-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_17786512-18014035

-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_8-snap.3287-T1
Valid prediction for GlimmerHMM_glimmerT_21285-T1
Valid prediction for GlimmerHMM_glimmerT_21315-T1
Valid prediction for CodingQuarry_transcript_59947-T1
Valid prediction for Augustus_model.g14199.t1
Valid prediction for Augustus_model.g14182.t1
Valid prediction for pasa_asmbl_53514.p1
Valid prediction for GlimmerHMM_glimmerT_21310-T1
Valid prediction for snap_scaffold_8-snap.3279-T1
Valid prediction for HiQ_model.g14180.t1
Valid prediction for Augustus_model.g14183.t1
Valid prediction for Augustus_model.g14190.t1
Valid prediction for GlimmerHMM_glimmerT_21297-T1
Valid prediction for snap_scaffold_8-snap.3308-T1
Valid prediction for CodingQuarry_transcript_59946-T1
Valid prediction for GlimmerHMM_glimmerT_21304-T1
Valid prediction for GlimmerHMM_glimmerT_21293-T1
Valid prediction for Augustus_model.g14197.t1
Valid prediction for snap_scaffold_8-snap.3301-T1
Valid prediction for snap_scaffold_8-snap.3269-T1
Valid prediction for GlimmerHMM_glimmerT_21296-T1
Valid prediction for GlimmerHMM_glimmerT_21306-T1
Valid prediction for snap_scaffold_8-snap.3306-T1
Valid prediction for snap_scaffold_8-snap.3276-T1
Valid prediction for snap_scaffold_8-snap.3296-T1
Valid prediction for pasa_asmbl_53507.p2
Valid prediction for snap_scaffold_8-snap.3304-T1
Valid prediction for CodingQuarry_transcript_59950-T1
Valid prediction for HiQ_model.g14192.t1
Valid prediction for snap_scaffold_8-snap.3278-T1
Valid prediction for Augustus_model.g14198.t1
Valid prediction for snap_scaffold_8-snap.3266-T1
Valid prediction for HiQ_model.g14187.t1
Valid prediction for GlimmerHMM_glimmerT_21303-T1
Valid prediction for CodingQuarry_transcript_59945-T1
Valid prediction for snap_scaffold_8-snap.3282-T1
Valid prediction for HiQ_model.g14185.t1
Valid prediction for pasa_asmbl_53516.p1
Valid prediction for CodingQuarry_transcript_59944-T1
Valid prediction for Augustus_model.g14200.t1
Valid prediction for GlimmerHMM_glimmerT_21289-T1
Valid prediction for GlimmerHMM_glimmerT_21307-T1
Valid prediction for snap_scaffold_8-snap.3295-T1
Valid prediction for snap_scaffold_8-snap.3294-T1
Valid prediction for GlimmerHMM_glimmerT_21316-T1
Valid prediction for snap_scaffold_8-snap.3280-T1
Valid prediction for pasa_asmbl_53506.p1
Valid prediction for snap_scaffold_8-snap.3284-T1
Valid prediction for snap_scaffold_8-snap.3311-T1
Valid prediction for CodingQuarry_transcript_59948-T1
Valid prediction for snap_scaffold_8-snap.3270-T1
Valid prediction for GlimmerHMM_glimmerT_21299-T1
Valid prediction for pasa_asmbl_53519.p1
Valid prediction for snap_scaffold_8-snap.3273-T1
Valid prediction for GlimmerHMM_glimmerT_21305-T1
Valid prediction for GlimmerHMM_glimmerT_21290-T1
Valid prediction for GlimmerHMM_glimmerT_21317-T1
Valid prediction for pasa_asmbl_53501.p1
Valid prediction for CodingQuarry_transcript_59949-T1
Valid prediction for snap_scaffold_8-snap.3288-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_8-snap.3307-T1
Valid prediction for GlimmerHMM_glimmerT_21295-T1
Valid prediction for snap_scaffold_8-snap.3271-T1
Valid prediction for snap_scaffold_8-snap.3291-T1
Valid prediction for GlimmerHMM_glimmerT_21302-T1
Valid prediction for snap_scaffold_8-snap.3305-T1
Valid prediction for snap_scaffold_8-snap.3298-T1
Valid prediction for GlimmerHMM_glimmerT_21312-T1
Valid prediction for GlimmerHMM_glimmerT_21298-T1
Valid prediction for snap_scaffold_8-snap.3277-T1
Valid prediction for snap_scaffold_8-snap.3268-T1
Couldn't classify 39092, 39227
Sorry, prediction pasa_asmbl_52498.p2 fails validation.
(GGA)	 CA	39092-39227	GT	AGG
(ATG)	 AG	40007-40118	GT	AGG
(AGA)	 AG	41796-41913	GA	AGG
add_exon() Sorry, pasa_asmbl_52498.p2 40007-40118-initial-1 is invalid.
-recovered pasa_asmbl_52498.p2, initial, 40007, 40118
-recovered pasa_asmbl_52498.p2, terminal, 41796, 41913
-recovered pasa_asmbl_52498.p2, internal, 40007, 40118
Valid prediction for snap_scaffold_8-snap.3302-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_8-snap.3289-T1
Valid prediction for GlimmerHMM_glimmerT_21291-T1
Valid prediction for snap_scaffold_8-snap.3290-T1
Valid prediction for Augustus_model.g14191.t1
Valid prediction for snap_scaffold_8-snap.3312-T1
Couldn't classify 131558, 131690
Couldn't classify 133296, 133426
Sorry, prediction pasa_asmbl_52493.p1 fails validation.
(ACC)	 CC	131558-131690	GT	AGG
(ACA)	 AG	132975-133175	GT	AGG
(GCT)	 AG	133296-133426	GG	ACG
-recovered pasa_asmbl_52493.p1, internal, 132975, 133175
Valid prediction for GlimmerHMM_glimmerT_21288-T1
Valid prediction for snap_scaffold_8-snap.3310-T1
Valid prediction for Augustus_model.g14188.t1
Valid prediction for GlimmerHMM_glimmerT_21309-T1
Valid prediction for HiQ_model.g14193.t1
Valid prediction for snap_scaffold_8-snap.3292-T1
Valid prediction for pasa_asmbl_52492.p1
Valid prediction for Augustus_model.g14186.t1
Valid prediction for snap_scaffold_8-snap.3285-T1
Valid prediction for Augustus_model.g14196.t1
Valid prediction for GlimmerHMM_glimmerT_21292-T1
Valid prediction for snap_scaffold_8-snap.3299-T1
Valid prediction for Augustus_model.g14189.t1
Valid prediction for GlimmerHMM_glimmerT_21287-T1
Valid prediction for snap_scaffold_8-snap.3293-T1
Valid prediction for snap_scaffold_8-snap.3274-T1
Valid prediction for GlimmerHMM_glimmerT_21308-T1
Valid prediction for GlimmerHMM_glimmerT_21314-T1
Valid prediction for Augustus_model.g14184.t1
Couldn't classify 30641, 30795
Couldn't classify 33231, 33356
Sorry, prediction pasa_asmbl_52500.p1 fails validation.
(GTA)	 AG	30641-30795	GT	AGG
(GCT)	 AG	31201-31346	GT	AGG
(GTG)	 AG	33019-33116	GT	GGG
(ATA)	 AG	33231-33356	GG	CAG
-recovered pasa_asmbl_52500.p1, internal, 30641, 30795
-recovered pasa_asmbl_52500.p1, internal, 31201, 31346
-recovered pasa_asmbl_52500.p1, internal, 33019, 33116
Valid prediction for Augustus_model.g14181.t1
Valid prediction for GlimmerHMM_glimmerT_21286-T1
Valid prediction for snap_scaffold_8-snap.3297-T1
Couldn't classify 58898, 59062
Sorry, prediction pasa_asmbl_52494.p1 fails validation.
(CAG)	 CT	58898-59062	GT	AGG
(ATC)	 AG	59873-60028	GT	CAG
(CTG)	 AG	60494-60638	GT	TGG
(GTA)	 AG	60752-60933	GT	TGG
(GTA)	 AG	61100-61228	GT	TGG
(TAC)	 AG	61305-61490	GT	AGG
(CCT)	 AG	61802-62046	GT	AGG
(GTA)	 AG	62183-62325	GT	AGG
(ATG)	 AG	62433-62663	GT	CGG
(ACA)	 AG	62822-63064	GT	TTG
(TGC)	 AG	63151-63299	GT	AGG
(AAT)	 AG	63387-63575	GT	ATG
(GGC)	 AG	63689-63889	GG	AGG
add_exon() Sorry, pasa_asmbl_52494.p1 62433-62663-initial-1 is invalid.
-recovered pasa_asmbl_52494.p1, initial, 62433, 62663
-recovered pasa_asmbl_52494.p1, terminal, 63689, 63889
-recovered pasa_asmbl_52494.p1, internal, 59873, 60028
-recovered pasa_asmbl_52494.p1, internal, 60494, 60638
-recovered pasa_asmbl_52494.p1, internal, 60752, 60933
-recovered pasa_asmbl_52494.p1, internal, 61100, 61228
-recovered pasa_asmbl_52494.p1, internal, 61305, 61490
-recovered pasa_asmbl_52494.p1, internal, 61802, 62046
-recovered pasa_asmbl_52494.p1, internal, 62183, 62325
-recovered pasa_asmbl_52494.p1, internal, 62433, 62663
-recovered pasa_asmbl_52494.p1, internal, 62822, 63064
-recovered pasa_asmbl_52494.p1, internal, 63151, 63299
-recovered pasa_asmbl_52494.p1, internal, 63387, 63575
Valid prediction for Augustus_model.g14194.t1
Valid prediction for Augustus_model.g14195.t1
Valid prediction for snap_scaffold_8-snap.3286-T1
Valid prediction for GlimmerHMM_glimmerT_21300-T1
Valid prediction for snap_scaffold_8-snap.3272-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_21294-T1
Valid prediction for snap_scaffold_8-snap.3283-T1
Valid prediction for snap_scaffold_8-snap.3281-T1
Valid prediction for GlimmerHMM_glimmerT_21311-T1
Valid prediction for GlimmerHMM_glimmerT_21313-T1
Valid prediction for snap_scaffold_8-snap.3275-T1
Valid prediction for GlimmerHMM_glimmerT_21301-T1
Valid prediction for snap_scaffold_8-snap.3300-T1
Valid prediction for snap_scaffold_8-snap.3267-T1
Couldn't classify 26145, 26852
Couldn't classify 27436, 27588
Sorry, prediction pasa_asmbl_52501.p1 fails validation.
(TCA)	 CC	26145-26852	GT	TGG
(GTA)	 AG	27436-27588	AA	AGA
Valid prediction for snap_scaffold_8-snap.3309-T1
Valid prediction for snap_scaffold_8-snap.3303-T1
Couldn't classify 153299, 153670
Sorry, prediction pasa_asmbl_52491.p1 fails validation.
(GAG)	 TG	153299-153670	CT	AGC

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 88969, rend_intergenic: 88056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92461, rend_intergenic: 89170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103167, rend_intergenic: 97956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144788, rend_intergenic: 137002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187531, rend_intergenic: 183994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189474, rend_intergenic: 187646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196414, rend_intergenic: 190371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201167, rend_intergenic: 197260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225789, rend_intergenic: 221259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227524
-exon list size: 414


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
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2.9    
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3.4    
3.6    
3.8    
4.1    
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8.9    
9.1    
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9.6    
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10.1    
10.3    
10.6    
10.8    
11.1    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
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13.2    
13.5    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.1    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.8    
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23.3    
23.6    
23.8    
24.0    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
26.0    
26.2    
26.4    
26.7    
26.9    
27.2    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
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    
44.2    
44.5    
44.7    
45.0    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.6    
46.9    
47.1    
47.4    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.6    
52.9    
53.1    
53.4    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.0    
55.3    
55.5    
55.8    
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    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.5    
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62.0    
62.3    
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63.0    
63.2    
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63.9    
64.2    
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65.1    
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66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
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68.0    
68.3    
68.5    
68.8    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
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73.1    
73.3    
73.6    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.4    
76.7    
76.9    
77.2    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.9    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.6    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 88969, rend_intergenic: 88056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92461, rend_intergenic: 89170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103167, rend_intergenic: 97956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144788, rend_intergenic: 137002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187531, rend_intergenic: 183994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189474, rend_intergenic: 187646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196414, rend_intergenic: 190371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201167, rend_intergenic: 197260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225789, rend_intergenic: 221259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support