-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_8698270-8923150

-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_1-snap.1589-T1
Valid prediction for snap_scaffold_1-snap.1609-T1
Couldn't classify 102305, 103099
Sorry, prediction pasa_asmbl_1937.p1 fails validation.
(ATG)	 CC	102305-103099	CA	TCC
Valid prediction for snap_scaffold_1-snap.1605-T1
Valid prediction for GeneMark_model.1702_t
Valid prediction for GeneMark_model.1685_t
Valid prediction for GlimmerHMM_glimmerT_1272-T1
Valid prediction for snap_scaffold_1-snap.1606-T1
Couldn't classify 103438, 103575
Couldn't classify 104825, 104980
Sorry, prediction pasa_asmbl_1938.p1 fails validation.
(GGC)	 CA	103438-103575	GT	AGG
(AGC)	 AG	103750-103863	GT	AGG
(AGC)	 AG	104080-104160	GT	CGG
(GAA)	 AG	104329-104451	GT	TGG
(GAT)	 AG	104623-104712	GC	AGG
(AGA)	 AG	104825-104980	CA	CCC
-recovered pasa_asmbl_1938.p1, internal, 103750, 103863
-recovered pasa_asmbl_1938.p1, internal, 104080, 104160
-recovered pasa_asmbl_1938.p1, internal, 104329, 104451
-recovered pasa_asmbl_1938.p1, internal, 104623, 104712
Valid prediction for Augustus_model.g915.t1
Valid prediction for snap_scaffold_1-snap.1596-T1
Valid prediction for GlimmerHMM_glimmerT_1268-T1
Valid prediction for GeneMark_model.1681_t
Couldn't classify 91400, 91547
Sorry, prediction pasa_asmbl_1934.p1 fails validation.
(GAG)	 CG	91400-91547	GT	GCG
(CTC)	 AG	91645-91788	GT	AGG
(TTC)	 AG	91992-92236	CC	GAC
-recovered pasa_asmbl_1934.p1, terminal, 91992, 92236
-recovered pasa_asmbl_1934.p1, internal, 91645, 91788
Valid prediction for GlimmerHMM_glimmerT_1274-T1
Valid prediction for CodingQuarry_transcript_2713-T1
Valid prediction for GeneMark_model.1691_t
Valid prediction for GeneMark_model.1696_t
Valid prediction for GlimmerHMM_glimmerT_1263-T1
Valid prediction for GeneMark_model.1694_t
Valid prediction for snap_scaffold_1-snap.1588-T1
Couldn't classify 105377, 105489
Sorry, prediction pasa_asmbl_1939.p1 fails validation.
(CCC)	 TC	105377-105489	GT	AGG
(GGA)	 AG	105576-105745	GT	AGG
(GCA)	 AG	105885-106015	GT	AGG
(GAC)	 AG	106131-106256	GT	AGG
(TCT)	 AG	106578-106634	GT	AGG
(ATG)	 AG	106746-106865	GT	AGG
(GGC)	 AG	107048-107215	CG	GAC
-recovered pasa_asmbl_1939.p1, initial, 106746, 106865
add_exon() Sorry, pasa_asmbl_1939.p1 105576-105745-terminal-2 is invalid.
-recovered pasa_asmbl_1939.p1, terminal, 105576, 105745
-recovered pasa_asmbl_1939.p1, terminal, 107048, 107215
-recovered pasa_asmbl_1939.p1, internal, 105576, 105745
-recovered pasa_asmbl_1939.p1, internal, 105885, 106015
-recovered pasa_asmbl_1939.p1, internal, 106131, 106256
-recovered pasa_asmbl_1939.p1, internal, 106578, 106634
-recovered pasa_asmbl_1939.p1, internal, 106746, 106865
Valid prediction for snap_scaffold_1-snap.1600-T1
Valid prediction for snap_scaffold_1-snap.1583-T1
Valid prediction for GlimmerHMM_glimmerT_1275-T1
Valid prediction for GeneMark_model.1699_t
Valid prediction for GeneMark_model.1704_t
Valid prediction for GeneMark_model.1679_t
Valid prediction for GlimmerHMM_glimmerT_1283-T1
Valid prediction for Augustus_model.g923.t1
Valid prediction for GlimmerHMM_glimmerT_1287-T1
Valid prediction for GeneMark_model.1687_t
Valid prediction for snap_scaffold_1-snap.1593-T1
Valid prediction for GlimmerHMM_glimmerT_1265-T1
Valid prediction for GeneMark_model.1689_t
Valid prediction for GeneMark_model.1693_t
Valid prediction for GlimmerHMM_glimmerT_1271-T1
Valid prediction for GlimmerHMM_glimmerT_1284-T1
Valid prediction for Augustus_model.g914.t1
Valid prediction for snap_scaffold_1-snap.1599-T1
Valid prediction for Augustus_model.g912.t1
Valid prediction for GeneMark_model.1674_t
Valid prediction for snap_scaffold_1-snap.1603-T1
Valid prediction for GeneMark_model.1677_t
Valid prediction for snap_scaffold_1-snap.1608-T1
Valid prediction for Augustus_model.g917.t1
Valid prediction for snap_scaffold_1-snap.1594-T1
Valid prediction for GeneMark_model.1692_t
Valid prediction for snap_scaffold_1-snap.1604-T1
Valid prediction for GlimmerHMM_glimmerT_1281-T1
Valid prediction for GeneMark_model.1672_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: -)Couldn't classify 124272, 124416
Couldn't classify 124929, 124972
Sorry, prediction pasa_asmbl_1301.p1 fails validation.
(TTT)	 CC	124272-124416	GT	TGG
(GGT)	 AG	124660-124809	GT	TGG
(GGC)	 AG	124929-124972	AA	CAA
-recovered pasa_asmbl_1301.p1, internal, 124660, 124809
Valid prediction for Augustus_model.g918.t1
Valid prediction for snap_scaffold_1-snap.1595-T1
Valid prediction for HiQ_model.g910.t1
Valid prediction for GlimmerHMM_glimmerT_1282-T1
Valid prediction for GlimmerHMM_glimmerT_1269-T1
Valid prediction for GlimmerHMM_glimmerT_1261-T1
Valid prediction for Augustus_model.g919.t1
Valid prediction for HiQ_model.g911.t1
Valid prediction for GeneMark_model.1676_t
Valid prediction for snap_scaffold_1-snap.1591-T1
Valid prediction for snap_scaffold_1-snap.1584-T1
Valid prediction for GeneMark_model.1698_t
Valid prediction for snap_scaffold_1-snap.1576-T1
Valid prediction for Augustus_model.g913.t1
Valid prediction for GeneMark_model.1665_t
Valid prediction for Augustus_model.g916.t1
Valid prediction for Augustus_model.g904.t1
Valid prediction for GeneMark_model.1670_t
Valid prediction for GeneMark_model.1683_t
Valid prediction for GeneMark_model.1675_t
Valid prediction for snap_scaffold_1-snap.1611-T1
Valid prediction for snap_scaffold_1-snap.1586-T1
Valid prediction for GlimmerHMM_glimmerT_1266-T1
Valid prediction for GeneMark_model.1680_t
Valid prediction for Augustus_model.g921.t1
Valid prediction for GeneMark_model.1688_t
Valid prediction for pasa_asmbl_497.p2
Valid prediction for GlimmerHMM_glimmerT_1285-T1
Valid prediction for snap_scaffold_1-snap.1578-T1
Valid prediction for snap_scaffold_1-snap.1590-T1
Valid prediction for GeneMark_model.1695_t
Valid prediction for pasa_asmbl_488.p1
Valid prediction for GlimmerHMM_glimmerT_1279-T1
Valid prediction for snap_scaffold_1-snap.1577-T1
Valid prediction for snap_scaffold_1-snap.1582-T1
Valid prediction for snap_scaffold_1-snap.1614-T1
Valid prediction for GeneMark_model.1684_t
Couldn't classify 221317, 221877
Sorry, prediction pasa_asmbl_487.p1 fails validation.
(TTC)	 TG	221317-221877	AA	AAA
Valid prediction for snap_scaffold_1-snap.1579-T1
Valid prediction for GeneMark_model.1686_t
Valid prediction for GlimmerHMM_glimmerT_1288-T1
Valid prediction for Augustus_model.g908.t1
Valid prediction for GeneMark_model.1678_t
Valid prediction for GlimmerHMM_glimmerT_1264-T1
Valid prediction for CodingQuarry_transcript_2711-T1
Valid prediction for snap_scaffold_1-snap.1585-T1
Valid prediction for GeneMark_model.1682_t
Couldn't classify 161573, 161573
Sorry, prediction CodingQuarry_transcript_2712-T1 fails validation.
(ATG)	 TC	158351-158440	GC	AGG
(GAT)	 AG	158565-158669	GT	ATG
(GTG)	 AG	158800-158892	GT	ATG
(GAT)	 AG	158981-159067	GT	AGG
(CAT)	 AG	159176-159262	GT	AGG
(TTC)	 AG	159377-159448	GT	TGG
(GTG)	 AG	159603-159710	GT	AGG
(CAT)	 AG	159810-159916	GT	CCG
(GGC)	 AG	160010-160085	GT	CTG
(GTA)	 AG	160399-160593	GT	AGG
(GGT)	 AG	160928-161013	GT	TGG
(ATT)	 AG	161573-161573	TT	GAT
-recovered CodingQuarry_transcript_2712-T1, initial, 158351, 158440
-recovered CodingQuarry_transcript_2712-T1, internal, 158565, 158669
-recovered CodingQuarry_transcript_2712-T1, internal, 158800, 158892
-recovered CodingQuarry_transcript_2712-T1, internal, 158981, 159067
-recovered CodingQuarry_transcript_2712-T1, internal, 159176, 159262
-recovered CodingQuarry_transcript_2712-T1, internal, 159377, 159448
-recovered CodingQuarry_transcript_2712-T1, internal, 159603, 159710
-recovered CodingQuarry_transcript_2712-T1, internal, 159810, 159916
-recovered CodingQuarry_transcript_2712-T1, internal, 160010, 160085
-recovered CodingQuarry_transcript_2712-T1, internal, 160399, 160593
-recovered CodingQuarry_transcript_2712-T1, internal, 160928, 161013
Valid prediction for snap_scaffold_1-snap.1580-T1
Valid prediction for GeneMark_model.1700_t
Valid prediction for HiQ_model.g909.t1
Valid prediction for Augustus_model.g922.t1
Valid prediction for GeneMark_model.1697_t
Couldn't classify 161573, 161573
Sorry, prediction pasa_asmbl_504.p1 fails validation.
(ATG)	 TC	158351-158440	GC	AGG
(GAT)	 AG	158565-158669	GT	ATG
(GTG)	 AG	158800-158892	GT	ATG
(GAT)	 AG	158981-159067	GT	AGG
(CAT)	 AG	159176-159262	GT	AGG
(TTC)	 AG	159377-159448	GT	TGG
(GTG)	 AG	159603-159710	GT	AGG
(CAT)	 AG	159810-159916	GT	CCG
(GGC)	 AG	160010-160085	GT	CTG
(GTA)	 AG	160399-160593	GT	AGG
(GGT)	 AG	160928-161013	GT	TGG
(ATT)	 AG	161573-161573	TT	GAT
-recovered pasa_asmbl_504.p1, initial, 158351, 158440
-recovered pasa_asmbl_504.p1, internal, 158565, 158669
-recovered pasa_asmbl_504.p1, internal, 158800, 158892
-recovered pasa_asmbl_504.p1, internal, 158981, 159067
-recovered pasa_asmbl_504.p1, internal, 159176, 159262
-recovered pasa_asmbl_504.p1, internal, 159377, 159448
-recovered pasa_asmbl_504.p1, internal, 159603, 159710
-recovered pasa_asmbl_504.p1, internal, 159810, 159916
-recovered pasa_asmbl_504.p1, internal, 160010, 160085
-recovered pasa_asmbl_504.p1, internal, 160399, 160593
-recovered pasa_asmbl_504.p1, internal, 160928, 161013
Valid prediction for GlimmerHMM_glimmerT_1259-T1
Valid prediction for Augustus_model.g903.t1
Couldn't classify 125178, 125226
Sorry, prediction pasa_asmbl_506.p1 fails validation.
(TGT)	 TC	125178-125226	GT	AGG
(AGG)	 AG	125368-125497	GT	AAG
(ACG)	 AG	125594-125768	AG	AAA
-recovered pasa_asmbl_506.p1, terminal, 125594, 125768
-recovered pasa_asmbl_506.p1, internal, 125368, 125497
Valid prediction for GeneMark_model.1701_t
Valid prediction for pasa_asmbl_1323.p1
Valid prediction for GeneMark_model.1703_t
Valid prediction for snap_scaffold_1-snap.1602-T1
Valid prediction for GlimmerHMM_glimmerT_1278-T1
Valid prediction for Augustus_model.g906.t1
Valid prediction for snap_scaffold_1-snap.1607-T1
Couldn't classify 140989, 141288
Sorry, prediction pasa_asmbl_1933.p1 fails validation.
(GGC)	 AA	140989-141288	CT	AAC
Valid prediction for GlimmerHMM_glimmerT_1273-T1
Valid prediction for snap_scaffold_1-snap.1612-T1
Valid prediction for GlimmerHMM_glimmerT_1276-T1
Valid prediction for GeneMark_model.1669_t
Valid prediction for snap_scaffold_1-snap.1597-T1
Valid prediction for snap_scaffold_1-snap.1615-T1
Valid prediction for snap_scaffold_1-snap.1610-T1
Valid prediction for GeneMark_model.1673_t
Valid prediction for snap_scaffold_1-snap.1592-T1
Valid prediction for GlimmerHMM_glimmerT_1277-T1
Valid prediction for GlimmerHMM_glimmerT_1286-T1
Valid prediction for Augustus_model.g924.t1
Valid prediction for GlimmerHMM_glimmerT_1258-T1
Valid prediction for snap_scaffold_1-snap.1601-T1
Valid prediction for GeneMark_model.1671_t
Valid prediction for GlimmerHMM_glimmerT_1289-T1
Valid prediction for CodingQuarry_transcript_2709-T1
Valid prediction for snap_scaffold_1-snap.1613-T1
Valid prediction for GlimmerHMM_glimmerT_1270-T1
Valid prediction for HiQ_model.g907.t1
Valid prediction for Augustus_model.g925.t1
Valid prediction for Augustus_model.g920.t1
Valid prediction for GlimmerHMM_glimmerT_1260-T1
Valid prediction for GeneMark_model.1667_t
Valid prediction for GeneMark_model.1690_t
Valid prediction for HiQ_model.g905.t1
Valid prediction for snap_scaffold_1-snap.1581-T1
Valid prediction for GlimmerHMM_glimmerT_1267-T1
Valid prediction for GlimmerHMM_glimmerT_1262-T1
Valid prediction for snap_scaffold_1-snap.1587-T1
Valid prediction for snap_scaffold_1-snap.1598-T1
Valid prediction for CodingQuarry_transcript_2710-T1
Valid prediction for GlimmerHMM_glimmerT_1280-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 51508, rend_intergenic: 46869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90837, rend_intergenic: 86331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107215, rend_intergenic: 104030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132086, rend_intergenic: 114169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156650, rend_intergenic: 148106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169186, rend_intergenic: 165287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224881
-exon list size: 548


building trellis

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85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
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: 51508, rend_intergenic: 46869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90837, rend_intergenic: 86331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107215, rend_intergenic: 104030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132086, rend_intergenic: 114169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156650, rend_intergenic: 148106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169186, rend_intergenic: 165287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 188709 - 224881
-exon list size: 37


building trellis

2.6    
5.1    
7.7    
10.3    
12.8    
15.4    
17.9    
20.5    
23.1    
25.6    
28.2    
30.8    
33.3    
35.9    
38.5    
41.0    
43.6    
46.2    
48.7    
51.3    
53.8    
56.4    
59.0    
61.5    
64.1    
66.7    
69.2    
71.8    
74.4    
76.9    
79.5    
82.1    
84.6    
87.2    
89.7    
92.3    
94.9    
97.4    
-found 2 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 198940 - 224881
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-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 200343 - 224881
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-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 201125 - 224881
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-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 206258 - 224881
-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 206326 - 224881
-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
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 213887 - 224881
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 214605 - 224881