-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_8221082-8518769

-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 Augustus_model.g17173.t1
Valid prediction for Augustus_model.g17174.t1
Valid prediction for pasa_asmbl_4591.p1
Valid prediction for GeneMark_model.43709_t
Valid prediction for Augustus_model.g17166.t1
Valid prediction for GeneMark_model.43726_t
Valid prediction for GlimmerHMM_glimmerT_25601-T1
Valid prediction for snap_scaffold_10-snap.1631-T1
Valid prediction for snap_scaffold_10-snap.1655-T1
Valid prediction for GeneMark_model.43733_t
Valid prediction for CodingQuarry_transcript_5482-T1
Valid prediction for GeneMark_model.43706_t
Valid prediction for pasa_asmbl_4601.p1
Valid prediction for GlimmerHMM_glimmerT_25572-T1
Valid prediction for GeneMark_model.43724_t
Valid prediction for GlimmerHMM_glimmerT_25576-T1
Valid prediction for GeneMark_model.43729_t
Valid prediction for GeneMark_model.43735_t
Valid prediction for Augustus_model.g17171.t1
Valid prediction for Augustus_model.g17164.t1
Valid prediction for snap_scaffold_10-snap.1633-T1
Couldn't classify 112687, 112755
Couldn't classify 115721, 115897
Sorry, prediction pasa_asmbl_4592.p1 fails validation.
(CAA)	 GA	112687-112755	GT	CGG
(ATG)	 AG	113760-113986	GT	AGG
(CTC)	 AG	114219-114414	GT	AGG
(AAG)	 AG	114654-114747	GT	AGG
(CAA)	 AG	115322-115429	GT	AGG
(GAA)	 AG	115521-115633	GT	AAG
(GAC)	 AG	115721-115897	TT	GCT
-recovered pasa_asmbl_4592.p1, initial, 113760, 113986
add_exon() Sorry, pasa_asmbl_4592.p1 114654-114747-terminal-3 is invalid.
-recovered pasa_asmbl_4592.p1, terminal, 114654, 114747
-recovered pasa_asmbl_4592.p1, internal, 113760, 113986
-recovered pasa_asmbl_4592.p1, internal, 114219, 114414
-recovered pasa_asmbl_4592.p1, internal, 114654, 114747
-recovered pasa_asmbl_4592.p1, internal, 115322, 115429
-recovered pasa_asmbl_4592.p1, internal, 115521, 115633
Valid prediction for snap_scaffold_10-snap.1662-T1
Valid prediction for GlimmerHMM_glimmerT_25599-T1
Valid prediction for CodingQuarry_transcript_5470-T1
Valid prediction for Augustus_model.g17181.t1
Valid prediction for snap_scaffold_10-snap.1639-T1
Valid prediction for snap_scaffold_10-snap.1654-T1
Couldn't classify 234975, 234992
Couldn't classify 235728, 235934
Sorry, prediction pasa_asmbl_4599.p1 fails validation.
(TGG)	 AA	234975-234992	GT	TGG
(GGA)	 AG	235419-235490	GT	AGG
(GAG)	 AG	235728-235934	AC	GGA
-recovered pasa_asmbl_4599.p1, internal, 235419, 235490
Valid prediction for GeneMark_model.43719_t
Valid prediction for GlimmerHMM_glimmerT_25595-T1
Valid prediction for GlimmerHMM_glimmerT_25596-T1
Valid prediction for GlimmerHMM_glimmerT_25574-T1
Valid prediction for GlimmerHMM_glimmerT_25598-T1
Valid prediction for Augustus_model.g17178.t1
Valid prediction for GeneMark_model.43714_t
Valid prediction for Augustus_model.g17176.t1
Valid prediction for GlimmerHMM_glimmerT_25569-T1
Valid prediction for HiQ_model.g17161.t1
Valid prediction for snap_scaffold_10-snap.1637-T1
Valid prediction for snap_scaffold_10-snap.1665-T1
Valid prediction for GeneMark_model.43725_t
Valid prediction for snap_scaffold_10-snap.1628-T1
Valid prediction for snap_scaffold_10-snap.1625-T1
Valid prediction for GeneMark_model.43728_t
Valid prediction for snap_scaffold_10-snap.1645-T1
Valid prediction for GlimmerHMM_glimmerT_25578-T1
Valid prediction for snap_scaffold_10-snap.1658-T1
Valid prediction for GlimmerHMM_glimmerT_25568-T1
Valid prediction for snap_scaffold_10-snap.1660-T1
Valid prediction for GlimmerHMM_glimmerT_25602-T1
Valid prediction for snap_scaffold_10-snap.1657-T1
Valid prediction for GlimmerHMM_glimmerT_25586-T1
Valid prediction for CodingQuarry_transcript_5478-T1
Valid prediction for GeneMark_model.43731_t
Valid prediction for pasa_asmbl_4594.p1
Valid prediction for HiQ_model.g17169.t1
Valid prediction for Augustus_model.g17177.t1
Valid prediction for GlimmerHMM_glimmerT_25593-T1
Couldn't classify 275159, 275306
Sorry, prediction pasa_asmbl_4602.p1 fails validation.
(GAC)	 AA	275159-275306	GT	AGG
(GGG)	 AG	275476-275619	GT	TAG
(ACA)	 AG	275730-275933	GT	TGG
(GTC)	 AG	276012-276151	GT	AGG
(GTG)	 AG	276386-276608	GT	AGG
(GAC)	 AG	276725-276972	TG	AAT
add_exon() Sorry, pasa_asmbl_4602.p1 276386-276608-terminal-3 is invalid.
-recovered pasa_asmbl_4602.p1, terminal, 276386, 276608
-recovered pasa_asmbl_4602.p1, terminal, 276725, 276972
-recovered pasa_asmbl_4602.p1, internal, 275476, 275619
-recovered pasa_asmbl_4602.p1, internal, 275730, 275933
-recovered pasa_asmbl_4602.p1, internal, 276012, 276151
-recovered pasa_asmbl_4602.p1, internal, 276386, 276608
Valid prediction for GeneMark_model.43712_t
Valid prediction for snap_scaffold_10-snap.1661-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 GeneMark_model.43713_t
Valid prediction for pasa_asmbl_3497.p1
Valid prediction for GlimmerHMM_glimmerT_25575-T1
Valid prediction for GlimmerHMM_glimmerT_25588-T1
Valid prediction for GlimmerHMM_glimmerT_25582-T1
Valid prediction for CodingQuarry_transcript_5475-T1
Valid prediction for HiQ_model.g17179.t1
Valid prediction for Augustus_model.g17168.t1
Valid prediction for GlimmerHMM_glimmerT_25581-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_25579-T1
Valid prediction for HiQ_model.g17180.t1
Valid prediction for snap_scaffold_10-snap.1641-T1
Valid prediction for snap_scaffold_10-snap.1646-T1
Valid prediction for GeneMark_model.43716_t
Valid prediction for snap_scaffold_10-snap.1636-T1
Valid prediction for pasa_asmbl_3503.p1
Valid prediction for CodingQuarry_transcript_5483-T1
Valid prediction for GeneMark_model.43707_t
Valid prediction for GeneMark_model.43711_t
Valid prediction for Augustus_model.g17163.t1
Valid prediction for snap_scaffold_10-snap.1656-T1
Valid prediction for GlimmerHMM_glimmerT_25591-T1
Valid prediction for GlimmerHMM_glimmerT_25585-T1
Valid prediction for HiQ_model.g17167.t1
Valid prediction for GeneMark_model.43705_t
Valid prediction for CodingQuarry_transcript_5472-T1
Valid prediction for GeneMark_model.43734_t
Valid prediction for snap_scaffold_10-snap.1643-T1
Valid prediction for GlimmerHMM_glimmerT_25589-T1
Valid prediction for CodingQuarry_transcript_5476-T1
Valid prediction for GlimmerHMM_glimmerT_25580-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.43722_t
Valid prediction for snap_scaffold_10-snap.1642-T1
Valid prediction for pasa_asmbl_3496.p1
Valid prediction for CodingQuarry_transcript_5477-T1
Valid prediction for HiQ_model.g17172.t1
Valid prediction for pasa_asmbl_3498.p1
Valid prediction for CodingQuarry_transcript_5471-T1
Valid prediction for pasa_asmbl_3489.p1
Valid prediction for GlimmerHMM_glimmerT_25573-T1
Valid prediction for CodingQuarry_transcript_5479-T1
Valid prediction for snap_scaffold_10-snap.1629-T1
Valid prediction for snap_scaffold_10-snap.1653-T1
Valid prediction for GlimmerHMM_glimmerT_25592-T1
Valid prediction for GlimmerHMM_glimmerT_25603-T1
Valid prediction for Augustus_model.g17170.t1
Valid prediction for GeneMark_model.43730_t
Valid prediction for snap_scaffold_10-snap.1635-T1
Valid prediction for pasa_asmbl_3485.p1
Valid prediction for snap_scaffold_10-snap.1626-T1
Valid prediction for GlimmerHMM_glimmerT_25571-T1
Valid prediction for GeneMark_model.43727_t
Couldn't classify 207200, 207308
Couldn't classify 207752, 207901
Sorry, prediction pasa_asmbl_4054.p1 fails validation.
(TAC)	 GC	207200-207308	GT	AGG
(GCT)	 AG	207531-207637	GT	AGG
(AAA)	 AG	207752-207901	GT	AGG
-recovered pasa_asmbl_4054.p1, internal, 207531, 207637
-recovered pasa_asmbl_4054.p1, internal, 207752, 207901
Valid prediction for snap_scaffold_10-snap.1644-T1
Valid prediction for pasa_asmbl_3505.p1
Couldn't classify 54175, 54176
Sorry, prediction CodingQuarry_transcript_5481-T1 fails validation.
(ATG)	 AG	54175-54176	GT	ATG
(GAC)	 AG	54730-54952	GT	GTG
(CTG)	 AG	55594-56070	AC	AAA
-recovered CodingQuarry_transcript_5481-T1, terminal, 55594, 56070
-recovered CodingQuarry_transcript_5481-T1, internal, 54175, 54176
-recovered CodingQuarry_transcript_5481-T1, internal, 54730, 54952
Valid prediction for GeneMark_model.43715_t
Valid prediction for GeneMark_model.43708_t
Valid prediction for GeneMark_model.43718_t
Valid prediction for snap_scaffold_10-snap.1640-T1
Valid prediction for GeneMark_model.43732_t
Valid prediction for HiQ_model.g17165.t1
Valid prediction for pasa_asmbl_3506.p1
Valid prediction for Augustus_model.g17182.t1
Valid prediction for GeneMark_model.43720_t
Valid prediction for GeneMark_model.43704_t
Valid prediction for CodingQuarry_transcript_5469-T1
Valid prediction for snap_scaffold_10-snap.1632-T1
Valid prediction for GlimmerHMM_glimmerT_25594-T1
Valid prediction for GeneMark_model.43703_t
Valid prediction for HiQ_model.g17175.t1
Valid prediction for GeneMark_model.43736_t
Valid prediction for snap_scaffold_10-snap.1666-T1
Valid prediction for GlimmerHMM_glimmerT_25567-T1
Valid prediction for snap_scaffold_10-snap.1648-T1
Valid prediction for snap_scaffold_10-snap.1659-T1
Valid prediction for GlimmerHMM_glimmerT_25584-T1
Valid prediction for snap_scaffold_10-snap.1663-T1
Valid prediction for CodingQuarry_transcript_5474-T1
Valid prediction for Augustus_model.g17162.t1
Couldn't classify 205278, 205449
Couldn't classify 206526, 206542
Sorry, prediction pasa_asmbl_3488.p1 fails validation.
(GTC)	 TG	205278-205449	GT	AGG
(TTT)	 AG	205926-206096	GT	TGG
(GCA)	 AG	206526-206542	TT	GCT
-recovered pasa_asmbl_3488.p1, internal, 205926, 206096
Valid prediction for GeneMark_model.43717_t
Valid prediction for snap_scaffold_10-snap.1647-T1
Valid prediction for HiQ_model.g17160.t1
Valid prediction for GlimmerHMM_glimmerT_25577-T1
Valid prediction for snap_scaffold_10-snap.1649-T1
Valid prediction for GlimmerHMM_glimmerT_25587-T1
Valid prediction for GeneMark_model.43723_t
Valid prediction for snap_scaffold_10-snap.1652-T1
Valid prediction for snap_scaffold_10-snap.1634-T1
Valid prediction for pasa_asmbl_3500.p1
Valid prediction for GeneMark_model.43702_t
Valid prediction for snap_scaffold_10-snap.1651-T1
Valid prediction for snap_scaffold_10-snap.1638-T1
Valid prediction for snap_scaffold_10-snap.1630-T1
Valid prediction for GlimmerHMM_glimmerT_25583-T1
Couldn't classify 208574, 208669
Sorry, prediction pasa_asmbl_3487.p1 fails validation.
(GTA)	 GC	208574-208669	GT	AGG
(GCA)	 AG	208822-209005	GT	GGG
(GCA)	 AG	209495-209556	CC	GAC
-recovered pasa_asmbl_3487.p1, terminal, 209495, 209556
-recovered pasa_asmbl_3487.p1, internal, 208822, 209005
Valid prediction for GlimmerHMM_glimmerT_25570-T1
Valid prediction for CodingQuarry_transcript_5480-T1
Valid prediction for snap_scaffold_10-snap.1664-T1
Valid prediction for GlimmerHMM_glimmerT_25600-T1
Valid prediction for GlimmerHMM_glimmerT_25597-T1
Valid prediction for GeneMark_model.43710_t
Valid prediction for GlimmerHMM_glimmerT_25590-T1
Valid prediction for snap_scaffold_10-snap.1627-T1
Valid prediction for CodingQuarry_transcript_5473-T1
Valid prediction for snap_scaffold_10-snap.1650-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 107560, rend_intergenic: 107557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139238, rend_intergenic: 138342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154263, rend_intergenic: 139307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 297688
-exon list size: 536


building trellis

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-found 37 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 107560, rend_intergenic: 107557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139238, rend_intergenic: 138342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154263, rend_intergenic: 139307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 27227
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-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 1 - 26991
-exon list size: 29


building trellis

3.2    
6.5    
9.7    
12.9    
16.1    
19.4    
22.6    
25.8    
29.0    
32.3    
35.5    
38.7    
41.9    
45.2    
48.4    
51.6    
54.8    
58.1    
61.3    
64.5    
67.7    
71.0    
74.2    
77.4    
80.6    
83.9    
87.1    
90.3    
93.5    
96.8    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 24976
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-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 1 - 10247
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-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

-building DP trellis

-building trellis in range 1 - 10034
-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
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 10254 - 24976
-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

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

-building DP trellis

-building trellis in range 11895 - 24976
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 13270 - 24976
-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

-building DP trellis

-building trellis in range 13998 - 24976
-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