118795	GT	CGG
(ACT)	 AG	118918-119039	GT	CGG
(ATC)	 AG	119283-119361	GT	AGG
(GAT)	 AG	119973-120143	GT	ATG
(GTA)	 AG	120270-120387	GT	AGG
(CTG)	 AG	120488-120639	GT	AGG
(GTT)	 AG	120751-121021	GG	GAG
-recovered pasa_asmbl_10702.p1, terminal, 120751, 121021
-recovered pasa_asmbl_10702.p1, internal, 117902, 117933
-recovered pasa_asmbl_10702.p1, internal, 118378, 118549
-recovered pasa_asmbl_10702.p1, internal, 118689, 118795
-recovered pasa_asmbl_10702.p1, internal, 118918, 119039
-recovered pasa_asmbl_10702.p1, internal, 119283, 119361
-recovered pasa_asmbl_10702.p1, internal, 119973, 120143
-recovered pasa_asmbl_10702.p1, internal, 120270, 120387
-recovered pasa_asmbl_10702.p1, internal, 120488, 120639
Valid prediction for GlimmerHMM_glimmerT_32121-T1
Valid prediction for CodingQuarry_transcript_12915-T1
Valid prediction for pasa_asmbl_10694.p1
Valid prediction for CodingQuarry_transcript_12913-T1
Valid prediction for GeneMark_model.54986_t
Valid prediction for CodingQuarry_transcript_12917-T1
Valid prediction for pasa_asmbl_10699.p1
Valid prediction for Augustus_model.g21480.t1
Valid prediction for pasa_asmbl_10691.p1
Valid prediction for snap_scaffold_13-snap.667-T1
Valid prediction for HiQ_model.g21466.t1
Valid prediction for Augustus_model.g21477.t1
Valid prediction for GeneMark_model.54997_t
Couldn't classify 113738, 113867
Couldn't classify 114624, 114730
Sorry, prediction pasa_asmbl_10700.p1 fails validation.
(CAG)	 CC	113738-113867	GT	CGG
(GTT)	 AG	114191-114400	GT	AGG
(GCC)	 AG	114624-114730	GC	AGG
-recovered pasa_asmbl_10700.p1, internal, 114191, 114400
-recovered pasa_asmbl_10700.p1, internal, 114624, 114730
Valid prediction for GlimmerHMM_glimmerT_32114-T1
Valid prediction for CodingQuarry_transcript_12920-T1
Valid prediction for HiQ_model.g21461.t1
Valid prediction for GeneMark_model.54988_t
Valid prediction for snap_scaffold_13-snap.653-T1
Valid prediction for GlimmerHMM_glimmerT_32118-T1
Valid prediction for snap_scaffold_13-snap.657-T1
Valid prediction for GeneMark_model.54993_t
Valid prediction for Augustus_model.g21468.t1
Valid prediction for GlimmerHMM_glimmerT_32099-T1
Valid prediction for GeneMark_model.54998_t
Valid prediction for GeneMark_model.54982_t
Valid prediction for pasa_asmbl_10684.p1
Valid prediction for CodingQuarry_transcript_12923-T1
Valid prediction for GeneMark_model.54996_t
Valid prediction for GlimmerHMM_glimmerT_32110-T1
Valid prediction for CodingQuarry_transcript_12916-T1
Valid prediction for snap_scaffold_13-snap.672-T1
Valid prediction for snap_scaffold_13-snap.669-T1
Valid prediction for HiQ_model.g21472.t1
Valid prediction for GlimmerHMM_glimmerT_32112-T1
Valid prediction for GlimmerHMM_glimmerT_32096-T1
Valid prediction for GeneMark_model.55002_t
Valid prediction for Augustus_model.g21478.t1
Valid prediction for GlimmerHMM_glimmerT_32116-T1
Valid prediction for GeneMark_model.55011_t
Valid prediction for snap_scaffold_13-snap.648-T1
Valid prediction for HiQ_model.g21473.t1
Valid prediction for GeneMark_model.54984_t
Valid prediction for snap_scaffold_13-snap.666-T1
Valid prediction for GeneMark_model.54987_t
Valid prediction for pasa_asmbl_10689.p1
Valid prediction for CodingQuarry_transcript_12911-T1
Valid prediction for GlimmerHMM_glimmerT_32113-T1
Valid prediction for GlimmerHMM_glimmerT_32106-T1
Valid prediction for snap_scaffold_13-snap.671-T1
Valid prediction for GlimmerHMM_glimmerT_32105-T1
Valid prediction for pasa_asmbl_10688.p1
Valid prediction for GlimmerHMM_glimmerT_32111-T1
Valid prediction for GlimmerHMM_glimmerT_32101-T1
Valid prediction for HiQ_model.g21474.t1
Valid prediction for GeneMark_model.55006_t
Valid prediction for pasa_asmbl_10697.p2
Couldn't classify 5354, 5431
Sorry, prediction pasa_asmbl_10683.p1 fails validation.
(ACT)	 TC	5354-5431	GT	AGG
(TGT)	 AG	5842-5915	GT	ACG
(TCT)	 AG	6010-6067	GT	CTG
(CGG)	 AG	6174-6246	GT	AGG
(ATC)	 AG	6341-6483	TC	AGT
-recovered pasa_asmbl_10683.p1, terminal, 6341, 6483
-recovered pasa_asmbl_10683.p1, internal, 5842, 5915
-recovered pasa_asmbl_10683.p1, internal, 6010, 6067
-recovered pasa_asmbl_10683.p1, internal, 6174, 6246
Valid prediction for GlimmerHMM_glimmerT_32120-T1
Valid prediction for CodingQuarry_transcript_12921-T1
Valid prediction for snap_scaffold_13-snap.661-T1
Valid prediction for GeneMark_model.54989_t
Valid prediction for GeneMark_model.55009_t
Valid prediction for HiQ_model.g21467.t1
Valid prediction for CodingQuarry_transcript_12922-T1
Valid prediction for snap_scaffold_13-snap.665-T1
Valid prediction for GeneMark_model.55005_t
Valid prediction for CodingQuarry_transcript_12918-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_13-snap.675-T1
Valid prediction for GeneMark_model.54985_t
Valid prediction for CodingQuarry_transcript_12914-T1
Valid prediction for Augustus_model.g21475.t1
Valid prediction for GlimmerHMM_glimmerT_32108-T1
Valid prediction for HiQ_model.g21471.t1
Valid prediction for GeneMark_model.55008_t
Valid prediction for GlimmerHMM_glimmerT_32109-T1
Valid prediction for CodingQuarry_transcript_12919-T1
Valid prediction for snap_scaffold_13-snap.658-T1
Valid prediction for snap_scaffold_13-snap.651-T1
Valid prediction for pasa_asmbl_9507.p1
Valid prediction for GlimmerHMM_glimmerT_32107-T1
Valid prediction for GeneMark_model.54992_t
Valid prediction for Augustus_model.g21470.t1
Valid prediction for GlimmerHMM_glimmerT_32093-T1
Valid prediction for GeneMark_model.54990_t
Valid prediction for GlimmerHMM_glimmerT_32115-T1
Valid prediction for snap_scaffold_13-snap.668-T1
Valid prediction for Augustus_model.g21476.t1
Valid prediction for snap_scaffold_13-snap.663-T1
Valid prediction for snap_scaffold_13-snap.662-T1
Valid prediction for pasa_asmbl_9510.p1
Valid prediction for Augustus_model.g21479.t1
Valid prediction for GlimmerHMM_glimmerT_32097-T1
Valid prediction for Augustus_model.g21460.t1
Valid prediction for snap_scaffold_13-snap.649-T1
Valid prediction for GeneMark_model.54995_t
Valid prediction for GlimmerHMM_glimmerT_32103-T1
Valid prediction for snap_scaffold_13-snap.670-T1
Valid prediction for HiQ_model.g21469.t1
Valid prediction for GeneMark_model.55010_t
Valid prediction for Augustus_model.g21481.t1
Valid prediction for GeneMark_model.54999_t
Valid prediction for snap_scaffold_13-snap.647-T1
Valid prediction for snap_scaffold_13-snap.674-T1
Valid prediction for GlimmerHMM_glimmerT_32095-T1
Valid prediction for CodingQuarry_transcript_12925-T1
Valid prediction for GlimmerHMM_glimmerT_32104-T1
Valid prediction for CodingQuarry_transcript_12912-T1
Valid prediction for GeneMark_model.54983_t
Valid prediction for GeneMark_model.55007_t
Valid prediction for GeneMark_model.54981_t
Valid prediction for GeneMark_model.55012_t
Valid prediction for Augustus_model.g21464.t1
Couldn't classify 98152, 98208
Sorry, prediction pasa_asmbl_9515.p1 fails validation.
(GTG)	 AG	98152-98208	GT	TGG
(AAC)	 AG	99060-99273	GT	AGG
(ACC)	 AG	99396-99564	GT	GGG
(ATG)	 AG	99811-99941	GT	GGG
(ACT)	 AG	100044-100126	GT	TGG
(GAA)	 AG	100227-100323	GT	AGG
(GAG)	 AG	100558-100634	CG	AGC
add_exon() Sorry, pasa_asmbl_9515.p1 99811-99941-initial-1 is invalid.
-recovered pasa_asmbl_9515.p1, initial, 99811, 99941
-recovered pasa_asmbl_9515.p1, terminal, 100558, 100634
-recovered pasa_asmbl_9515.p1, internal, 98152, 98208
-recovered pasa_asmbl_9515.p1, internal, 99060, 99273
-recovered pasa_asmbl_9515.p1, internal, 99396, 99564
-recovered pasa_asmbl_9515.p1, internal, 99811, 99941
-recovered pasa_asmbl_9515.p1, internal, 100044, 100126
-recovered pasa_asmbl_9515.p1, internal, 100227, 100323
Valid prediction for HiQ_model.g21462.t1
Valid prediction for snap_scaffold_13-snap.659-T1
Valid prediction for GlimmerHMM_glimmerT_32117-T1
Valid prediction for snap_scaffold_13-snap.664-T1
Valid prediction for GlimmerHMM_glimmerT_32102-T1
Valid prediction for GeneMark_model.55004_t
Couldn't classify 77311, 77427
Couldn't classify 77799, 77828
Sorry, prediction CodingQuarry_transcript_12924-T1 fails validation.
(ATG)	 AA	73130-73187	GT	AGG
(GCT)	 AG	73641-73786	GT	AGG
(GAT)	 AG	73919-74141	GT	CAG
(ACC)	 AG	74345-74477	GT	GGG
(GTC)	 AG	74786-74927	GT	ATG
(AGT)	 AG	75344-75407	GT	CGG
(GTA)	 AG	75541-75638	GT	AGG
(ACC)	 AG	75789-75849	GT	AGG
(CTC)	 AG	76288-76409	GT	CCG
(AAT)	 AG	76641-76715	GT	AGG
(ATC)	 AG	77311-77427	AT	TCA
(GAT)	 TC	77799-77828	GT	AGG
(ACG)	 AG	77939-78040	GT	CGG
(GTT)	 AG	78170-78196	CG	GAC
-recovered CodingQuarry_transcript_12924-T1, initial, 73130, 73187
-recovered CodingQuarry_transcript_12924-T1, terminal, 78170, 78196
-recovered CodingQuarry_transcript_12924-T1, internal, 73641, 73786
-recovered CodingQuarry_transcript_12924-T1, internal, 73919, 74141
-recovered CodingQuarry_transcript_12924-T1, internal, 74345, 74477
-recovered CodingQuarry_transcript_12924-T1, internal, 74786, 74927
-recovered CodingQuarry_transcript_12924-T1, internal, 75344, 75407
-recovered CodingQuarry_transcript_12924-T1, internal, 75541, 75638
-recovered CodingQuarry_transcript_12924-T1, internal, 75789, 75849
-recovered CodingQuarry_transcript_12924-T1, internal, 76288, 76409
-recovered CodingQuarry_transcript_12924-T1, internal, 76641, 76715
-recovered CodingQuarry_transcript_12924-T1, internal, 77939, 78040
Valid prediction for pasa_asmbl_9518.p1
Valid prediction for snap_scaffold_13-snap.652-T1
Valid prediction for GeneMark_model.55001_t
Valid prediction for GlimmerHMM_glimmerT_32119-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 152978, rend_intergenic: 148849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173271
-exon list size: 465


building trellis

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21.6    
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23.8    
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24.4    
24.6    
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25.5    
25.7    
25.9    
26.1    
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26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 152978, rend_intergenic: 148849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 162283 - 173271
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-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