-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_11819119-12050360

-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_6-snap.2526-T1
Valid prediction for snap_scaffold_6-snap.2504-T1
Valid prediction for snap_scaffold_6-snap.2510-T1
Valid prediction for GeneMark_model.26756_t
Valid prediction for GeneMark_model.26771_t
Valid prediction for Augustus_model.g10678.t1
Valid prediction for CodingQuarry_transcript_55094-T1
Valid prediction for snap_scaffold_6-snap.2523-T1
Valid prediction for GeneMark_model.26761_t
Valid prediction for CodingQuarry_transcript_55095-T1
Valid prediction for GlimmerHMM_glimmerT_15927-T1
Valid prediction for snap_scaffold_6-snap.2524-T1
Valid prediction for snap_scaffold_6-snap.2509-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 162089, 162184
Couldn't classify 163831, 163953
Sorry, prediction pasa_asmbl_47301.p1 fails validation.
(TGT)	 CA	162089-162184	GT	AGG
(GCC)	 AG	162542-162703	GT	AGG
(AAC)	 AG	162901-162993	GT	AGG
(GTA)	 AG	163473-163676	GT	TGG
(GTG)	 AG	163831-163953	AT	CCA
-recovered pasa_asmbl_47301.p1, internal, 162542, 162703
-recovered pasa_asmbl_47301.p1, internal, 162901, 162993
-recovered pasa_asmbl_47301.p1, internal, 163473, 163676
Valid prediction for GlimmerHMM_glimmerT_15925-T1
Valid prediction for Augustus_model.g10690.t1
Valid prediction for GeneMark_model.26775_t
Valid prediction for GlimmerHMM_glimmerT_15916-T1
Valid prediction for Augustus_model.g10691.t1
Valid prediction for snap_scaffold_6-snap.2520-T1
Valid prediction for GlimmerHMM_glimmerT_15932-T1
Valid prediction for snap_scaffold_6-snap.2502-T1
Valid prediction for GlimmerHMM_glimmerT_15914-T1
Valid prediction for snap_scaffold_6-snap.2503-T1
Valid prediction for snap_scaffold_6-snap.2521-T1
Valid prediction for GeneMark_model.26765_t
Valid prediction for GlimmerHMM_glimmerT_15939-T1
Valid prediction for snap_scaffold_6-snap.2515-T1
Valid prediction for snap_scaffold_6-snap.2514-T1
Valid prediction for Augustus_model.g10674.t1
Valid prediction for snap_scaffold_6-snap.2513-T1
Valid prediction for snap_scaffold_6-snap.2508-T1
Valid prediction for snap_scaffold_6-snap.2499-T1
Valid prediction for GlimmerHMM_glimmerT_15929-T1
Valid prediction for GlimmerHMM_glimmerT_15921-T1
Valid prediction for GeneMark_model.26758_t
Valid prediction for GlimmerHMM_glimmerT_15918-T1
Valid prediction for GlimmerHMM_glimmerT_15936-T1
Valid prediction for Augustus_model.g10680.t1
Valid prediction for Augustus_model.g10682.t1
Valid prediction for GlimmerHMM_glimmerT_15922-T1
Couldn't classify 155990, 156064
Couldn't classify 157888, 158113
Sorry, prediction pasa_asmbl_47891.p1 fails validation.
(CTT)	 TG	155990-156064	GT	AGG
(CCC)	 AG	156350-156475	GT	CAG
(AAT)	 AG	157237-157298	GT	GGG
(GCT)	 AG	157585-157716	GT	AGG
(GCT)	 AG	157888-158113	AG	TCA
-recovered pasa_asmbl_47891.p1, internal, 156350, 156475
-recovered pasa_asmbl_47891.p1, internal, 157237, 157298
-recovered pasa_asmbl_47891.p1, internal, 157585, 157716
Valid prediction for Augustus_model.g10686.t1
Valid prediction for snap_scaffold_6-snap.2522-T1
Valid prediction for GeneMark_model.26751_t
Valid prediction for GlimmerHMM_glimmerT_15937-T1
Valid prediction for GlimmerHMM_glimmerT_15915-T1
Valid prediction for GeneMark_model.26762_t
Couldn't classify 190105, 190300
Sorry, prediction pasa_asmbl_47306.p1 fails validation.
(ATG)	 TC	178980-179093	GT	AGG
(GGA)	 AG	179258-179425	GT	GGG
(ACT)	 AG	180567-180744	GT	CGG
(AAG)	 AG	181364-181411	GT	AGG
(ACA)	 AG	182752-182803	GT	GGG
(CTC)	 AG	183187-183301	GT	GGG
(GTG)	 AG	183995-184202	GT	AGG
(GGG)	 AG	184344-184654	GT	AGG
(AGG)	 AG	185142-185341	GT	CGG
(TTG)	 AG	185528-185654	GT	AGG
(CTG)	 AG	186235-186336	GT	AGG
(GCT)	 AG	186490-186636	GT	AGG
(GTA)	 AG	186859-187017	GC	AGG
(GAC)	 AG	187799-187965	GT	AGG
(TCT)	 AG	190105-190300	TA	GGT
-recovered pasa_asmbl_47306.p1, initial, 178980, 179093
-recovered pasa_asmbl_47306.p1, internal, 179258, 179425
-recovered pasa_asmbl_47306.p1, internal, 180567, 180744
-recovered pasa_asmbl_47306.p1, internal, 181364, 181411
-recovered pasa_asmbl_47306.p1, internal, 182752, 182803
-recovered pasa_asmbl_47306.p1, internal, 183187, 183301
-recovered pasa_asmbl_47306.p1, internal, 183995, 184202
-recovered pasa_asmbl_47306.p1, internal, 184344, 184654
-recovered pasa_asmbl_47306.p1, internal, 185142, 185341
-recovered pasa_asmbl_47306.p1, internal, 185528, 185654
-recovered pasa_asmbl_47306.p1, internal, 186235, 186336
-recovered pasa_asmbl_47306.p1, internal, 186490, 186636
-recovered pasa_asmbl_47306.p1, internal, 186859, 187017
-recovered pasa_asmbl_47306.p1, internal, 187799, 187965
Valid prediction for snap_scaffold_6-snap.2505-T1
Valid prediction for snap_scaffold_6-snap.2516-T1
Valid prediction for GeneMark_model.26766_t
Valid prediction for Augustus_model.g10685.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_6-snap.2525-T1
Valid prediction for Augustus_model.g10684.t1
Valid prediction for Augustus_model.g10675.t1
Valid prediction for GeneMark_model.26773_t
Couldn't classify 10759, 10968
Couldn't classify 15398, 15550
Sorry, prediction pasa_asmbl_48715.p1 fails validation.
(TCC)	 AG	10759-10968	GT	AGG
(ATG)	 AG	11128-11184	GT	AGG
(ACG)	 AG	13874-14009	GT	AGG
(ACC)	 AG	14218-14322	GT	TGG
(AGC)	 AG	14523-14651	GT	CTG
(ATG)	 AG	15120-15169	GT	AGG
(GAG)	 AG	15398-15550	GT	AGG
-recovered pasa_asmbl_48715.p1, initial, 11128, 11184
add_exon() Sorry, pasa_asmbl_48715.p1 15120-15169-initial-1 is invalid.
-recovered pasa_asmbl_48715.p1, initial, 15120, 15169
-recovered pasa_asmbl_48715.p1, internal, 10759, 10968
-recovered pasa_asmbl_48715.p1, internal, 11128, 11184
-recovered pasa_asmbl_48715.p1, internal, 13874, 14009
-recovered pasa_asmbl_48715.p1, internal, 14218, 14322
-recovered pasa_asmbl_48715.p1, internal, 14523, 14651
-recovered pasa_asmbl_48715.p1, internal, 15120, 15169
-recovered pasa_asmbl_48715.p1, internal, 15398, 15550
Valid prediction for GlimmerHMM_glimmerT_15920-T1
Valid prediction for GlimmerHMM_glimmerT_15933-T1
Valid prediction for snap_scaffold_6-snap.2506-T1
Valid prediction for GeneMark_model.26769_t
Valid prediction for Augustus_model.g10689.t1
Valid prediction for GeneMark_model.26750_t
Valid prediction for GlimmerHMM_glimmerT_15924-T1
Valid prediction for GeneMark_model.26754_t
Valid prediction for snap_scaffold_6-snap.2527-T1
Valid prediction for snap_scaffold_6-snap.2501-T1
Valid prediction for GeneMark_model.26749_t
Valid prediction for snap_scaffold_6-snap.2528-T1
Valid prediction for GeneMark_model.26760_t
Valid prediction for snap_scaffold_6-snap.2512-T1
Sorry, intron length (8) is less than minimum required (10)
Couldn't classify 19870, 19932
Sorry, prediction pasa_asmbl_48710.p1 fails validation.
(TTC)	 AC	19870-19932	GT	CGG
(TAT)	 AG	20090-20143	GT	AGG
(GCC)	 AG	20354-20419	GT	AGG
(GTG)	 AG	20940-21016	GT	AAG
(GTA)	 AG	21165-21375	GT	ACG
(ATC)	 AG	23028-23099	GT	AGG
(GCA)	 AG	23816-23919	GT	GGG
(AAC)	 AG	24170-24248	GT	AGG
(CTG)	 AG	24700-24829	GT	AGG
(TGT)	 AG	24994-25130	TC	GAT
-recovered pasa_asmbl_48710.p1, terminal, 24994, 25130
-recovered pasa_asmbl_48710.p1, internal, 20090, 20143
-recovered pasa_asmbl_48710.p1, internal, 20354, 20419
-recovered pasa_asmbl_48710.p1, internal, 20940, 21016
-recovered pasa_asmbl_48710.p1, internal, 21165, 21375
-recovered pasa_asmbl_48710.p1, internal, 23028, 23099
-recovered pasa_asmbl_48710.p1, internal, 23816, 23919
-recovered pasa_asmbl_48710.p1, internal, 24170, 24248
-recovered pasa_asmbl_48710.p1, internal, 24700, 24829
Valid prediction for Augustus_model.g10681.t1
Valid prediction for GeneMark_model.26755_t
Valid prediction for snap_scaffold_6-snap.2496-T1
Valid prediction for GeneMark_model.26753_t
Valid prediction for GeneMark_model.26759_t
Valid prediction for snap_scaffold_6-snap.2530-T1
Valid prediction for Augustus_model.g10679.t1
Valid prediction for GlimmerHMM_glimmerT_15942-T1
Valid prediction for Augustus_model.g10695.t1
Valid prediction for snap_scaffold_6-snap.2498-T1
Valid prediction for HiQ_model.g10693.t1
Valid prediction for Augustus_model.g10673.t1
Valid prediction for GlimmerHMM_glimmerT_15919-T1
Valid prediction for GlimmerHMM_glimmerT_15935-T1
Valid prediction for CodingQuarry_transcript_55096-T1
Valid prediction for GeneMark_model.26752_t
Valid prediction for snap_scaffold_6-snap.2519-T1
Valid prediction for GeneMark_model.26763_t
Valid prediction for snap_scaffold_6-snap.2517-T1
Valid prediction for GlimmerHMM_glimmerT_15941-T1
Valid prediction for Augustus_model.g10676.t1
Valid prediction for Augustus_model.g10692.t1
Valid prediction for GlimmerHMM_glimmerT_15931-T1
Valid prediction for GlimmerHMM_glimmerT_15940-T1
Valid prediction for GlimmerHMM_glimmerT_15926-T1
Valid prediction for snap_scaffold_6-snap.2495-T1
Valid prediction for GeneMark_model.26764_t
Valid prediction for snap_scaffold_6-snap.2518-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2507-T1
Valid prediction for snap_scaffold_6-snap.2531-T1
Valid prediction for GeneMark_model.26757_t
Valid prediction for Augustus_model.g10677.t1
Valid prediction for GeneMark_model.26772_t
Valid prediction for snap_scaffold_6-snap.2529-T1
Valid prediction for GeneMark_model.26767_t
Valid prediction for GeneMark_model.26774_t
Valid prediction for snap_scaffold_6-snap.2500-T1
Valid prediction for snap_scaffold_6-snap.2532-T1
Valid prediction for Augustus_model.g10688.t1
Valid prediction for snap_scaffold_6-snap.2533-T1
Valid prediction for Augustus_model.g10694.t1
Valid prediction for GlimmerHMM_glimmerT_15930-T1
Valid prediction for Augustus_model.g10683.t1
Valid prediction for Augustus_model.g10687.t1
Valid prediction for snap_scaffold_6-snap.2497-T1
Valid prediction for snap_scaffold_6-snap.2511-T1
Valid prediction for GlimmerHMM_glimmerT_15938-T1
Valid prediction for GlimmerHMM_glimmerT_15917-T1
Valid prediction for GlimmerHMM_glimmerT_15923-T1
Valid prediction for GeneMark_model.26768_t
Valid prediction for GeneMark_model.26770_t
Valid prediction for GlimmerHMM_glimmerT_15928-T1
Valid prediction for GlimmerHMM_glimmerT_15934-T1
Sorry, intron length (4) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 165223, rend_intergenic: 165220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56503, rend_intergenic: 54053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231242
-exon list size: 363


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.5    
2.7    
3.0    
3.3    
3.6    
3.8    
4.1    
4.4    
4.7    
4.9    
5.2    
5.5    
5.8    
6.0    
6.3    
6.6    
6.8    
7.1    
7.4    
7.7    
7.9    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.9    
10.1    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.2    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.3    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.1    
21.4    
21.6    
21.9    
22.2    
22.5    
22.7    
23.0    
23.3    
23.6    
23.8    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.8    
26.0    
26.3    
26.6    
26.8    
27.1    
27.4    
27.7    
27.9    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.9    
30.1    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.1    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.8    
47.1    
47.4    
47.7    
47.9    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.1    
52.3    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
64.9    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.9    
70.1    
70.4    
70.7    
71.0    
71.2    
71.5    
71.8    
72.1    
72.3    
72.6    
72.9    
73.2    
73.4    
73.7    
74.0    
74.2    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.2    
76.4    
76.7    
77.0    
77.3    
77.5    
77.8    
78.1    
78.4    
78.6    
78.9    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.7    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.2    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.1    
95.3    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 28 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 165223, rend_intergenic: 165220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56503, rend_intergenic: 54053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14222
-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 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 2699 - 14222
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 2699 - 14122
-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