-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_15116317-15349909

-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 GlimmerHMM_glimmerT_28949-T1
Valid prediction for GeneMark_model.49969_t
Valid prediction for snap_scaffold_11-snap.3138-T1
Couldn't classify 145765, 146041
Sorry, prediction pasa_asmbl_6092.p1 fails validation.
(GAG)	 AG	145765-146041	GT	CAG
(AAG)	 AG	147234-147286	GT	TGG
(GAT)	 AG	147568-147640	GT	AGG
(GAA)	 AG	147757-147863	GT	AGG
(AAC)	 AG	147947-148108	GT	AGG
(ATT)	 AG	148916-149014	GT	AGG
(GTA)	 AG	149103-149370	GT	AGG
(CAA)	 AG	150086-150171	GT	AGG
(GAC)	 AG	150341-150514	TG	AGT
-recovered pasa_asmbl_6092.p1, terminal, 150341, 150514
-recovered pasa_asmbl_6092.p1, internal, 145765, 146041
-recovered pasa_asmbl_6092.p1, internal, 147234, 147286
-recovered pasa_asmbl_6092.p1, internal, 147568, 147640
-recovered pasa_asmbl_6092.p1, internal, 147757, 147863
-recovered pasa_asmbl_6092.p1, internal, 147947, 148108
-recovered pasa_asmbl_6092.p1, internal, 148916, 149014
-recovered pasa_asmbl_6092.p1, internal, 149103, 149370
-recovered pasa_asmbl_6092.p1, internal, 150086, 150171
Valid prediction for GeneMark_model.49947_t
Valid prediction for GlimmerHMM_glimmerT_28944-T1
Valid prediction for GlimmerHMM_glimmerT_28942-T1
Valid prediction for GlimmerHMM_glimmerT_28948-T1
Valid prediction for GeneMark_model.49942_t
Valid prediction for HiQ_model.g19332.t1
Valid prediction for snap_scaffold_11-snap.3115-T1
Valid prediction for snap_scaffold_11-snap.3143-T1
Valid prediction for snap_scaffold_11-snap.3134-T1
Valid prediction for GeneMark_model.49944_t
Valid prediction for snap_scaffold_11-snap.3140-T1
Valid prediction for GlimmerHMM_glimmerT_28930-T1
Valid prediction for GeneMark_model.49958_t
Valid prediction for snap_scaffold_11-snap.3131-T1
Valid prediction for GlimmerHMM_glimmerT_28931-T1
Valid prediction for GlimmerHMM_glimmerT_28941-T1
Valid prediction for GeneMark_model.49967_t
Valid prediction for snap_scaffold_11-snap.3135-T1
Valid prediction for snap_scaffold_11-snap.3130-T1
Valid prediction for Augustus_model.g19326.t1
Valid prediction for GeneMark_model.49961_t
Valid prediction for Augustus_model.g19333.t1
Valid prediction for GeneMark_model.49957_t
Valid prediction for GlimmerHMM_glimmerT_28950-T1
Valid prediction for GlimmerHMM_glimmerT_28945-T1
Valid prediction for Augustus_model.g19330.t1
Valid prediction for GeneMark_model.49968_t
Valid prediction for snap_scaffold_11-snap.3127-T1
Valid prediction for snap_scaffold_11-snap.3137-T1
Valid prediction for Augustus_model.g19331.t1
Valid prediction for GlimmerHMM_glimmerT_28932-T1
Valid prediction for GlimmerHMM_glimmerT_28946-T1
Valid prediction for GlimmerHMM_glimmerT_28938-T1
Valid prediction for GlimmerHMM_glimmerT_28929-T1
Valid prediction for GeneMark_model.49946_t
Valid prediction for snap_scaffold_11-snap.3118-T1
Valid prediction for snap_scaffold_11-snap.3132-T1
Valid prediction for GeneMark_model.49949_t
Valid prediction for snap_scaffold_11-snap.3121-T1
Valid prediction for GeneMark_model.49955_t
Valid prediction for GeneMark_model.49951_t
Valid prediction for GlimmerHMM_glimmerT_28936-T1
Valid prediction for snap_scaffold_11-snap.3120-T1
Valid prediction for GeneMark_model.49963_t
Valid prediction for Augustus_model.g19329.t1
Valid prediction for GeneMark_model.49965_t
Valid prediction for GeneMark_model.49960_t
Valid prediction for GlimmerHMM_glimmerT_28939-T1
Valid prediction for snap_scaffold_11-snap.3113-T1
Valid prediction for GlimmerHMM_glimmerT_28927-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 Augustus_model.g19323.t1
Valid prediction for GeneMark_model.49970_t
Valid prediction for GlimmerHMM_glimmerT_28934-T1
Valid prediction for snap_scaffold_11-snap.3114-T1
Valid prediction for GeneMark_model.49941_t
Couldn't classify 124744, 124911
Sorry, prediction pasa_asmbl_7173.p1 fails validation.
(GGC)	 AG	124744-124911	GT	TGG
(GAC)	 AG	125381-125480	GT	TGG
(AGC)	 AG	125674-125790	GT	AGG
(GTG)	 AG	125915-126096	AG	AGA
-recovered pasa_asmbl_7173.p1, terminal, 125915, 126096
-recovered pasa_asmbl_7173.p1, internal, 124744, 124911
-recovered pasa_asmbl_7173.p1, internal, 125381, 125480
-recovered pasa_asmbl_7173.p1, internal, 125674, 125790
Valid prediction for snap_scaffold_11-snap.3112-T1
Valid prediction for snap_scaffold_11-snap.3139-T1
Valid prediction for pasa_asmbl_7163.p1
Valid prediction for CodingQuarry_transcript_8284-T1
Valid prediction for snap_scaffold_11-snap.3142-T1
Valid prediction for CodingQuarry_transcript_8283-T1
Valid prediction for GlimmerHMM_glimmerT_28933-T1
Valid prediction for snap_scaffold_11-snap.3141-T1
Valid prediction for GeneMark_model.49959_t
Valid prediction for snap_scaffold_11-snap.3128-T1
Valid prediction for GeneMark_model.49943_t
Valid prediction for GeneMark_model.49956_t
Valid prediction for GeneMark_model.49972_t
Valid prediction for GeneMark_model.49964_t
Valid prediction for GlimmerHMM_glimmerT_28940-T1
Valid prediction for GeneMark_model.49948_t
Valid prediction for Augustus_model.g19328.t1
Valid prediction for snap_scaffold_11-snap.3117-T1
Valid prediction for snap_scaffold_11-snap.3125-T1
Valid prediction for snap_scaffold_11-snap.3122-T1
Valid prediction for Augustus_model.g19321.t1
Valid prediction for GlimmerHMM_glimmerT_28943-T1
Valid prediction for GeneMark_model.49952_t
Valid prediction for Augustus_model.g19325.t1
Valid prediction for Augustus_model.g19327.t1
Valid prediction for GeneMark_model.49953_t
Valid prediction for GeneMark_model.49971_t
Valid prediction for snap_scaffold_11-snap.3123-T1
Valid prediction for snap_scaffold_11-snap.3136-T1
Valid prediction for snap_scaffold_11-snap.3116-T1
Valid prediction for snap_scaffold_11-snap.3133-T1
Couldn't classify 190714, 190809
Sorry, prediction pasa_asmbl_7165.p1 fails validation.
(ATG)	 AG	188945-189058	GT	AGG
(ATT)	 AG	189287-189443	GT	CGG
(AGT)	 AG	189910-190040	GT	AGG
(CTC)	 AG	190714-190809	CC	CGC
-recovered pasa_asmbl_7165.p1, initial, 188945, 189058
-recovered pasa_asmbl_7165.p1, internal, 188945, 189058
-recovered pasa_asmbl_7165.p1, internal, 189287, 189443
-recovered pasa_asmbl_7165.p1, internal, 189910, 190040
Valid prediction for GeneMark_model.49962_t
Valid prediction for pasa_asmbl_7168.p1
Valid prediction for snap_scaffold_11-snap.3126-T1
Couldn't classify 154090, 154125
Sorry, prediction pasa_asmbl_7171.p1 fails validation.
(ACC)	 GC	154090-154125	GT	TCG
(TCC)	 AG	155169-155288	GT	TGG
(GGT)	 AG	155447-155506	GT	ATG
(TCT)	 AG	156184-156252	GT	TGG
(GTG)	 AG	156365-156511	GT	AGG
(AAT)	 AG	157878-158002	GT	CGG
(AGA)	 AG	158783-158970	GT	TGG
(GGA)	 AG	159071-159157	GT	AGG
(GTG)	 AG	160172-160467	TG	GAT
-recovered pasa_asmbl_7171.p1, terminal, 160172, 160467
-recovered pasa_asmbl_7171.p1, internal, 155169, 155288
-recovered pasa_asmbl_7171.p1, internal, 155447, 155506
-recovered pasa_asmbl_7171.p1, internal, 156184, 156252
-recovered pasa_asmbl_7171.p1, internal, 156365, 156511
-recovered pasa_asmbl_7171.p1, internal, 157878, 158002
-recovered pasa_asmbl_7171.p1, internal, 158783, 158970
-recovered pasa_asmbl_7171.p1, internal, 159071, 159157
Valid prediction for snap_scaffold_11-snap.3129-T1
Couldn't classify 184479, 184502
Couldn't classify 186027, 186179
Sorry, prediction pasa_asmbl_7167.p1 fails validation.
(AGT)	 AG	184479-184502	GT	AAG
(TGC)	 AG	184942-185103	GT	AGG
(AGT)	 AG	185236-185392	GT	TGG
(GGA)	 AG	185731-185858	GT	AGG
(CTC)	 AG	186027-186179	CA	AGC
-recovered pasa_asmbl_7167.p1, internal, 184479, 184502
-recovered pasa_asmbl_7167.p1, internal, 184942, 185103
-recovered pasa_asmbl_7167.p1, internal, 185236, 185392
-recovered pasa_asmbl_7167.p1, internal, 185731, 185858
Valid prediction for Augustus_model.g19322.t1
Valid prediction for snap_scaffold_11-snap.3119-T1
Valid prediction for snap_scaffold_11-snap.3124-T1
Valid prediction for GeneMark_model.49945_t
Valid prediction for GeneMark_model.49954_t
Couldn't classify 192048, 193712
Sorry, prediction pasa_asmbl_7164.p1 fails validation.
(GGG)	 GA	192048-193712	TC	AAT
Valid prediction for Augustus_model.g19320.t1
Valid prediction for GlimmerHMM_glimmerT_28928-T1
Valid prediction for snap_scaffold_11-snap.3144-T1
Valid prediction for GeneMark_model.49950_t
Valid prediction for GlimmerHMM_glimmerT_28937-T1
Valid prediction for GlimmerHMM_glimmerT_28935-T1
Valid prediction for GlimmerHMM_glimmerT_28947-T1
Valid prediction for HiQ_model.g19324.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10869, rend_intergenic: 8934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14842, rend_intergenic: 11557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15961, rend_intergenic: 15775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33262, rend_intergenic: 31978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52690, rend_intergenic: 42680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96624, rend_intergenic: 90506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128700, rend_intergenic: 126872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143961, rend_intergenic: 141327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145413, rend_intergenic: 144298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184170, rend_intergenic: 181265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233593
-exon list size: 417


building trellis

0.2    
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11.9    
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15.8    
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17.2    
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17.7    
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18.4    
18.6    
18.9    
19.1    
19.3    
19.6    
19.8    
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20.8    
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22.9    
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23.6    
23.9    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.8    
30.1    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.2    
37.5    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.6    
44.9    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.6    
51.8    
52.0    
52.3    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.1    
55.4    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.0    
57.3    
57.5    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.9    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.5    
62.8    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.4    
64.7    
64.9    
65.2    
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65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
69.9    
70.2    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.2    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 10869, rend_intergenic: 8934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14842, rend_intergenic: 11557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15961, rend_intergenic: 15775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33262, rend_intergenic: 31978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52690, rend_intergenic: 42680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96624, rend_intergenic: 90506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128700, rend_intergenic: 126872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143961, rend_intergenic: 141327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145413, rend_intergenic: 144298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184170, rend_intergenic: 181265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 212124 - 233593
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 212124 - 227459
-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