-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_671872-906920

-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_9-snap.166-T1
Valid prediction for GlimmerHMM_glimmerT_21535-T1
Valid prediction for snap_scaffold_9-snap.195-T1
Valid prediction for Augustus_model.g14325.t1
Valid prediction for snap_scaffold_9-snap.189-T1
Valid prediction for Augustus_model.g14323.t1
Valid prediction for snap_scaffold_9-snap.174-T1
Valid prediction for GlimmerHMM_glimmerT_21534-T1
Valid prediction for snap_scaffold_9-snap.161-T1
Valid prediction for snap_scaffold_9-snap.199-T1
Valid prediction for snap_scaffold_9-snap.165-T1
Valid prediction for GlimmerHMM_glimmerT_21532-T1
Valid prediction for GlimmerHMM_glimmerT_21531-T1
Valid prediction for Augustus_model.g14321.t1
Valid prediction for snap_scaffold_9-snap.170-T1
Valid prediction for GlimmerHMM_glimmerT_21521-T1
Valid prediction for snap_scaffold_9-snap.175-T1
Valid prediction for snap_scaffold_9-snap.178-T1
Valid prediction for snap_scaffold_9-snap.176-T1
Couldn't classify 35191, 35370
Sorry, prediction pasa_asmbl_53792.p1 fails validation.
(TGG)	 AG	35191-35370	GT	AGG
(GTG)	 AG	35675-35793	GT	AAG
(TGT)	 AG	36742-36816	GT	AAG
(ACA)	 AG	37352-37515	GT	GGG
(CCA)	 AG	38184-38248	GT	AGG
(ATG)	 AG	38903-39044	GT	AGG
(GAG)	 AG	39254-39401	GT	AGG
(TGA)	 AG	41924-42095	GT	AGG
(GAC)	 AG	43531-43620	GT	AGG
(GTA)	 AG	44721-44893	GT	CGG
(GGC)	 AG	45309-45432	GT	GGG
(GTG)	 AG	45527-45637	TA	GAT
-recovered pasa_asmbl_53792.p1, initial, 38903, 39044
add_exon() Sorry, pasa_asmbl_53792.p1 38903-39044-terminal-3 is invalid.
-recovered pasa_asmbl_53792.p1, terminal, 38903, 39044
-recovered pasa_asmbl_53792.p1, terminal, 45527, 45637
-recovered pasa_asmbl_53792.p1, internal, 35191, 35370
-recovered pasa_asmbl_53792.p1, internal, 35675, 35793
-recovered pasa_asmbl_53792.p1, internal, 36742, 36816
-recovered pasa_asmbl_53792.p1, internal, 37352, 37515
-recovered pasa_asmbl_53792.p1, internal, 38184, 38248
-recovered pasa_asmbl_53792.p1, internal, 38903, 39044
-recovered pasa_asmbl_53792.p1, internal, 39254, 39401
-recovered pasa_asmbl_53792.p1, internal, 41924, 42095
-recovered pasa_asmbl_53792.p1, internal, 43531, 43620
-recovered pasa_asmbl_53792.p1, internal, 44721, 44893
-recovered pasa_asmbl_53792.p1, internal, 45309, 45432
Valid prediction for GlimmerHMM_glimmerT_21533-T1
Valid prediction for Augustus_model.g14317.t1
Valid prediction for snap_scaffold_9-snap.183-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.193-T1
Valid prediction for snap_scaffold_9-snap.186-T1
Valid prediction for snap_scaffold_9-snap.179-T1
Valid prediction for snap_scaffold_9-snap.190-T1
Valid prediction for Augustus_model.g14318.t1
Valid prediction for HiQ_model.g14319.t1
Valid prediction for GlimmerHMM_glimmerT_21525-T1
Valid prediction for GlimmerHMM_glimmerT_21539-T1
Valid prediction for snap_scaffold_9-snap.168-T1
Valid prediction for GlimmerHMM_glimmerT_21527-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_9-snap.187-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.194-T1
Valid prediction for snap_scaffold_9-snap.169-T1
Valid prediction for Augustus_model.g14326.t1
Valid prediction for snap_scaffold_9-snap.198-T1
Valid prediction for GlimmerHMM_glimmerT_21543-T1
Valid prediction for GlimmerHMM_glimmerT_21529-T1
Valid prediction for snap_scaffold_9-snap.162-T1
Valid prediction for snap_scaffold_9-snap.171-T1
Valid prediction for snap_scaffold_9-snap.182-T1
Valid prediction for snap_scaffold_9-snap.167-T1
Valid prediction for snap_scaffold_9-snap.173-T1
Valid prediction for snap_scaffold_9-snap.184-T1
Valid prediction for Augustus_model.g14322.t1
Valid prediction for GlimmerHMM_glimmerT_21530-T1
Valid prediction for Augustus_model.g14329.t1
Valid prediction for snap_scaffold_9-snap.160-T1
Valid prediction for Augustus_model.g14327.t1
Couldn't classify 23109, 23164
Sorry, prediction pasa_asmbl_55767.p1 fails validation.
(GTG)	 GG	23109-23164	GT	AGG
(TAT)	 AG	23677-23833	GT	TGG
(TCT)	 AG	24206-24303	GT	TTG
(CAT)	 AG	24520-24632	GT	CTG
(TGG)	 AG	24810-24857	GT	AGG
(GTG)	 AG	25234-25300	GT	GAG
(ATG)	 AG	26571-26574	CA	GAC
-recovered pasa_asmbl_55767.p1, terminal, 26571, 26574
-recovered pasa_asmbl_55767.p1, internal, 23677, 23833
-recovered pasa_asmbl_55767.p1, internal, 24206, 24303
-recovered pasa_asmbl_55767.p1, internal, 24520, 24632
-recovered pasa_asmbl_55767.p1, internal, 24810, 24857
-recovered pasa_asmbl_55767.p1, internal, 25234, 25300
Valid prediction for GlimmerHMM_glimmerT_21542-T1
Valid prediction for GlimmerHMM_glimmerT_21528-T1
Valid prediction for snap_scaffold_9-snap.197-T1
Couldn't classify 18296, 18470
Couldn't classify 21444, 21541
Sorry, prediction pasa_asmbl_54814.p1 fails validation.
(GCG)	 TG	18296-18470	GT	CGG
(GTA)	 AG	18658-18710	GT	AGG
(GAC)	 AG	19077-19189	GT	AGG
(GTT)	 AG	19560-19602	GT	AGG
(GTG)	 AG	19748-19815	GT	GGG
(GAT)	 AG	19937-20045	GT	TGG
(GGC)	 AG	20456-20558	GT	TGG
(GTG)	 AG	21444-21541	GG	CAG
-recovered pasa_asmbl_54814.p1, internal, 18658, 18710
-recovered pasa_asmbl_54814.p1, internal, 19077, 19189
-recovered pasa_asmbl_54814.p1, internal, 19560, 19602
-recovered pasa_asmbl_54814.p1, internal, 19748, 19815
-recovered pasa_asmbl_54814.p1, internal, 19937, 20045
-recovered pasa_asmbl_54814.p1, internal, 20456, 20558
Valid prediction for snap_scaffold_9-snap.192-T1
Valid prediction for snap_scaffold_9-snap.180-T1
Valid prediction for snap_scaffold_9-snap.181-T1
Valid prediction for GlimmerHMM_glimmerT_21537-T1
Valid prediction for GlimmerHMM_glimmerT_21544-T1
Valid prediction for Augustus_model.g14324.t1
Valid prediction for Augustus_model.g14331.t1
Valid prediction for GlimmerHMM_glimmerT_21526-T1
Valid prediction for GlimmerHMM_glimmerT_21536-T1
Valid prediction for snap_scaffold_9-snap.177-T1
Valid prediction for snap_scaffold_9-snap.185-T1
Couldn't classify 152633, 153388
Sorry, prediction pasa_asmbl_54807.p1 fails validation.
(CCT)	 CC	152633-153388	CT	AAC
Valid prediction for Augustus_model.g14320.t1
Valid prediction for GlimmerHMM_glimmerT_21540-T1
Valid prediction for Augustus_model.g14328.t1
Couldn't classify 109066, 110037
Sorry, prediction pasa_asmbl_54808.p1 fails validation.
(ATG)	 TG	106830-106841	GT	CGG
(GAC)	 AG	109066-110037	TG	CGT
-recovered pasa_asmbl_54808.p1, initial, 106830, 106841
Valid prediction for snap_scaffold_9-snap.163-T1
Valid prediction for GlimmerHMM_glimmerT_21522-T1
Valid prediction for snap_scaffold_9-snap.196-T1
Valid prediction for snap_scaffold_9-snap.172-T1
Valid prediction for snap_scaffold_9-snap.164-T1
Valid prediction for GlimmerHMM_glimmerT_21524-T1
Valid prediction for CodingQuarry_transcript_62101-T1
Valid prediction for snap_scaffold_9-snap.191-T1
Valid prediction for GlimmerHMM_glimmerT_21538-T1
Valid prediction for snap_scaffold_9-snap.188-T1
Valid prediction for GlimmerHMM_glimmerT_21523-T1
Valid prediction for Augustus_model.g14332.t1
Valid prediction for GlimmerHMM_glimmerT_21541-T1
Valid prediction for Augustus_model.g14333.t1
Valid prediction for Augustus_model.g14330.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29807, rend_intergenic: 5831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47261, rend_intergenic: 29817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53805, rend_intergenic: 51160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63989, rend_intergenic: 62780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66002, rend_intergenic: 64176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75511, rend_intergenic: 68056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92168, rend_intergenic: 81801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95563, rend_intergenic: 94408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114035, rend_intergenic: 95936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126020, rend_intergenic: 114810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138947, rend_intergenic: 131317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141858, rend_intergenic: 139009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155781, rend_intergenic: 141889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174389, rend_intergenic: 156060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202440, rend_intergenic: 174756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212961, rend_intergenic: 206704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215953, rend_intergenic: 212992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229430, rend_intergenic: 218897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230870, rend_intergenic: 229434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 235049
-exon list size: 343


building trellis

0.3    
0.6    
0.9    
1.2    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.2    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.8    
99.1    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 29807, rend_intergenic: 5831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47261, rend_intergenic: 29817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53805, rend_intergenic: 51160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63989, rend_intergenic: 62780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66002, rend_intergenic: 64176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75511, rend_intergenic: 68056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92168, rend_intergenic: 81801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95563, rend_intergenic: 94408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114035, rend_intergenic: 95936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126020, rend_intergenic: 114810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138947, rend_intergenic: 131317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141858, rend_intergenic: 139009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155781, rend_intergenic: 141889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174389, rend_intergenic: 156060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202440, rend_intergenic: 174756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212961, rend_intergenic: 206704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215953, rend_intergenic: 212992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229430, rend_intergenic: 218897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230870, rend_intergenic: 229434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support