-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_17755237-17893539

-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 GeneMark_model.13714_t
Valid prediction for snap_scaffold_3-snap.3471-T1
Valid prediction for pasa_asmbl_40652.p1
Valid prediction for snap_scaffold_3-snap.3487-T1
Valid prediction for snap_scaffold_3-snap.3475-T1
Valid prediction for GeneMark_model.13720_t
Valid prediction for snap_scaffold_3-snap.3493-T1
Valid prediction for GeneMark_model.13703_t
Valid prediction for snap_scaffold_3-snap.3477-T1
Valid prediction for Augustus_model.g5608.t1
Valid prediction for Augustus_model.g5594.t1
Valid prediction for snap_scaffold_3-snap.3485-T1
Valid prediction for Augustus_model.g5595.t1
Valid prediction for snap_scaffold_3-snap.3473-T1
Valid prediction for snap_scaffold_3-snap.3502-T1
Valid prediction for GlimmerHMM_glimmerT_8429-T1
Valid prediction for snap_scaffold_3-snap.3491-T1
Valid prediction for GeneMark_model.13700_t
Valid prediction for CodingQuarry_transcript_46350-T1
Valid prediction for snap_scaffold_3-snap.3498-T1
Valid prediction for GeneMark_model.13718_t
Valid prediction for Augustus_model.g5596.t1
Couldn't classify 95416, 95497
Couldn't classify 95815, 95873
Sorry, prediction CodingQuarry_transcript_46352-T1 fails validation.
(ATG)	 CC	94806-94877	GT	AAG
(GTA)	 AG	95181-95275	GT	AGG
(ATT)	 AG	95416-95497	CG	GCC
(TTT)	 GG	95815-95873	GT	AAG
(GTA)	 AG	95962-96010	GT	AGG
(GTC)	 AG	96166-96286	GT	AGG
(GTC)	 AG	97197-97303	GT	AGG
(GCG)	 AG	97693-97778	GT	AGG
(GAA)	 AG	97967-98795	GT	GAG
-recovered CodingQuarry_transcript_46352-T1, initial, 94806, 94877
-recovered CodingQuarry_transcript_46352-T1, terminal, 97967, 98795
-recovered CodingQuarry_transcript_46352-T1, internal, 95181, 95275
-recovered CodingQuarry_transcript_46352-T1, internal, 95962, 96010
-recovered CodingQuarry_transcript_46352-T1, internal, 96166, 96286
-recovered CodingQuarry_transcript_46352-T1, internal, 97197, 97303
-recovered CodingQuarry_transcript_46352-T1, internal, 97693, 97778
-recovered CodingQuarry_transcript_46352-T1, internal, 97967, 98795
Valid prediction for GlimmerHMM_glimmerT_8435-T1
Valid prediction for snap_scaffold_3-snap.3500-T1
Valid prediction for GlimmerHMM_glimmerT_8446-T1
Valid prediction for Augustus_model.g5600.t1
Valid prediction for GlimmerHMM_glimmerT_8434-T1
Valid prediction for GeneMark_model.13726_t
Valid prediction for snap_scaffold_3-snap.3496-T1
Valid prediction for HiQ_model.g5593.t1
Valid prediction for snap_scaffold_3-snap.3488-T1
Valid prediction for snap_scaffold_3-snap.3495-T1
Valid prediction for snap_scaffold_3-snap.3484-T1
Valid prediction for GeneMark_model.13706_t
Valid prediction for GlimmerHMM_glimmerT_8442-T1
Couldn't classify 97967, 98084
Sorry, prediction pasa_asmbl_40669.p1 fails validation.
(ATG)	 CC	94806-94877	GT	AAG
(GTA)	 AG	95181-95275	GT	AGG
(ATT)	 AG	95416-95489	GT	AGG
(AAG)	 AG	95622-95635	GT	AGG
(GAT)	 AG	95821-95873	GT	AAG
(GTA)	 AG	95962-96010	GT	AGG
(GTC)	 AG	96166-96286	GT	AGG
(GTC)	 AG	97197-97303	GT	AGG
(GCG)	 AG	97693-97778	GT	AGG
(GAA)	 AG	97967-98084	TC	CCT
-recovered pasa_asmbl_40669.p1, initial, 94806, 94877
-recovered pasa_asmbl_40669.p1, internal, 95181, 95275
-recovered pasa_asmbl_40669.p1, internal, 95416, 95489
-recovered pasa_asmbl_40669.p1, internal, 95622, 95635
-recovered pasa_asmbl_40669.p1, internal, 95821, 95873
-recovered pasa_asmbl_40669.p1, internal, 95962, 96010
-recovered pasa_asmbl_40669.p1, internal, 96166, 96286
-recovered pasa_asmbl_40669.p1, internal, 97197, 97303
-recovered pasa_asmbl_40669.p1, internal, 97693, 97778
Valid prediction for GlimmerHMM_glimmerT_8440-T1
Couldn't classify 85403, 85728
Sorry, prediction pasa_asmbl_40665.p1 fails validation.
(GTC)	 TG	85403-85728	GT	CTG
(GTT)	 AG	86325-86493	GT	TGG
(GTC)	 AG	86600-86755	GT	TGG
(GTT)	 AG	87268-87351	GT	AAG
(TTT)	 AG	87471-87591	GT	AGG
(GGT)	 AG	87741-87825	GT	GGG
(GCT)	 AG	87990-88080	GT	AGG
(ATG)	 AG	88523-88724	GC	AGG
(ATT)	 AG	88912-89001	GT	AGG
(GTC)	 AG	89483-89613	GT	CTG
(AAC)	 AG	89727-89822	GT	AGG
(GGT)	 AG	89918-89982	GT	AGG
(GTT)	 AG	90065-90202	GT	AGG
(GTG)	 AG	90605-90803	GG	AGG
-recovered pasa_asmbl_40665.p1, initial, 88523, 88724
-recovered pasa_asmbl_40665.p1, terminal, 90605, 90803
-recovered pasa_asmbl_40665.p1, internal, 86325, 86493
-recovered pasa_asmbl_40665.p1, internal, 86600, 86755
-recovered pasa_asmbl_40665.p1, internal, 87268, 87351
-recovered pasa_asmbl_40665.p1, internal, 87471, 87591
-recovered pasa_asmbl_40665.p1, internal, 87741, 87825
-recovered pasa_asmbl_40665.p1, internal, 87990, 88080
-recovered pasa_asmbl_40665.p1, internal, 88523, 88724
-recovered pasa_asmbl_40665.p1, internal, 88912, 89001
-recovered pasa_asmbl_40665.p1, internal, 89483, 89613
-recovered pasa_asmbl_40665.p1, internal, 89727, 89822
-recovered pasa_asmbl_40665.p1, internal, 89918, 89982
-recovered pasa_asmbl_40665.p1, internal, 90065, 90202
Valid prediction for pasa_asmbl_40658.p1
Valid prediction for GlimmerHMM_glimmerT_8444-T1
Couldn't classify 85329, 85352
Sorry, prediction pasa_asmbl_40663.p1 fails validation.
(ATG)	 CC	84635-84940	GT	AGG
(TGG)	 AG	85329-85352	AC	CTA
-recovered pasa_asmbl_40663.p1, initial, 84635, 84940
Valid prediction for HiQ_model.g5602.t1
Valid prediction for GeneMark_model.13730_t
Valid prediction for CodingQuarry_transcript_46349-T1
Valid prediction for GeneMark_model.13722_t
Valid prediction for Augustus_model.g5607.t1
Couldn't classify 98064, 98795
Sorry, prediction pasa_asmbl_40671.p1 fails validation.
(AGC)	 GC	98064-98795	GT	GAG
Couldn't classify 110273, 110399
Sorry, prediction pasa_asmbl_40672.p1 fails validation.
(ATG)	 AA	107749-107763	GT	AGG
(GCA)	 AG	107865-107956	GT	GGG
(GAA)	 AG	109541-109684	GT	AGG
(CAA)	 AG	110273-110399	CG	CAC
-recovered pasa_asmbl_40672.p1, initial, 107749, 107763
-recovered pasa_asmbl_40672.p1, internal, 107865, 107956
-recovered pasa_asmbl_40672.p1, internal, 109541, 109684
Valid prediction for GlimmerHMM_glimmerT_8439-T1
Valid prediction for GlimmerHMM_glimmerT_8432-T1
Valid prediction for GlimmerHMM_glimmerT_8445-T1
Valid prediction for snap_scaffold_3-snap.3490-T1
Valid prediction for Augustus_model.g5604.t1
Valid prediction for snap_scaffold_3-snap.3470-T1
Couldn't classify 29761, 29844
Couldn't classify 32653, 32713
Sorry, prediction pasa_asmbl_40656.p1 fails validation.
(TGT)	 AC	29761-29844	GT	AGG
(TTA)	 AG	30929-31072	GT	AGG
(GAG)	 AG	32052-32230	GT	GTG
(TCC)	 AG	32653-32713	AC	TCA
-recovered pasa_asmbl_40656.p1, internal, 30929, 31072
-recovered pasa_asmbl_40656.p1, internal, 32052, 32230
Valid prediction for GlimmerHMM_glimmerT_8428-T1
Valid prediction for GeneMark_model.13707_t
Valid prediction for snap_scaffold_3-snap.3486-T1
Valid prediction for HiQ_model.g5601.t1
Valid prediction for GeneMark_model.13723_t
Valid prediction for GlimmerHMM_glimmerT_8431-T1
Valid prediction for GlimmerHMM_glimmerT_8438-T1
Valid prediction for snap_scaffold_3-snap.3472-T1
Valid prediction for snap_scaffold_3-snap.3476-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_46348-T1
Valid prediction for CodingQuarry_transcript_46346-T1
Valid prediction for GeneMark_model.13725_t
Valid prediction for GeneMark_model.13719_t
Valid prediction for GeneMark_model.13708_t
Valid prediction for GeneMark_model.13728_t
Valid prediction for GeneMark_model.13704_t
Valid prediction for HiQ_model.g5606.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 CodingQuarry_transcript_46351-T1
Valid prediction for GeneMark_model.13721_t
Valid prediction for Augustus_model.g5592.t1
Valid prediction for GeneMark_model.13716_t
Valid prediction for GeneMark_model.13717_t
Valid prediction for GlimmerHMM_glimmerT_8441-T1
Valid prediction for GeneMark_model.13712_t
Valid prediction for Augustus_model.g5598.t1
Valid prediction for snap_scaffold_3-snap.3479-T1
Valid prediction for snap_scaffold_3-snap.3483-T1
Valid prediction for GeneMark_model.13701_t
Valid prediction for Augustus_model.g5597.t1
Valid prediction for GeneMark_model.13729_t
Valid prediction for snap_scaffold_3-snap.3499-T1
Valid prediction for GeneMark_model.13702_t
Valid prediction for HiQ_model.g5605.t1
Valid prediction for GeneMark_model.13715_t
Valid prediction for GeneMark_model.13727_t
Valid prediction for snap_scaffold_3-snap.3482-T1
Valid prediction for GlimmerHMM_glimmerT_8436-T1
Valid prediction for Augustus_model.g5609.t1
Valid prediction for snap_scaffold_3-snap.3481-T1
Valid prediction for GeneMark_model.13724_t
Valid prediction for snap_scaffold_3-snap.3497-T1
Valid prediction for GlimmerHMM_glimmerT_8447-T1
Valid prediction for snap_scaffold_3-snap.3494-T1
Valid prediction for GlimmerHMM_glimmerT_8430-T1
Valid prediction for GlimmerHMM_glimmerT_8433-T1
Valid prediction for GeneMark_model.13711_t
Valid prediction for GlimmerHMM_glimmerT_8443-T1
Valid prediction for snap_scaffold_3-snap.3469-T1
Valid prediction for pasa_asmbl_39524.p1
Valid prediction for snap_scaffold_3-snap.3501-T1
Valid prediction for GeneMark_model.13713_t
Valid prediction for GlimmerHMM_glimmerT_8437-T1
Valid prediction for snap_scaffold_3-snap.3480-T1
Valid prediction for snap_scaffold_3-snap.3492-T1
Valid prediction for GeneMark_model.13710_t
Valid prediction for snap_scaffold_3-snap.3489-T1
Valid prediction for Augustus_model.g5599.t1
Valid prediction for HiQ_model.g5603.t1
Valid prediction for snap_scaffold_3-snap.3503-T1
Valid prediction for snap_scaffold_3-snap.3474-T1
Valid prediction for GeneMark_model.13705_t
Valid prediction for snap_scaffold_3-snap.3478-T1
Sorry, intron length (9) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 81165, rend_intergenic: 78448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121588, rend_intergenic: 120082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126431, rend_intergenic: 122957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131364, rend_intergenic: 128435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135816, rend_intergenic: 134038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 138303
-exon list size: 404


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
3.0    
3.2    
3.4    
3.7    
3.9    
4.2    
4.4    
4.7    
4.9    
5.2    
5.4    
5.7    
5.9    
6.2    
6.4    
6.7    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.1    
10.3    
10.6    
10.8    
11.1    
11.3    
11.6    
11.8    
12.1    
12.3    
12.6    
12.8    
13.1    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.3    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.2    
22.4    
22.7    
22.9    
23.2    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 81165, rend_intergenic: 78448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121588, rend_intergenic: 120082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126431, rend_intergenic: 122957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131364, rend_intergenic: 128435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135816, rend_intergenic: 134038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support