-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_7098385-7334062

-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: +)Couldn't classify 168866, 168985
Couldn't classify 169545, 169755
Sorry, prediction pasa_asmbl_4548.p1 fails validation.
(AAC)	 GG	168866-168985	GT	AGG
(CTG)	 AG	169164-169357	GT	AGG
(AAC)	 AG	169545-169755	AG	GCA
-recovered pasa_asmbl_4548.p1, internal, 169164, 169357
Valid prediction for snap_scaffold_10-snap.1483-T1
Valid prediction for Augustus_model.g17095.t1
Valid prediction for snap_scaffold_10-snap.1471-T1
Valid prediction for snap_scaffold_10-snap.1479-T1
Valid prediction for GeneMark_model.43530_t
Valid prediction for GeneMark_model.43531_t
Valid prediction for snap_scaffold_10-snap.1481-T1
Valid prediction for snap_scaffold_10-snap.1458-T1
Valid prediction for GlimmerHMM_glimmerT_25467-T1
Couldn't classify 166858, 166945
Couldn't classify 168375, 168518
Sorry, prediction pasa_asmbl_4547.p1 fails validation.
(GAG)	 AG	166858-166945	GT	TTG
(GTC)	 AG	167056-167200	GT	AGG
(AAA)	 AG	167422-167798	GT	AGG
(AGT)	 AG	168005-168261	GT	AGG
(AGT)	 AG	168375-168518	TA	GGT
add_exon() Sorry, pasa_asmbl_4547.p1 167422-167798-terminal-2 is invalid.
-recovered pasa_asmbl_4547.p1, terminal, 167422, 167798
-recovered pasa_asmbl_4547.p1, internal, 166858, 166945
-recovered pasa_asmbl_4547.p1, internal, 167056, 167200
-recovered pasa_asmbl_4547.p1, internal, 167422, 167798
-recovered pasa_asmbl_4547.p1, internal, 168005, 168261
Valid prediction for GeneMark_model.43524_t
Valid prediction for GlimmerHMM_glimmerT_25453-T1
Couldn't classify 164226, 164477
Couldn't classify 165059, 165157
Sorry, prediction pasa_asmbl_4546.p2 fails validation.
(CAG)	 AC	164226-164477	GT	AGG
(GTG)	 AG	165059-165157	CG	AGC
Valid prediction for Augustus_model.g17102.t1
Valid prediction for GlimmerHMM_glimmerT_25463-T1
Valid prediction for GeneMark_model.43532_t
Valid prediction for Augustus_model.g17099.t1
Valid prediction for snap_scaffold_10-snap.1474-T1
Valid prediction for GeneMark_model.43537_t
Valid prediction for GlimmerHMM_glimmerT_25474-T1
Valid prediction for Augustus_model.g17104.t1
Valid prediction for snap_scaffold_10-snap.1459-T1
Valid prediction for GeneMark_model.43521_t
Couldn't classify 11715, 11970
Sorry, prediction pasa_asmbl_4542.p1 fails validation.
(CCC)	 CT	11715-11970	GT	AGG
(GTG)	 AG	12708-12990	GT	AGG
(TGA)	 AG	13114-13300	GT	GAG
(CCC)	 AG	13501-13740	GT	AGG
(ATG)	 AG	13931-14936	GT	AGG
(ATG)	 AG	15058-15139	GT	AGG
(GTT)	 AG	15280-15373	CA	GAC
-recovered pasa_asmbl_4542.p1, initial, 13931, 14936
-recovered pasa_asmbl_4542.p1, initial, 15058, 15139
add_exon() Sorry, pasa_asmbl_4542.p1 13931-14936-terminal-3 is invalid.
-recovered pasa_asmbl_4542.p1, terminal, 13931, 14936
-recovered pasa_asmbl_4542.p1, terminal, 15280, 15373
-recovered pasa_asmbl_4542.p1, internal, 12708, 12990
-recovered pasa_asmbl_4542.p1, internal, 13114, 13300
-recovered pasa_asmbl_4542.p1, internal, 13501, 13740
-recovered pasa_asmbl_4542.p1, internal, 13931, 14936
-recovered pasa_asmbl_4542.p1, internal, 15058, 15139
Valid prediction for CodingQuarry_transcript_5451-T1
Valid prediction for snap_scaffold_10-snap.1464-T1
Valid prediction for Augustus_model.g17108.t1
Valid prediction for GlimmerHMM_glimmerT_25460-T1
Valid prediction for GlimmerHMM_glimmerT_25464-T1
Valid prediction for GeneMark_model.43529_t
Valid prediction for GlimmerHMM_glimmerT_25475-T1
Valid prediction for snap_scaffold_10-snap.1465-T1
Valid prediction for GlimmerHMM_glimmerT_25469-T1
Valid prediction for GeneMark_model.43520_t
Couldn't classify 5177, 5197
Couldn't classify 6847, 6868
Sorry, prediction pasa_asmbl_4537.p1 fails validation.
(GAC)	 CG	5177-5197	GT	AGG
(ACT)	 AG	5559-5792	GT	CGG
(AAC)	 AG	6084-6259	GT	CGG
(GGA)	 AG	6847-6868	CG	AGC
-recovered pasa_asmbl_4537.p1, internal, 5559, 5792
-recovered pasa_asmbl_4537.p1, internal, 6084, 6259
Valid prediction for Augustus_model.g17086.t1
Valid prediction for Augustus_model.g17111.t1
Valid prediction for GlimmerHMM_glimmerT_25476-T1
Valid prediction for GeneMark_model.43516_t
Valid prediction for GlimmerHMM_glimmerT_25461-T1
Valid prediction for Augustus_model.g17103.t1
Valid prediction for Augustus_model.g17093.t1
Valid prediction for Augustus_model.g17094.t1
Valid prediction for snap_scaffold_10-snap.1467-T1
Valid prediction for snap_scaffold_10-snap.1486-T1
Valid prediction for GeneMark_model.43528_t
Valid prediction for GlimmerHMM_glimmerT_25458-T1
Valid prediction for GlimmerHMM_glimmerT_25470-T1
Valid prediction for snap_scaffold_10-snap.1463-T1
Valid prediction for snap_scaffold_10-snap.1475-T1
Valid prediction for Augustus_model.g17097.t1
Valid prediction for snap_scaffold_10-snap.1493-T1
Valid prediction for snap_scaffold_10-snap.1487-T1
Valid prediction for GeneMark_model.43545_t
Valid prediction for snap_scaffold_10-snap.1460-T1
Couldn't classify 170878, 170977
Couldn't classify 171524, 171614
Sorry, prediction pasa_asmbl_4549.p1 fails validation.
(AGC)	 CC	170878-170977	GT	TGG
(GGT)	 AG	171229-171409	GT	AGG
(ACC)	 AG	171524-171614	AC	ACA
-recovered pasa_asmbl_4549.p1, internal, 171229, 171409
Valid prediction for snap_scaffold_10-snap.1482-T1
Valid prediction for Augustus_model.g17090.t1
Valid prediction for Augustus_model.g17096.t1
Valid prediction for GeneMark_model.43533_t
Valid prediction for Augustus_model.g17106.t1
Valid prediction for GeneMark_model.43526_t
Valid prediction for GlimmerHMM_glimmerT_25456-T1
Valid prediction for GeneMark_model.43535_t
Valid prediction for snap_scaffold_10-snap.1466-T1
Valid prediction for snap_scaffold_10-snap.1500-T1
Valid prediction for snap_scaffold_10-snap.1470-T1
Couldn't classify 176190, 176243
Sorry, prediction pasa_asmbl_4556.p1 fails validation.
(AAA)	 AA	176190-176243	GT	AGG
(GAC)	 AG	176521-176656	GT	TAG
(GCT)	 AG	176756-176904	GT	AGG
(ATA)	 AG	177049-177121	GT	TGG
(TGA)	 AG	177269-177462	GT	TGG
(GAG)	 AG	177776-177868	GT	AGG
(GAG)	 AG	177978-178101	GT	AGG
(AAA)	 AG	178456-178481	AA	GAA
-recovered pasa_asmbl_4556.p1, terminal, 178456, 178481
-recovered pasa_asmbl_4556.p1, internal, 176521, 176656
-recovered pasa_asmbl_4556.p1, internal, 176756, 176904
-recovered pasa_asmbl_4556.p1, internal, 177049, 177121
-recovered pasa_asmbl_4556.p1, internal, 177269, 177462
-recovered pasa_asmbl_4556.p1, internal, 177776, 177868
-recovered pasa_asmbl_4556.p1, internal, 177978, 178101
Valid prediction for Augustus_model.g17100.t1
Valid prediction for GeneMark_model.43518_t
Valid prediction for snap_scaffold_10-snap.1499-T1
Valid prediction for Augustus_model.g17092.t1
Valid prediction for snap_scaffold_10-snap.1480-T1
Valid prediction for GeneMark_model.43542_t
Valid prediction for snap_scaffold_10-snap.1472-T1
Couldn't classify 171675, 171864
Sorry, prediction pasa_asmbl_4551.p1 fails validation.
(AAG)	 CC	171675-171864	GT	AGG
(GGC)	 AG	172093-172254	GT	AGG
(CCT)	 AG	172546-172602	GT	AGG
(ATG)	 AG	173076-173248	GT	AGG
(GAC)	 AG	173421-173552	GT	CGG
(GAG)	 AG	174339-174465	GT	AGG
(GGG)	 AG	175084-175175	GT	AGG
(GAG)	 AG	175301-175435	GT	AGG
(GAC)	 AG	175899-176105	GT	AGG
(GAA)	 AG	176187-176243	GT	AGG
(GAC)	 AG	176521-176656	GT	TAG
(GCT)	 AG	176756-176904	GT	AGG
(ATA)	 AG	177049-177121	GT	TGG
(TGA)	 AG	177269-177474	GT	ATG
(GAG)	 AG	177776-177868	GT	AGG
(GAG)	 AG	177978-178101	GT	AGG
(AAA)	 AG	178456-178481	AA	GAA
add_exon() Sorry, pasa_asmbl_4551.p1 173076-173248-initial-1 is invalid.
-recovered pasa_asmbl_4551.p1, initial, 173076, 173248
add_exon() Sorry, pasa_asmbl_4551.p1 174339-174465-terminal-3 is invalid.
-recovered pasa_asmbl_4551.p1, terminal, 174339, 174465
-recovered pasa_asmbl_4551.p1, terminal, 178456, 178481
-recovered pasa_asmbl_4551.p1, internal, 172093, 172254
-recovered pasa_asmbl_4551.p1, internal, 172546, 172602
-recovered pasa_asmbl_4551.p1, internal, 173076, 173248
-recovered pasa_asmbl_4551.p1, internal, 173421, 173552
-recovered pasa_asmbl_4551.p1, internal, 174339, 174465
-recovered pasa_asmbl_4551.p1, internal, 175084, 175175
-recovered pasa_asmbl_4551.p1, internal, 175301, 175435
-recovered pasa_asmbl_4551.p1, internal, 175899, 176105
-recovered pasa_asmbl_4551.p1, internal, 176187, 176243
-recovered pasa_asmbl_4551.p1, internal, 176521, 176656
-recovered pasa_asmbl_4551.p1, internal, 176756, 176904
-recovered pasa_asmbl_4551.p1, internal, 177049, 177121
-recovered pasa_asmbl_4551.p1, internal, 177269, 177474
-recovered pasa_asmbl_4551.p1, internal, 177776, 177868
-recovered pasa_asmbl_4551.p1, internal, 177978, 178101
Valid prediction for snap_scaffold_10-snap.1477-T1
Valid prediction for GlimmerHMM_glimmerT_25472-T1
Valid prediction for snap_scaffold_10-snap.1476-T1
Valid prediction for GlimmerHMM_glimmerT_25459-T1
Valid prediction for snap_scaffold_10-snap.1484-T1
Valid prediction for GeneMark_model.43525_t
Valid prediction for GlimmerHMM_glimmerT_25465-T1
Valid prediction for Augustus_model.g17089.t1
Valid prediction for GeneMark_model.43539_t
Valid prediction for snap_scaffold_10-snap.1488-T1
Valid prediction for Augustus_model.g17101.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_10-snap.1462-T1
Valid prediction for CodingQuarry_transcript_5452-T1
Valid prediction for CodingQuarry_transcript_5450-T1
Valid prediction for GeneMark_model.43522_t
Valid prediction for GeneMark_model.43527_t
Valid prediction for GeneMark_model.43523_t
Valid prediction for pasa_asmbl_3446.p1
Valid prediction for GeneMark_model.43546_t
Valid prediction for GeneMark_model.43547_t
Valid prediction for GeneMark_model.43517_t
Valid prediction for snap_scaffold_10-snap.1468-T1
Valid prediction for GeneMark_model.43540_t
Valid prediction for GeneMark_model.43534_t
Valid prediction for GlimmerHMM_glimmerT_25473-T1
Valid prediction for snap_scaffold_10-snap.1469-T1
Valid prediction for GlimmerHMM_glimmerT_25466-T1
Valid prediction for pasa_asmbl_3448.p1
Valid prediction for snap_scaffold_10-snap.1492-T1
Couldn't classify 77666, 77741
Sorry, prediction pasa_asmbl_3454.p1 fails validation.
(ATG)	 TG	75826-75959	GT	AGG
(AAC)	 AG	77007-77215	GT	TGG
(ATG)	 AG	77334-77496	GT	AGG
(ATC)	 AG	77666-77741	AC	CCA
-recovered pasa_asmbl_3454.p1, initial, 75826, 75959
-recovered pasa_asmbl_3454.p1, initial, 77334, 77496
-recovered pasa_asmbl_3454.p1, internal, 77007, 77215
-recovered pasa_asmbl_3454.p1, internal, 77334, 77496
Valid prediction for Augustus_model.g17098.t1
Valid prediction for snap_scaffold_10-snap.1497-T1
Valid prediction for snap_scaffold_10-snap.1478-T1
Valid prediction for Augustus_model.g17091.t1
Valid prediction for GeneMark_model.43541_t
Valid prediction for GlimmerHMM_glimmerT_25457-T1
Valid prediction for snap_scaffold_10-snap.1498-T1
Valid prediction for GeneMark_model.43519_t
Valid prediction for GlimmerHMM_glimmerT_25471-T1
Valid prediction for pasa_asmbl_3457.p1
Valid prediction for GlimmerHMM_glimmerT_25462-T1
Valid prediction for GeneMark_model.43536_t
Valid prediction for snap_scaffold_10-snap.1473-T1
Valid prediction for snap_scaffold_10-snap.1501-T1
Valid prediction for snap_scaffold_10-snap.1494-T1
Valid prediction for snap_scaffold_10-snap.1491-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for HiQ_model.g17109.t1
Couldn't classify 78045, 78087
Sorry, prediction pasa_asmbl_3449.p1 fails validation.
(GTG)	 CA	78045-78087	GT	GGG
(GGT)	 AG	78223-78337	GT	AGG
(GAG)	 AG	78426-78483	GT	CAG
(CTT)	 AG	78722-78889	GT	CTG
(GTC)	 AG	79030-79275	GT	AGG
(GTG)	 AG	79978-80098	GT	CGG
(GTT)	 AG	80212-80315	GT	AGG
(TCA)	 AG	80441-80536	GT	AGG
(GTA)	 AG	80674-80861	GT	CCG
(CGA)	 AG	81183-81412	GT	GGG
(GCT)	 AG	83609-83751	TT	GAT
-recovered pasa_asmbl_3449.p1, terminal, 83609, 83751
-recovered pasa_asmbl_3449.p1, internal, 78223, 78337
-recovered pasa_asmbl_3449.p1, internal, 78426, 78483
-recovered pasa_asmbl_3449.p1, internal, 78722, 78889
-recovered pasa_asmbl_3449.p1, internal, 79030, 79275
-recovered pasa_asmbl_3449.p1, internal, 79978, 80098
-recovered pasa_asmbl_3449.p1, internal, 80212, 80315
-recovered pasa_asmbl_3449.p1, internal, 80441, 80536
-recovered pasa_asmbl_3449.p1, internal, 80674, 80861
-recovered pasa_asmbl_3449.p1, internal, 81183, 81412
Valid prediction for GlimmerHMM_glimmerT_25468-T1
Valid prediction for snap_scaffold_10-snap.1495-T1
Valid prediction for snap_scaffold_10-snap.1496-T1
Valid prediction for Augustus_model.g17088.t1
Valid prediction for GeneMark_model.43543_t
Valid prediction for GlimmerHMM_glimmerT_25454-T1
Valid prediction for CodingQuarry_transcript_5453-T1
Valid prediction for HiQ_model.g17110.t1
Valid prediction for CodingQuarry_transcript_5449-T1
Valid prediction for Augustus_model.g17107.t1
Valid prediction for snap_scaffold_10-snap.1502-T1
Valid prediction for pasa_asmbl_4049.p1
Valid prediction for GlimmerHMM_glimmerT_25455-T1
Valid prediction for GeneMark_model.43538_t
Valid prediction for HiQ_model.g17087.t1
Valid prediction for snap_scaffold_10-snap.1489-T1
Valid prediction for snap_scaffold_10-snap.1490-T1
Valid prediction for snap_scaffold_10-snap.1485-T1
Valid prediction for HiQ_model.g17105.t1
Valid prediction for GeneMark_model.43544_t
Valid prediction for snap_scaffold_10-snap.1461-T1
Valid prediction for CodingQuarry_transcript_5448-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 64010, rend_intergenic: 62100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178481, rend_intergenic: 163780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 235678
-exon list size: 547


building trellis

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67.8    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.0    
69.2    
69.4    
69.6    
69.8    
69.9    
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    
72.9    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.9    
85.1    
85.2    
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    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 64010, rend_intergenic: 62100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178481, rend_intergenic: 163780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 218066 - 235678
-exon list size: 28


building trellis

3.3    
6.7    
10.0    
13.3    
16.7    
20.0    
23.3    
26.7    
30.0    
33.3    
36.7    
40.0    
43.3    
46.7    
50.0    
53.3    
56.7    
60.0    
63.3    
66.7    
70.0    
73.3    
76.7    
80.0    
83.3    
86.7    
90.0    
93.3    
96.7    
-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 218066 - 229084
-exon list size: 26


building trellis

3.6    
7.1    
10.7    
14.3    
17.9    
21.4    
25.0    
28.6    
32.1    
35.7    
39.3    
42.9    
46.4    
50.0    
53.6    
57.1    
60.7    
64.3    
67.9    
71.4    
75.0    
78.6    
82.1    
85.7    
89.3    
92.9    
96.4    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 218066 - 228807
-exon list size: 24


building trellis

3.8    
7.7    
11.5    
15.4    
19.2    
23.1    
26.9    
30.8    
34.6    
38.5    
42.3    
46.2    
50.0    
53.8    
57.7    
61.5    
65.4    
69.2    
73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-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