-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_17338644-17522371

-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_13520-T1
Valid prediction for Augustus_model.g8988.t1
Valid prediction for pasa_asmbl_46180.p1
Valid prediction for GlimmerHMM_glimmerT_13500-T1
Valid prediction for GlimmerHMM_glimmerT_13530-T1
Couldn't classify 21639, 21653
Couldn't classify 24035, 24183
Sorry, prediction pasa_asmbl_46176.p1 fails validation.
(GAG)	 TG	21639-21653	GT	CAG
(CAG)	 AG	22002-22071	GT	CGG
(TGG)	 AG	22426-22589	GT	AGG
(ATG)	 AG	22701-22797	GT	CAG
(AGA)	 AG	23647-23871	GT	AGG
(ACA)	 AG	24035-24183	GT	AGG
-recovered pasa_asmbl_46176.p1, initial, 22701, 22797
-recovered pasa_asmbl_46176.p1, internal, 22002, 22071
-recovered pasa_asmbl_46176.p1, internal, 22426, 22589
-recovered pasa_asmbl_46176.p1, internal, 22701, 22797
-recovered pasa_asmbl_46176.p1, internal, 23647, 23871
-recovered pasa_asmbl_46176.p1, internal, 24035, 24183
Valid prediction for snap_scaffold_5-snap.3216-T1
Valid prediction for Augustus_model.g8985.t1
Valid prediction for snap_scaffold_5-snap.3238-T1
Valid prediction for Augustus_model.g8977.t1
Valid prediction for snap_scaffold_5-snap.3231-T1
Valid prediction for snap_scaffold_5-snap.3218-T1
Valid prediction for GlimmerHMM_glimmerT_13531-T1
Valid prediction for snap_scaffold_5-snap.3235-T1
Valid prediction for snap_scaffold_5-snap.3242-T1
Valid prediction for snap_scaffold_5-snap.3225-T1
Valid prediction for GlimmerHMM_glimmerT_13505-T1
Valid prediction for GlimmerHMM_glimmerT_13526-T1
Valid prediction for GlimmerHMM_glimmerT_13522-T1
Valid prediction for GlimmerHMM_glimmerT_13518-T1
Valid prediction for GlimmerHMM_glimmerT_13504-T1
Valid prediction for GlimmerHMM_glimmerT_13499-T1
Valid prediction for snap_scaffold_5-snap.3226-T1
Valid prediction for snap_scaffold_5-snap.3224-T1
Valid prediction for HiQ_model.g8979.t1
Couldn't classify 21020, 21049
Couldn't classify 21456, 21653
Sorry, prediction pasa_asmbl_46402.p1 fails validation.
(GAG)	 AC	21020-21049	GT	CGG
(GAA)	 AG	21247-21324	GT	AGG
(TGT)	 AG	21456-21653	GT	CAG
-recovered pasa_asmbl_46402.p1, internal, 21247, 21324
-recovered pasa_asmbl_46402.p1, internal, 21456, 21653
Valid prediction for GlimmerHMM_glimmerT_13510-T1
Couldn't classify 19560, 19629
Sorry, prediction pasa_asmbl_46175.p1 fails validation.
(ATG)	 AC	17423-17536	GT	AGG
(CAT)	 AG	17737-17859	GT	ATG
(GAG)	 AG	18257-18358	GT	AGG
(GTG)	 AG	18418-18605	GT	TGG
(GCG)	 AG	19560-19629	AC	TGA
-recovered pasa_asmbl_46175.p1, initial, 17423, 17536
-recovered pasa_asmbl_46175.p1, internal, 17737, 17859
-recovered pasa_asmbl_46175.p1, internal, 18257, 18358
-recovered pasa_asmbl_46175.p1, internal, 18418, 18605
Valid prediction for snap_scaffold_5-snap.3236-T1
Valid prediction for GlimmerHMM_glimmerT_13511-T1
Valid prediction for snap_scaffold_5-snap.3246-T1
Valid prediction for snap_scaffold_5-snap.3230-T1
Valid prediction for snap_scaffold_5-snap.3233-T1
Valid prediction for Augustus_model.g8980.t1
Valid prediction for snap_scaffold_5-snap.3229-T1
Valid prediction for snap_scaffold_5-snap.3247-T1
Valid prediction for snap_scaffold_5-snap.3253-T1
Valid prediction for snap_scaffold_5-snap.3249-T1
Valid prediction for GlimmerHMM_glimmerT_13514-T1
Valid prediction for Augustus_model.g8987.t1
Valid prediction for snap_scaffold_5-snap.3255-T1
Valid prediction for GlimmerHMM_glimmerT_13515-T1
Valid prediction for GlimmerHMM_glimmerT_13509-T1
Valid prediction for CodingQuarry_transcript_52434-T1
Couldn't classify 24277, 24388
Couldn't classify 25321, 25371
Sorry, prediction pasa_asmbl_46177.p1 fails validation.
(CTG)	 TG	24277-24388	GT	AGG
(CTG)	 AG	24836-24997	GT	AGG
(GGT)	 AG	25102-25190	GT	GGG
(GAT)	 AG	25321-25371	GT	CGG
-recovered pasa_asmbl_46177.p1, internal, 24836, 24997
-recovered pasa_asmbl_46177.p1, internal, 25102, 25190
-recovered pasa_asmbl_46177.p1, internal, 25321, 25371
Valid prediction for snap_scaffold_5-snap.3227-T1
Valid prediction for Augustus_model.g8976.t1
Valid prediction for snap_scaffold_5-snap.3243-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.g8983.t1
Valid prediction for snap_scaffold_5-snap.3239-T1
Valid prediction for GlimmerHMM_glimmerT_13524-T1
Valid prediction for snap_scaffold_5-snap.3248-T1
Valid prediction for snap_scaffold_5-snap.3219-T1
Valid prediction for GlimmerHMM_glimmerT_13506-T1
Valid prediction for GlimmerHMM_glimmerT_13529-T1
Valid prediction for pasa_asmbl_44802.p1
Valid prediction for snap_scaffold_5-snap.3222-T1
Valid prediction for snap_scaffold_5-snap.3232-T1
Valid prediction for snap_scaffold_5-snap.3256-T1
Valid prediction for snap_scaffold_5-snap.3237-T1
Valid prediction for GlimmerHMM_glimmerT_13513-T1
Valid prediction for GlimmerHMM_glimmerT_13521-T1
Valid prediction for GlimmerHMM_glimmerT_13528-T1
Valid prediction for GlimmerHMM_glimmerT_13501-T1
Valid prediction for snap_scaffold_5-snap.3217-T1
Valid prediction for snap_scaffold_5-snap.3254-T1
Valid prediction for snap_scaffold_5-snap.3240-T1
Valid prediction for snap_scaffold_5-snap.3234-T1
Valid prediction for GlimmerHMM_glimmerT_13525-T1
Valid prediction for snap_scaffold_5-snap.3245-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g8986.t1
Valid prediction for GlimmerHMM_glimmerT_13527-T1
Valid prediction for Augustus_model.g8982.t1
Valid prediction for GlimmerHMM_glimmerT_13532-T1
Valid prediction for GlimmerHMM_glimmerT_13512-T1
Valid prediction for snap_scaffold_5-snap.3250-T1
Valid prediction for GlimmerHMM_glimmerT_13523-T1
Valid prediction for snap_scaffold_5-snap.3241-T1
Valid prediction for snap_scaffold_5-snap.3244-T1
Valid prediction for GlimmerHMM_glimmerT_13502-T1
Valid prediction for GlimmerHMM_glimmerT_13508-T1
Valid prediction for GlimmerHMM_glimmerT_13516-T1
Valid prediction for snap_scaffold_5-snap.3223-T1
Valid prediction for GlimmerHMM_glimmerT_13503-T1
Valid prediction for Augustus_model.g8978.t1
Valid prediction for GlimmerHMM_glimmerT_13519-T1
Valid prediction for Augustus_model.g8984.t1
Valid prediction for Augustus_model.g8989.t1
Valid prediction for snap_scaffold_5-snap.3228-T1
Valid prediction for snap_scaffold_5-snap.3252-T1
Valid prediction for GlimmerHMM_glimmerT_13507-T1
Valid prediction for snap_scaffold_5-snap.3251-T1
Valid prediction for snap_scaffold_5-snap.3220-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g8981.t1
Valid prediction for snap_scaffold_5-snap.3221-T1
Valid prediction for GlimmerHMM_glimmerT_13517-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27524, rend_intergenic: 9644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69562, rend_intergenic: 69324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80613, rend_intergenic: 80138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93031, rend_intergenic: 92262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98623, rend_intergenic: 93441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122494, rend_intergenic: 108646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135248, rend_intergenic: 122755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137518, rend_intergenic: 135386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150844, rend_intergenic: 143074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150974, rend_intergenic: 150875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153885, rend_intergenic: 152297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164212, rend_intergenic: 154859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169096, rend_intergenic: 165686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169607, rend_intergenic: 169224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175210, rend_intergenic: 169710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180753, rend_intergenic: 175603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183728
-exon list size: 407


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.4    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.2    
4.4    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.8    
7.1    
7.3    
7.6    
7.8    
8.1    
8.3    
8.6    
8.8    
9.0    
9.3    
9.5    
9.8    
10.0    
10.3    
10.5    
10.8    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.7    
13.0    
13.2    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.4    
15.6    
15.9    
16.1    
16.4    
16.6    
16.9    
17.1    
17.4    
17.6    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.8    
22.0    
22.2    
22.5    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
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    
35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.3    
53.5    
53.8    
54.0    
54.3    
54.5    
54.8    
55.0    
55.3    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.9    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.6    
63.8    
64.1    
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    
68.9    
69.2    
69.4    
69.7    
69.9    
70.2    
70.4    
70.7    
70.9    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.3    
73.6    
73.8    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
77.8    
78.0    
78.2    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.4    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.0    
87.3    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 27524, rend_intergenic: 9644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69562, rend_intergenic: 69324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80613, rend_intergenic: 80138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93031, rend_intergenic: 92262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98623, rend_intergenic: 93441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122494, rend_intergenic: 108646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135248, rend_intergenic: 122755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137518, rend_intergenic: 135386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150844, rend_intergenic: 143074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150974, rend_intergenic: 150875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153885, rend_intergenic: 152297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164212, rend_intergenic: 154859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169096, rend_intergenic: 165686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169607, rend_intergenic: 169224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175210, rend_intergenic: 169710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180753, rend_intergenic: 175603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support