-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_9044971-9259316

-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 CodingQuarry_transcript_55157-T1
Valid prediction for snap_scaffold_6-snap.2037-T1
Valid prediction for pasa_asmbl_47206.p1
Couldn't classify 13556, 13618
Couldn't classify 14685, 14726
Sorry, prediction pasa_asmbl_47195.p1 fails validation.
(GAT)	 TG	13556-13618	GT	AGG
(ACG)	 AG	13768-13902	GT	AGG
(TTT)	 AG	14093-14245	GT	ACG
(AAC)	 AG	14388-14546	GC	AGG
(GTC)	 AG	14685-14726	AC	ACA
-recovered pasa_asmbl_47195.p1, internal, 13768, 13902
-recovered pasa_asmbl_47195.p1, internal, 14093, 14245
-recovered pasa_asmbl_47195.p1, internal, 14388, 14546
Valid prediction for HiQ_model.g10121.t1
Valid prediction for GlimmerHMM_glimmerT_15247-T1
Valid prediction for GlimmerHMM_glimmerT_15246-T1
Valid prediction for snap_scaffold_6-snap.2009-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2019-T1
Valid prediction for Augustus_model.g10124.t1
Valid prediction for snap_scaffold_6-snap.2010-T1
Valid prediction for HiQ_model.g10108.t1
Valid prediction for GlimmerHMM_glimmerT_15240-T1
Valid prediction for CodingQuarry_transcript_55160-T1
Couldn't classify 48381, 48597
Sorry, prediction pasa_asmbl_47202.p1 fails validation.
(GTT)	 GT	48381-48597	GT	GAG
(CAA)	 AG	48826-48895	GT	AGG
(GTT)	 AG	51043-51175	GT	AGG
(GTG)	 AG	52237-52311	GT	GGG
(GCC)	 AG	53273-53426	GT	AAG
(CAG)	 AG	53602-53683	GT	AGG
(CCT)	 AG	53799-53936	GT	AGG
(GCC)	 AG	54370-54526	GT	AGG
(ATA)	 AG	54932-55038	GT	CTG
(GTA)	 AG	55410-55539	GT	AGG
(GCC)	 AG	56065-56254	GT	AAG
(CCA)	 AG	56367-56559	GT	AGG
(GCT)	 AG	56957-57122	GA	AGG
-recovered pasa_asmbl_47202.p1, terminal, 56957, 57122
-recovered pasa_asmbl_47202.p1, internal, 48826, 48895
-recovered pasa_asmbl_47202.p1, internal, 51043, 51175
-recovered pasa_asmbl_47202.p1, internal, 52237, 52311
-recovered pasa_asmbl_47202.p1, internal, 53273, 53426
-recovered pasa_asmbl_47202.p1, internal, 53602, 53683
-recovered pasa_asmbl_47202.p1, internal, 53799, 53936
-recovered pasa_asmbl_47202.p1, internal, 54370, 54526
-recovered pasa_asmbl_47202.p1, internal, 54932, 55038
-recovered pasa_asmbl_47202.p1, internal, 55410, 55539
-recovered pasa_asmbl_47202.p1, internal, 56065, 56254
-recovered pasa_asmbl_47202.p1, internal, 56367, 56559
Valid prediction for pasa_asmbl_47224.p1
Couldn't classify 11364, 11509
Sorry, prediction pasa_asmbl_47949.p2 fails validation.
(ATG)	 AC	10827-10948	GT	GGG
(GGT)	 AG	11045-11214	GT	AGG
(ACA)	 AG	11364-11509	AC	CCA
-recovered pasa_asmbl_47949.p2, initial, 10827, 10948
-recovered pasa_asmbl_47949.p2, internal, 11045, 11214
Valid prediction for snap_scaffold_6-snap.2025-T1
Valid prediction for pasa_asmbl_47197.p1
Valid prediction for GlimmerHMM_glimmerT_15227-T1
Valid prediction for snap_scaffold_6-snap.2012-T1
Valid prediction for snap_scaffold_6-snap.2016-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_15248-T1
Valid prediction for snap_scaffold_6-snap.2014-T1
Valid prediction for snap_scaffold_6-snap.2036-T1
Valid prediction for GlimmerHMM_glimmerT_15252-T1
Valid prediction for GlimmerHMM_glimmerT_15228-T1
Valid prediction for Augustus_model.g10122.t1
Valid prediction for CodingQuarry_transcript_55156-T1
Valid prediction for CodingQuarry_transcript_55164-T1
Valid prediction for snap_scaffold_6-snap.2031-T1
Valid prediction for HiQ_model.g10112.t1
Valid prediction for snap_scaffold_6-snap.2024-T1
Valid prediction for HiQ_model.g10119.t1
Valid prediction for snap_scaffold_6-snap.2017-T1
Valid prediction for snap_scaffold_6-snap.2021-T1
Valid prediction for Augustus_model.g10106.t1
Valid prediction for GlimmerHMM_glimmerT_15241-T1
Valid prediction for snap_scaffold_6-snap.2030-T1
Valid prediction for Augustus_model.g10125.t1
Valid prediction for pasa_asmbl_47201.p1
Valid prediction for GlimmerHMM_glimmerT_15229-T1
Valid prediction for pasa_asmbl_47215.p1
Valid prediction for GlimmerHMM_glimmerT_15230-T1
Valid prediction for snap_scaffold_6-snap.2013-T1
Valid prediction for HiQ_model.g10118.t1
Valid prediction for HiQ_model.g10114.t1
Valid prediction for snap_scaffold_6-snap.2035-T1
Valid prediction for snap_scaffold_6-snap.2039-T1
Valid prediction for snap_scaffold_6-snap.2038-T1
Valid prediction for GlimmerHMM_glimmerT_15235-T1
Valid prediction for pasa_asmbl_47225.p1
Valid prediction for snap_scaffold_6-snap.2026-T1
Valid prediction for GlimmerHMM_glimmerT_15237-T1
Valid prediction for CodingQuarry_transcript_55165-T1
Valid prediction for GlimmerHMM_glimmerT_15232-T1
Valid prediction for snap_scaffold_6-snap.2032-T1
Valid prediction for HiQ_model.g10110.t1
Valid prediction for GlimmerHMM_glimmerT_15233-T1
Valid prediction for Augustus_model.g10107.t1
Valid prediction for pasa_asmbl_47200.p1
Valid prediction for GlimmerHMM_glimmerT_15231-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 GlimmerHMM_glimmerT_15226-T1
Valid prediction for GlimmerHMM_glimmerT_15245-T1
Valid prediction for snap_scaffold_6-snap.2033-T1
Valid prediction for CodingQuarry_transcript_55158-T1
Valid prediction for snap_scaffold_6-snap.2015-T1
Valid prediction for GlimmerHMM_glimmerT_15254-T1
Valid prediction for GlimmerHMM_glimmerT_15238-T1
Valid prediction for GlimmerHMM_glimmerT_15243-T1
Valid prediction for pasa_asmbl_48607.p1
Valid prediction for snap_scaffold_6-snap.2028-T1
Valid prediction for CodingQuarry_transcript_55162-T1
Couldn't classify 173632, 173765
Sorry, prediction pasa_asmbl_48605.p1 fails validation.
(TAT)	 AT	173632-173765	GT	AGG
(ATG)	 AG	173872-174094	GT	GGG
(CTG)	 AG	174246-174374	GC	AAG
add_exon() Sorry, pasa_asmbl_48605.p1 173872-174094-initial-1 is invalid.
-recovered pasa_asmbl_48605.p1, initial, 173872, 174094
-recovered pasa_asmbl_48605.p1, terminal, 174246, 174374
-recovered pasa_asmbl_48605.p1, internal, 173872, 174094
-recovered pasa_asmbl_48605.p1, internal, 174246, 174374
Couldn't classify 81282, 81441
Couldn't classify 81490, 82193
Sorry, prediction CodingQuarry_transcript_55166-T1 fails validation.
(ATG)	 CC	80376-80491	GT	AAG
(GCC)	 AG	80946-81111	GT	AGG
(GTT)	 AG	81282-81441	AC	CAA
(GCC)	 CA	81490-82193	GT	AGG
(ACA)	 AG	82852-83037	GT	AGG
(ACG)	 AG	83131-83262	GT	AGG
(TTT)	 AG	83345-83405	GT	AGG
(AGA)	 AG	83494-83993	GA	GAG
-recovered CodingQuarry_transcript_55166-T1, initial, 80376, 80491
-recovered CodingQuarry_transcript_55166-T1, terminal, 83494, 83993
-recovered CodingQuarry_transcript_55166-T1, internal, 80946, 81111
-recovered CodingQuarry_transcript_55166-T1, internal, 82852, 83037
-recovered CodingQuarry_transcript_55166-T1, internal, 83131, 83262
-recovered CodingQuarry_transcript_55166-T1, internal, 83345, 83405
Valid prediction for Augustus_model.g10116.t1
Valid prediction for GlimmerHMM_glimmerT_15236-T1
Valid prediction for snap_scaffold_6-snap.2011-T1
Valid prediction for snap_scaffold_6-snap.2027-T1
Valid prediction for HiQ_model.g10120.t1
Valid prediction for CodingQuarry_transcript_55159-T1
Valid prediction for snap_scaffold_6-snap.2034-T1
Valid prediction for snap_scaffold_6-snap.2040-T1
Valid prediction for snap_scaffold_6-snap.2022-T1
Valid prediction for GlimmerHMM_glimmerT_15249-T1
Valid prediction for Augustus_model.g10123.t1
Valid prediction for snap_scaffold_6-snap.2018-T1
Valid prediction for CodingQuarry_transcript_55161-T1
Valid prediction for Augustus_model.g10126.t1
Valid prediction for snap_scaffold_6-snap.2020-T1
Valid prediction for snap_scaffold_6-snap.2023-T1
Valid prediction for GlimmerHMM_glimmerT_15253-T1
Valid prediction for Augustus_model.g10113.t1
Valid prediction for GlimmerHMM_glimmerT_15250-T1
Valid prediction for CodingQuarry_transcript_55163-T1
Couldn't classify 77773, 77778
Sorry, prediction pasa_asmbl_48614.p1 fails validation.
(GCA)	 GG	77773-77778	GT	GGG
(ACT)	 AG	77907-77982	GT	AGG
(AGA)	 AG	78209-78370	GT	CGG
(ATG)	 AG	78597-78775	GT	AGG
(TAC)	 AG	79149-79289	GT	AGG
(CAA)	 AG	80244-80491	GT	AAG
(GCC)	 AG	80946-81111	GT	AGG
(GTT)	 AG	81282-82193	GT	AGG
(ACA)	 AG	82852-83037	GT	AGG
(ACG)	 AG	83131-83262	GT	AGG
(TTT)	 AG	83345-83405	GT	AGG
(AGA)	 AG	83494-83993	GA	GAG
-recovered pasa_asmbl_48614.p1, initial, 78597, 78775
-recovered pasa_asmbl_48614.p1, terminal, 83494, 83993
-recovered pasa_asmbl_48614.p1, internal, 77907, 77982
-recovered pasa_asmbl_48614.p1, internal, 78209, 78370
-recovered pasa_asmbl_48614.p1, internal, 78597, 78775
-recovered pasa_asmbl_48614.p1, internal, 79149, 79289
-recovered pasa_asmbl_48614.p1, internal, 80244, 80491
-recovered pasa_asmbl_48614.p1, internal, 80946, 81111
-recovered pasa_asmbl_48614.p1, internal, 81282, 82193
-recovered pasa_asmbl_48614.p1, internal, 82852, 83037
-recovered pasa_asmbl_48614.p1, internal, 83131, 83262
-recovered pasa_asmbl_48614.p1, internal, 83345, 83405
Valid prediction for pasa_asmbl_48608.p1
Valid prediction for HiQ_model.g10111.t1
Valid prediction for GlimmerHMM_glimmerT_15244-T1
Valid prediction for GlimmerHMM_glimmerT_15234-T1
Valid prediction for Augustus_model.g10105.t1
Valid prediction for HiQ_model.g10117.t1
Valid prediction for snap_scaffold_6-snap.2029-T1
Valid prediction for HiQ_model.g10109.t1
Valid prediction for GlimmerHMM_glimmerT_15239-T1
Valid prediction for GlimmerHMM_glimmerT_15251-T1
Valid prediction for Augustus_model.g10115.t1
Valid prediction for GlimmerHMM_glimmerT_15242-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12477, rend_intergenic: 4795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32215, rend_intergenic: 27129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214346
-exon list size: 326


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 12477, rend_intergenic: 4795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32215, rend_intergenic: 27129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 194651 - 214346
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 200975 - 214346
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 200975 - 211091
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support