-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_7193305-7470014

-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_19-snap.1466-T1
Valid prediction for snap_scaffold_19-snap.1468-T1
Valid prediction for GeneMark_model.79285_t
Valid prediction for GeneMark_model.79278_t
Valid prediction for GeneMark_model.79275_t
Valid prediction for snap_scaffold_19-snap.1448-T1
Valid prediction for Augustus_model.g30253.t1
Valid prediction for Augustus_model.g30248.t1
Valid prediction for snap_scaffold_19-snap.1450-T1
Valid prediction for GlimmerHMM_glimmerT_45380-T1
Valid prediction for GlimmerHMM_glimmerT_45373-T1
Valid prediction for GeneMark_model.79286_t
Valid prediction for GlimmerHMM_glimmerT_45375-T1
Valid prediction for snap_scaffold_19-snap.1454-T1
Valid prediction for snap_scaffold_19-snap.1465-T1
Valid prediction for GlimmerHMM_glimmerT_45388-T1
Valid prediction for snap_scaffold_19-snap.1439-T1
Couldn't classify 261694, 261733
Sorry, prediction pasa_asmbl_22719.p1 fails validation.
(GGA)	 CA	261694-261733	GT	TCG
(AGG)	 AG	261863-261913	GT	AGG
(GTA)	 AG	262909-262947	GT	AGG
(GGG)	 AG	263099-263277	AA	GAA
-recovered pasa_asmbl_22719.p1, terminal, 263099, 263277
-recovered pasa_asmbl_22719.p1, internal, 261863, 261913
-recovered pasa_asmbl_22719.p1, internal, 262909, 262947
Valid prediction for snap_scaffold_19-snap.1461-T1
Valid prediction for snap_scaffold_19-snap.1445-T1
Valid prediction for snap_scaffold_19-snap.1437-T1
Valid prediction for Augustus_model.g30250.t1
Valid prediction for snap_scaffold_19-snap.1444-T1
Valid prediction for snap_scaffold_19-snap.1449-T1
Valid prediction for GeneMark_model.79277_t
Valid prediction for GlimmerHMM_glimmerT_45366-T1
Couldn't classify 232345, 232377
Sorry, prediction pasa_asmbl_22258.p1 fails validation.
(AAG)	 AT	232345-232377	GT	ACG
(TAT)	 AG	232647-232802	GT	GGG
(CAA)	 AG	232882-233031	GC	AGG
-recovered pasa_asmbl_22258.p1, terminal, 232882, 233031
-recovered pasa_asmbl_22258.p1, internal, 232647, 232802
-recovered pasa_asmbl_22258.p1, internal, 232882, 233031
Valid prediction for GeneMark_model.79296_t
Valid prediction for snap_scaffold_19-snap.1470-T1
Valid prediction for snap_scaffold_19-snap.1441-T1
Valid prediction for snap_scaffold_19-snap.1458-T1
Valid prediction for snap_scaffold_19-snap.1440-T1
Valid prediction for snap_scaffold_19-snap.1464-T1
Couldn't classify 184574, 184687
Couldn't classify 184983, 185129
Sorry, prediction pasa_asmbl_22732.p1 fails validation.
(GGA)	 GG	184574-184687	GT	AAG
(AAC)	 AG	184777-184842	GT	AGG
(ATC)	 AG	184983-185129	CT	TGC
-recovered pasa_asmbl_22732.p1, internal, 184777, 184842
Valid prediction for GlimmerHMM_glimmerT_45376-T1
Valid prediction for Augustus_model.g30245.t1
Valid prediction for GlimmerHMM_glimmerT_45362-T1
Couldn't classify 181557, 181600
Couldn't classify 183001, 183036
Sorry, prediction pasa_asmbl_22256.p1 fails validation.
(TTT)	 TC	181557-181600	GT	ATG
(CAA)	 AG	181725-181851	GT	AAG
(GTG)	 AG	181945-182067	GT	AGG
(GAC)	 AG	182151-182247	GT	GGG
(ATG)	 AG	182346-182470	GT	AGG
(GAA)	 AG	182584-182717	GT	AAG
(GAC)	 AG	182801-182888	GT	AGG
(GTG)	 AG	183001-183036	GA	TCG
add_exon() Sorry, pasa_asmbl_22256.p1 182346-182470-initial-1 is invalid.
-recovered pasa_asmbl_22256.p1, initial, 182346, 182470
-recovered pasa_asmbl_22256.p1, internal, 181725, 181851
-recovered pasa_asmbl_22256.p1, internal, 181945, 182067
-recovered pasa_asmbl_22256.p1, internal, 182151, 182247
-recovered pasa_asmbl_22256.p1, internal, 182346, 182470
-recovered pasa_asmbl_22256.p1, internal, 182584, 182717
-recovered pasa_asmbl_22256.p1, internal, 182801, 182888
Valid prediction for CodingQuarry_transcript_25647-T1
Valid prediction for Augustus_model.g30255.t1
Valid prediction for GlimmerHMM_glimmerT_45387-T1
Valid prediction for Augustus_model.g30256.t1
Valid prediction for snap_scaffold_19-snap.1457-T1
Valid prediction for snap_scaffold_19-snap.1459-T1
Valid prediction for snap_scaffold_19-snap.1452-T1
Valid prediction for GlimmerHMM_glimmerT_45370-T1
Valid prediction for snap_scaffold_19-snap.1455-T1
Couldn't classify 170515, 171240
Sorry, prediction pasa_asmbl_22255.p1 fails validation.
(ACG)	 CC	170515-171240	GT	TGG
(CTC)	 AG	171393-171425	TG	GAT
-recovered pasa_asmbl_22255.p1, terminal, 171393, 171425
Valid prediction for GeneMark_model.79273_t
Valid prediction for GlimmerHMM_glimmerT_45379-T1
Valid prediction for GlimmerHMM_glimmerT_45372-T1
Valid prediction for GlimmerHMM_glimmerT_45369-T1
Valid prediction for GeneMark_model.79290_t
Valid prediction for snap_scaffold_19-snap.1443-T1
Valid prediction for snap_scaffold_19-snap.1438-T1
Valid prediction for Augustus_model.g30246.t1
Valid prediction for Augustus_model.g30243.t1
Valid prediction for GlimmerHMM_glimmerT_45389-T1
Valid prediction for snap_scaffold_19-snap.1453-T1
Valid prediction for GeneMark_model.79279_t
Valid prediction for GlimmerHMM_glimmerT_45384-T1
Valid prediction for snap_scaffold_19-snap.1446-T1
Valid prediction for GeneMark_model.79281_t
Valid prediction for snap_scaffold_19-snap.1451-T1
Valid prediction for snap_scaffold_19-snap.1442-T1
Valid prediction for Augustus_model.g30244.t1
Valid prediction for GeneMark_model.79288_t
Valid prediction for GlimmerHMM_glimmerT_45365-T1
Valid prediction for GlimmerHMM_glimmerT_45377-T1
Valid prediction for GeneMark_model.79283_t
Valid prediction for snap_scaffold_19-snap.1467-T1
Valid prediction for Augustus_model.g30254.t1
Valid prediction for GeneMark_model.79292_t

-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 HiQ_model.g30247.t1
Valid prediction for snap_scaffold_19-snap.1469-T1
Valid prediction for snap_scaffold_19-snap.1435-T1
Valid prediction for GeneMark_model.79274_t
Valid prediction for snap_scaffold_19-snap.1456-T1
Valid prediction for snap_scaffold_19-snap.1436-T1
Valid prediction for pasa_asmbl_21450.p1
Valid prediction for GeneMark_model.79287_t
Valid prediction for GeneMark_model.79280_t
Valid prediction for CodingQuarry_transcript_25646-T1
Valid prediction for GeneMark_model.79284_t
Valid prediction for GlimmerHMM_glimmerT_45386-T1
Valid prediction for GlimmerHMM_glimmerT_45378-T1
Valid prediction for GlimmerHMM_glimmerT_45367-T1
Valid prediction for HiQ_model.g30249.t1
Couldn't classify 212625, 212735
Couldn't classify 216096, 216122
Sorry, prediction pasa_asmbl_21446.p1 fails validation.
(AGG)	 AC	212625-212735	GT	AGG
(GGC)	 AG	214719-214817	GC	AGG
(TAT)	 AG	214937-215010	GT	GCG
(GCT)	 AG	215143-215195	GT	TGG
(AAA)	 AG	215409-215494	GT	AGG
(ATT)	 AG	215682-215912	GT	CTG
(TGT)	 AG	216096-216122	CG	TGC
-recovered pasa_asmbl_21446.p1, internal, 214719, 214817
-recovered pasa_asmbl_21446.p1, internal, 214937, 215010
-recovered pasa_asmbl_21446.p1, internal, 215143, 215195
-recovered pasa_asmbl_21446.p1, internal, 215409, 215494
-recovered pasa_asmbl_21446.p1, internal, 215682, 215912
Valid prediction for GeneMark_model.79294_t
Valid prediction for GlimmerHMM_glimmerT_45371-T1
Valid prediction for CodingQuarry_transcript_25645-T1
Valid prediction for snap_scaffold_19-snap.1434-T1
Valid prediction for snap_scaffold_19-snap.1460-T1
Valid prediction for snap_scaffold_19-snap.1471-T1
Couldn't classify 55763, 55814
Couldn't classify 55932, 58303
Sorry, prediction pasa_asmbl_21452.p1 fails validation.
(CTC)	 CA	55763-55814	GT	AGG
(TGC)	 AG	55932-58303	AT	TCA
Valid prediction for GeneMark_model.79276_t
Valid prediction for GeneMark_model.79271_t
Valid prediction for snap_scaffold_19-snap.1463-T1
Valid prediction for GlimmerHMM_glimmerT_45383-T1
Valid prediction for snap_scaffold_19-snap.1447-T1
Valid prediction for GlimmerHMM_glimmerT_45363-T1
Valid prediction for GeneMark_model.79291_t
Valid prediction for GeneMark_model.79295_t
Valid prediction for pasa_asmbl_21913.p1
Valid prediction for GeneMark_model.79289_t
Valid prediction for GlimmerHMM_glimmerT_45385-T1
Valid prediction for GlimmerHMM_glimmerT_45364-T1
Valid prediction for GeneMark_model.79282_t
Valid prediction for Augustus_model.g30252.t1
Valid prediction for HiQ_model.g30251.t1
Valid prediction for GlimmerHMM_glimmerT_45374-T1
Valid prediction for GlimmerHMM_glimmerT_45368-T1
Valid prediction for GlimmerHMM_glimmerT_45382-T1
Valid prediction for snap_scaffold_19-snap.1462-T1
Valid prediction for Augustus_model.g30241.t1
Valid prediction for GeneMark_model.79293_t
Valid prediction for Augustus_model.g30242.t1
Valid prediction for GlimmerHMM_glimmerT_45381-T1
Couldn't classify 62159, 62413
Sorry, prediction pasa_asmbl_21451.p1 fails validation.
(GAT)	 GA	62159-62413	GT	AGG
(TCA)	 AG	62593-62817	GA	GAG
-recovered pasa_asmbl_21451.p1, terminal, 62593, 62817
Valid prediction for GeneMark_model.79272_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 134731, rend_intergenic: 117819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 145629, rend_intergenic: 145626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 276710
-exon list size: 554


building trellis

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26.8    
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28.2    
28.4    
28.6    
28.8    
29.0    
29.1    
29.3    
29.5    
29.7    
29.9    
30.0    
30.2    
30.4    
30.6    
30.8    
30.9    
31.1    
31.3    
31.5    
31.7    
31.8    
32.0    
32.2    
32.4    
32.6    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.4    
34.5    
34.7    
34.9    
35.1    
35.3    
35.4    
35.6    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
37.9    
38.1    
38.3    
38.5    
38.7    
38.8    
39.0    
39.2    
39.4    
39.6    
39.7    
39.9    
40.1    
40.3    
40.5    
40.6    
40.8    
41.0    
41.2    
41.4    
41.5    
41.7    
41.9    
42.1    
42.3    
42.4    
42.6    
42.8    
43.0    
43.2    
43.3    
43.5    
43.7    
43.9    
44.1    
44.2    
44.4    
44.6    
44.8    
45.0    
45.1    
45.3    
45.5    
45.7    
45.9    
46.0    
46.2    
46.4    
46.6    
46.8    
46.9    
47.1    
47.3    
47.5    
47.7    
47.8    
48.0    
48.2    
48.4    
48.6    
48.7    
48.9    
49.1    
49.3    
49.5    
49.6    
49.8    
50.0    
50.2    
50.4    
50.5    
50.7    
50.9    
51.1    
51.3    
51.4    
51.6    
51.8    
52.0    
52.2    
52.3    
52.5    
52.7    
52.9    
53.1    
53.2    
53.4    
53.6    
53.8    
54.0    
54.1    
54.3    
54.5    
54.7    
54.9    
55.0    
55.2    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
56.5    
56.7    
56.8    
57.0    
57.2    
57.4    
57.6    
57.7    
57.9    
58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.1    
60.3    
60.4    
60.6    
60.8    
61.0    
61.2    
61.3    
61.5    
61.7    
61.9    
62.1    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.4    
64.6    
64.7    
64.9    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.8    
70.0    
70.1    
70.3    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.6    
71.8    
71.9    
72.1    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.4    
73.6    
73.7    
73.9    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.2    
77.3    
77.5    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.8    
79.0    
79.1    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 134731, rend_intergenic: 117819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 145629, rend_intergenic: 145626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 30911
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 3865 - 30911
-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 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 3865 - 30750
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 3865 - 25860
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 10762 - 25860
-exon list size: 1


building trellis

33.3    
66.7    
-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
	-no exons in range 14062 - 25860

-building DP trellis

-building trellis in range 263278 - 276710
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support