-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_18864291-19083020

-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_3-snap.3725-T1
Valid prediction for snap_scaffold_3-snap.3718-T1
Valid prediction for snap_scaffold_3-snap.3717-T1
Valid prediction for GlimmerHMM_glimmerT_8421-T1
Couldn't classify 196105, 196262
Couldn't classify 200384, 200536
Sorry, prediction pasa_asmbl_40849.p1 fails validation.
(CAA)	 AG	196105-196262	GT	AGG
(GAT)	 AG	197570-197649	GT	TGG
(CTC)	 AG	199116-199231	GT	TGG
(GCC)	 AG	199798-199847	GT	GGG
(GTT)	 AG	199938-200025	GT	AGG
(GTA)	 AG	200384-200536	CC	CTC
-recovered pasa_asmbl_40849.p1, internal, 196105, 196262
-recovered pasa_asmbl_40849.p1, internal, 197570, 197649
-recovered pasa_asmbl_40849.p1, internal, 199116, 199231
-recovered pasa_asmbl_40849.p1, internal, 199798, 199847
-recovered pasa_asmbl_40849.p1, internal, 199938, 200025
Valid prediction for Augustus_model.g5549.t1
Valid prediction for HiQ_model.g5538.t1
Valid prediction for snap_scaffold_3-snap.3703-T1
Valid prediction for snap_scaffold_3-snap.3748-T1
Valid prediction for Augustus_model.g5540.t1
Valid prediction for Augustus_model.g5546.t1
Valid prediction for CodingQuarry_transcript_46481-T1
Valid prediction for Augustus_model.g5533.t1
Valid prediction for snap_scaffold_3-snap.3712-T1
Valid prediction for Augustus_model.g5534.t1
Valid prediction for snap_scaffold_3-snap.3714-T1
Valid prediction for snap_scaffold_3-snap.3719-T1
Valid prediction for GlimmerHMM_glimmerT_8422-T1
Valid prediction for GlimmerHMM_glimmerT_8429-T1
Valid prediction for Augustus_model.g5536.t1
Valid prediction for pasa_asmbl_40751.p1
Valid prediction for Augustus_model.g5544.t1
Valid prediction for snap_scaffold_3-snap.3728-T1
Valid prediction for snap_scaffold_3-snap.3743-T1
Valid prediction for snap_scaffold_3-snap.3733-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_46480-T1
Valid prediction for GlimmerHMM_glimmerT_8420-T1
Valid prediction for snap_scaffold_3-snap.3721-T1
Valid prediction for GlimmerHMM_glimmerT_8416-T1
Valid prediction for snap_scaffold_3-snap.3715-T1
Valid prediction for snap_scaffold_3-snap.3737-T1
Valid prediction for snap_scaffold_3-snap.3722-T1
Valid prediction for snap_scaffold_3-snap.3711-T1
Valid prediction for snap_scaffold_3-snap.3702-T1
Valid prediction for snap_scaffold_3-snap.3706-T1
Valid prediction for snap_scaffold_3-snap.3747-T1
Valid prediction for snap_scaffold_3-snap.3730-T1
Valid prediction for pasa_asmbl_40761.p1
Valid prediction for GlimmerHMM_glimmerT_8417-T1
Valid prediction for GlimmerHMM_glimmerT_8423-T1
Valid prediction for GlimmerHMM_glimmerT_8432-T1
Valid prediction for Augustus_model.g5535.t1
Valid prediction for snap_scaffold_3-snap.3713-T1
Valid prediction for snap_scaffold_3-snap.3744-T1
Valid prediction for GlimmerHMM_glimmerT_8435-T1
Valid prediction for Augustus_model.g5537.t1
Valid prediction for GlimmerHMM_glimmerT_8436-T1
Valid prediction for snap_scaffold_3-snap.3707-T1
Valid prediction for CodingQuarry_transcript_46483-T1
Valid prediction for Augustus_model.g5548.t1
Valid prediction for GlimmerHMM_glimmerT_8438-T1
Valid prediction for snap_scaffold_3-snap.3708-T1
Valid prediction for snap_scaffold_3-snap.3716-T1
Valid prediction for Augustus_model.g5550.t1
Valid prediction for HiQ_model.g5539.t1
Valid prediction for snap_scaffold_3-snap.3738-T1
Valid prediction for GlimmerHMM_glimmerT_8419-T1
Valid prediction for snap_scaffold_3-snap.3729-T1
Valid prediction for snap_scaffold_3-snap.3710-T1
Valid prediction for snap_scaffold_3-snap.3726-T1
Couldn't classify 79513, 79608
Sorry, prediction pasa_asmbl_40754.p1 fails validation.
(TAT)	 CC	79513-79608	GT	AGG
(TCC)	 AG	79888-79985	GT	AGG
(CGA)	 AG	80095-80224	GT	AGG
(AAA)	 AG	80345-80383	GT	ATG
(TAT)	 AG	80686-80784	GT	ATG
(GGA)	 AG	80937-81007	GT	ATG
(ATA)	 AG	81107-81160	GT	AAG
(GCT)	 AG	81486-81610	GT	CGG
(GAC)	 AG	81794-81844	GT	AGG
(AAC)	 AG	82092-82190	GT	TGG
(ATC)	 AG	82705-82774	GT	GTG
(GTA)	 AG	82874-83068	GT	AGG
(AGA)	 AG	83232-83286	GT	GGG
(TCA)	 AG	83430-83529	GT	TGG
(ATG)	 AG	83616-83674	GT	TGG
(AAT)	 AG	83792-83864	GT	CGG
(ACA)	 AG	84033-84106	GT	TGG
(TGG)	 AG	84408-84509	AA	AAA
add_exon() Sorry, pasa_asmbl_40754.p1 83616-83674-initial-1 is invalid.
-recovered pasa_asmbl_40754.p1, initial, 83616, 83674
-recovered pasa_asmbl_40754.p1, terminal, 84408, 84509
-recovered pasa_asmbl_40754.p1, internal, 79888, 79985
-recovered pasa_asmbl_40754.p1, internal, 80095, 80224
-recovered pasa_asmbl_40754.p1, internal, 80345, 80383
-recovered pasa_asmbl_40754.p1, internal, 80686, 80784
-recovered pasa_asmbl_40754.p1, internal, 80937, 81007
-recovered pasa_asmbl_40754.p1, internal, 81107, 81160
-recovered pasa_asmbl_40754.p1, internal, 81486, 81610
-recovered pasa_asmbl_40754.p1, internal, 81794, 81844
-recovered pasa_asmbl_40754.p1, internal, 82092, 82190
-recovered pasa_asmbl_40754.p1, internal, 82705, 82774
-recovered pasa_asmbl_40754.p1, internal, 82874, 83068
-recovered pasa_asmbl_40754.p1, internal, 83232, 83286
-recovered pasa_asmbl_40754.p1, internal, 83430, 83529
-recovered pasa_asmbl_40754.p1, internal, 83616, 83674
-recovered pasa_asmbl_40754.p1, internal, 83792, 83864
-recovered pasa_asmbl_40754.p1, internal, 84033, 84106

-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 GlimmerHMM_glimmerT_8418-T1
Valid prediction for Augustus_model.g5541.t1
Valid prediction for GlimmerHMM_glimmerT_8437-T1
Valid prediction for Augustus_model.g5547.t1
Valid prediction for snap_scaffold_3-snap.3709-T1
Valid prediction for Augustus_model.g5543.t1
Valid prediction for snap_scaffold_3-snap.3731-T1
Valid prediction for snap_scaffold_3-snap.3723-T1
Valid prediction for snap_scaffold_3-snap.3724-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3746-T1
Valid prediction for GlimmerHMM_glimmerT_8424-T1
Valid prediction for GlimmerHMM_glimmerT_8430-T1
Valid prediction for snap_scaffold_3-snap.3740-T1
Valid prediction for GlimmerHMM_glimmerT_8425-T1
Valid prediction for Augustus_model.g5532.t1
Valid prediction for snap_scaffold_3-snap.3732-T1
Valid prediction for GlimmerHMM_glimmerT_8426-T1
Valid prediction for HiQ_model.g5545.t1
Valid prediction for Augustus_model.g5531.t1
Couldn't classify 56497, 56711
Sorry, prediction pasa_asmbl_39636.p1 fails validation.
(ATG)	 GG	53901-53999	GT	AGG
(ACG)	 AG	54477-54582	GT	AGG
(GAG)	 AG	54731-54813	GT	AGG
(GAG)	 AG	55632-55696	GT	AAG
(CAA)	 AG	55779-55897	GT	CGG
(AGC)	 AG	56497-56711	AA	GGA
-recovered pasa_asmbl_39636.p1, initial, 53901, 53999
-recovered pasa_asmbl_39636.p1, internal, 54477, 54582
-recovered pasa_asmbl_39636.p1, internal, 54731, 54813
-recovered pasa_asmbl_39636.p1, internal, 55632, 55696
-recovered pasa_asmbl_39636.p1, internal, 55779, 55897
Valid prediction for GlimmerHMM_glimmerT_8427-T1
Valid prediction for GlimmerHMM_glimmerT_8431-T1
Valid prediction for snap_scaffold_3-snap.3734-T1
Valid prediction for snap_scaffold_3-snap.3701-T1
Valid prediction for GlimmerHMM_glimmerT_8434-T1
Valid prediction for GlimmerHMM_glimmerT_8433-T1
Valid prediction for snap_scaffold_3-snap.3700-T1
Valid prediction for snap_scaffold_3-snap.3741-T1
Valid prediction for snap_scaffold_3-snap.3705-T1
Valid prediction for snap_scaffold_3-snap.3742-T1
Valid prediction for snap_scaffold_3-snap.3727-T1
Valid prediction for snap_scaffold_3-snap.3704-T1
Valid prediction for snap_scaffold_3-snap.3745-T1
Valid prediction for snap_scaffold_3-snap.3739-T1
Valid prediction for Augustus_model.g5542.t1
Couldn't classify 56497, 56677
Couldn't classify 56714, 56846
Couldn't classify 56919, 57170
Sorry, prediction CodingQuarry_transcript_46482-T1 fails validation.
(ATG)	 GG	53901-53999	GT	AGG
(ACG)	 AG	54477-54582	GT	AGG
(GAG)	 AG	54731-54813	GT	AGG
(GAG)	 AG	55632-55696	GT	AAG
(CAA)	 AG	55779-55897	GT	CGG
(AGC)	 AG	56497-56677	CC	GCC
(GGA)	 AA	56714-56846	CT	ACC
(CTG)	 AC	56919-57170	GT	AGG
(CCT)	 AG	57841-58002	CT	AAC
-recovered CodingQuarry_transcript_46482-T1, initial, 53901, 53999
-recovered CodingQuarry_transcript_46482-T1, terminal, 57841, 58002
-recovered CodingQuarry_transcript_46482-T1, internal, 54477, 54582
-recovered CodingQuarry_transcript_46482-T1, internal, 54731, 54813
-recovered CodingQuarry_transcript_46482-T1, internal, 55632, 55696
-recovered CodingQuarry_transcript_46482-T1, internal, 55779, 55897
Valid prediction for snap_scaffold_3-snap.3720-T1
Valid prediction for GlimmerHMM_glimmerT_8428-T1
Valid prediction for snap_scaffold_3-snap.3735-T1
Valid prediction for snap_scaffold_3-snap.3736-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25659, rend_intergenic: 19525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40245, rend_intergenic: 38083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98877, rend_intergenic: 92489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100603, rend_intergenic: 99070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114222, rend_intergenic: 104401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126022, rend_intergenic: 116761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162216, rend_intergenic: 160729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170381, rend_intergenic: 166755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177907, rend_intergenic: 174433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202194, rend_intergenic: 188548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 218730
-exon list size: 385


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.8    
3.1    
3.4    
3.6    
3.9    
4.1    
4.4    
4.7    
4.9    
5.2    
5.4    
5.7    
5.9    
6.2    
6.5    
6.7    
7.0    
7.2    
7.5    
7.8    
8.0    
8.3    
8.5    
8.8    
9.0    
9.3    
9.6    
9.8    
10.1    
10.3    
10.6    
10.9    
11.1    
11.4    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.5    
15.8    
16.0    
16.3    
16.5    
16.8    
17.1    
17.3    
17.6    
17.8    
18.1    
18.3    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
22.0    
22.2    
22.5    
22.7    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
31.0    
31.3    
31.5    
31.8    
32.0    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.0    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.6    
63.8    
64.1    
64.3    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
68.0    
68.2    
68.5    
68.7    
69.0    
69.3    
69.5    
69.8    
70.0    
70.3    
70.5    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.3    
77.5    
77.8    
78.0    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.2    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.4    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 25659, rend_intergenic: 19525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40245, rend_intergenic: 38083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98877, rend_intergenic: 92489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100603, rend_intergenic: 99070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114222, rend_intergenic: 104401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126022, rend_intergenic: 116761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162216, rend_intergenic: 160729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170381, rend_intergenic: 166755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177907, rend_intergenic: 174433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202194, rend_intergenic: 188548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support