-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_9862961-10036408

-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 HiQ_model.g38328.t1
Valid prediction for snap_scaffold_27-snap.2291-T1
Valid prediction for snap_scaffold_27-snap.2286-T1
Valid prediction for snap_scaffold_27-snap.2268-T1
Valid prediction for snap_scaffold_27-snap.2295-T1
Valid prediction for snap_scaffold_27-snap.2270-T1
Couldn't classify 140278, 140292
Sorry, prediction pasa_asmbl_36560.p1 fails validation.
(AAA)	 AG	140278-140292	GT	AGG
(GAT)	 AG	140627-140810	GT	AGG
(ATA)	 AG	140997-141082	GT	AGG
(AGC)	 AG	141416-141556	AA	GAA
-recovered pasa_asmbl_36560.p1, terminal, 141416, 141556
-recovered pasa_asmbl_36560.p1, internal, 140278, 140292
-recovered pasa_asmbl_36560.p1, internal, 140627, 140810
-recovered pasa_asmbl_36560.p1, internal, 140997, 141082
Valid prediction for CodingQuarry_transcript_41975-T1
Couldn't classify 76629, 76645
Sorry, prediction pasa_asmbl_36545.p1 fails validation.
(GCC)	 GT	76629-76645	GT	CGG
(GAG)	 AG	77026-77074	GT	ATG
(GAA)	 AG	77562-77598	GT	AGG
(ACA)	 AG	77710-77752	GT	AGG
(GAT)	 AG	78573-78645	GC	AGG
(GAC)	 AG	78758-78815	GT	AGG
(CAT)	 AG	78978-79015	CA	AGC
-recovered pasa_asmbl_36545.p1, terminal, 78978, 79015
-recovered pasa_asmbl_36545.p1, internal, 77026, 77074
-recovered pasa_asmbl_36545.p1, internal, 77562, 77598
-recovered pasa_asmbl_36545.p1, internal, 77710, 77752
-recovered pasa_asmbl_36545.p1, internal, 78573, 78645
-recovered pasa_asmbl_36545.p1, internal, 78758, 78815
Valid prediction for pasa_asmbl_36552.p1
Valid prediction for snap_scaffold_27-snap.2290-T1
Valid prediction for snap_scaffold_27-snap.2281-T1
Valid prediction for CodingQuarry_transcript_41976-T1
Valid prediction for pasa_asmbl_36541.p1
Valid prediction for HiQ_model.g38331.t1
Valid prediction for snap_scaffold_27-snap.2293-T1
Valid prediction for GlimmerHMM_glimmerT_57914-T1
Valid prediction for Augustus_model.g38329.t1
Valid prediction for snap_scaffold_27-snap.2296-T1
Valid prediction for Augustus_model.g38325.t1
Couldn't classify 128789, 129085
Couldn't classify 140146, 140277
Sorry, prediction pasa_asmbl_36558.p1 fails validation.
(CTA)	 CT	128789-129085	GT	TGG
(GAG)	 AG	129418-129633	GT	AGG
(GCA)	 AG	131757-131891	GT	AGG
(ATG)	 AG	131979-132110	GT	AGG
(GGT)	 AG	132387-132512	GT	AGG
(GAA)	 AG	132592-132702	GT	GAG
(GAG)	 AG	132793-132882	GT	AGG
(CAC)	 AG	135117-135251	GT	AGG
(GGC)	 AG	138033-138126	GT	GAG
(CTG)	 AG	138454-138652	GT	AGG
(TGC)	 AG	139001-139091	GT	GGG
(GAG)	 AG	140146-140277	AA	AGA
-recovered pasa_asmbl_36558.p1, initial, 131979, 132110
-recovered pasa_asmbl_36558.p1, internal, 129418, 129633
-recovered pasa_asmbl_36558.p1, internal, 131757, 131891
-recovered pasa_asmbl_36558.p1, internal, 131979, 132110
-recovered pasa_asmbl_36558.p1, internal, 132387, 132512
-recovered pasa_asmbl_36558.p1, internal, 132592, 132702
-recovered pasa_asmbl_36558.p1, internal, 132793, 132882
-recovered pasa_asmbl_36558.p1, internal, 135117, 135251
-recovered pasa_asmbl_36558.p1, internal, 138033, 138126
-recovered pasa_asmbl_36558.p1, internal, 138454, 138652
-recovered pasa_asmbl_36558.p1, internal, 139001, 139091
Valid prediction for GlimmerHMM_glimmerT_57921-T1
Valid prediction for Augustus_model.g38333.t1
Valid prediction for snap_scaffold_27-snap.2264-T1
Valid prediction for snap_scaffold_27-snap.2265-T1
Valid prediction for HiQ_model.g38330.t1
Valid prediction for snap_scaffold_27-snap.2278-T1
Valid prediction for CodingQuarry_transcript_41974-T1
Valid prediction for CodingQuarry_transcript_41979-T1
Couldn't classify 86308, 86376
Sorry, prediction pasa_asmbl_36548.p1 fails validation.
(ATG)	 CC	83134-83179	GT	AGG
(GCG)	 AG	83895-84023	GT	AGG
(AGT)	 AG	84297-84408	GT	AGG
(AGA)	 AG	85513-85663	GT	TGG
(ACT)	 AG	85791-85922	GT	AGG
(GAT)	 AG	86138-86203	GT	CTG
(ACC)	 AG	86308-86376	GT	AGG
-recovered pasa_asmbl_36548.p1, initial, 83134, 83179
-recovered pasa_asmbl_36548.p1, internal, 83895, 84023
-recovered pasa_asmbl_36548.p1, internal, 84297, 84408
-recovered pasa_asmbl_36548.p1, internal, 85513, 85663
-recovered pasa_asmbl_36548.p1, internal, 85791, 85922
-recovered pasa_asmbl_36548.p1, internal, 86138, 86203
-recovered pasa_asmbl_36548.p1, internal, 86308, 86376
Valid prediction for GlimmerHMM_glimmerT_57919-T1
Valid prediction for snap_scaffold_27-snap.2284-T1
Valid prediction for Augustus_model.g38323.t1
Valid prediction for GlimmerHMM_glimmerT_57916-T1
Valid prediction for snap_scaffold_27-snap.2267-T1
Couldn't classify 155553, 155673
Sorry, prediction GlimmerHMM_glimmerT_57927-T1 fails validation.
(ATG)	 AG	152404-152434	GT	CGG
(TTA)	 AG	154274-154368	GT	CGG
(TTT)	 AG	154570-154690	GT	TGG
(CTG)	 AG	155274-155343	GT	ATG
(GGT)	 AG	155553-155673	GT	CAG
-recovered GlimmerHMM_glimmerT_57927-T1, initial, 152404, 152434
-recovered GlimmerHMM_glimmerT_57927-T1, internal, 152404, 152434
-recovered GlimmerHMM_glimmerT_57927-T1, internal, 154274, 154368
-recovered GlimmerHMM_glimmerT_57927-T1, internal, 154570, 154690
-recovered GlimmerHMM_glimmerT_57927-T1, internal, 155274, 155343
-recovered GlimmerHMM_glimmerT_57927-T1, internal, 155553, 155673
Valid prediction for pasa_asmbl_36544.p1
Valid prediction for snap_scaffold_27-snap.2288-T1
Valid prediction for GlimmerHMM_glimmerT_57918-T1
Valid prediction for CodingQuarry_transcript_41980-T1
Valid prediction for snap_scaffold_27-snap.2292-T1
Valid prediction for GlimmerHMM_glimmerT_57923-T1
Valid prediction for CodingQuarry_transcript_41978-T1
Valid prediction for CodingQuarry_transcript_41981-T1
Couldn't classify 5768, 5794
Couldn't classify 6555, 6704
Sorry, prediction pasa_asmbl_36533.p1 fails validation.
(TCA)	 CC	5768-5794	GT	AGG
(CCT)	 AG	6119-6469	GT	AGG
(GTG)	 AG	6555-6704	AT	CCA
-recovered pasa_asmbl_36533.p1, internal, 6119, 6469
Valid prediction for snap_scaffold_27-snap.2279-T1
Valid prediction for snap_scaffold_27-snap.2273-T1
Valid prediction for CodingQuarry_transcript_41977-T1
Valid prediction for GlimmerHMM_glimmerT_57920-T1
Valid prediction for snap_scaffold_27-snap.2277-T1
Valid prediction for GlimmerHMM_glimmerT_57925-T1
Valid prediction for CodingQuarry_transcript_41982-T1
Valid prediction for pasa_asmbl_36551.p1
Valid prediction for snap_scaffold_27-snap.2275-T1
Valid prediction for snap_scaffold_27-snap.2274-T1
Valid prediction for Augustus_model.g38327.t1
Valid prediction for snap_scaffold_27-snap.2260-T1
Valid prediction for GlimmerHMM_glimmerT_57911-T1
Valid prediction for Augustus_model.g38321.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_27-snap.2272-T1
Valid prediction for snap_scaffold_27-snap.2280-T1
Valid prediction for Augustus_model.g38324.t1
Valid prediction for snap_scaffold_27-snap.2297-T1
Valid prediction for snap_scaffold_27-snap.2283-T1
Valid prediction for snap_scaffold_27-snap.2262-T1
Valid prediction for snap_scaffold_27-snap.2263-T1
Valid prediction for Augustus_model.g38334.t1
Valid prediction for snap_scaffold_27-snap.2271-T1
Valid prediction for GlimmerHMM_glimmerT_57926-T1
Valid prediction for snap_scaffold_27-snap.2285-T1
Valid prediction for Augustus_model.g38322.t1
Valid prediction for GlimmerHMM_glimmerT_57922-T1
Valid prediction for GlimmerHMM_glimmerT_57924-T1
Valid prediction for snap_scaffold_27-snap.2276-T1
Valid prediction for GlimmerHMM_glimmerT_57917-T1
Valid prediction for snap_scaffold_27-snap.2294-T1
Valid prediction for GlimmerHMM_glimmerT_57912-T1
Valid prediction for snap_scaffold_27-snap.2269-T1
Valid prediction for snap_scaffold_27-snap.2282-T1
Valid prediction for snap_scaffold_27-snap.2266-T1
Valid prediction for snap_scaffold_27-snap.2261-T1
Valid prediction for snap_scaffold_27-snap.2289-T1
Valid prediction for GlimmerHMM_glimmerT_57913-T1
Couldn't classify 151002, 152804
Sorry, prediction pasa_asmbl_37214.p1 fails validation.
(CTG)	 GC	151002-152804	TG	GAT
Valid prediction for Augustus_model.g38332.t1
Valid prediction for snap_scaffold_27-snap.2287-T1
Valid prediction for GlimmerHMM_glimmerT_57915-T1
Valid prediction for Augustus_model.g38326.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6746, rend_intergenic: 4263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34290, rend_intergenic: 30277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55331, rend_intergenic: 44084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72201, rend_intergenic: 71921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86424, rend_intergenic: 84283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112688, rend_intergenic: 111878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121547, rend_intergenic: 112916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129267, rend_intergenic: 127080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134234, rend_intergenic: 131943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136486, rend_intergenic: 135052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141516, rend_intergenic: 138009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150005, rend_intergenic: 147985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173448
-exon list size: 315


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
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    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
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    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 6746, rend_intergenic: 4263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34290, rend_intergenic: 30277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55331, rend_intergenic: 44084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72201, rend_intergenic: 71921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86424, rend_intergenic: 84283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112688, rend_intergenic: 111878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121547, rend_intergenic: 112916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129267, rend_intergenic: 127080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134234, rend_intergenic: 131943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136486, rend_intergenic: 135052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141516, rend_intergenic: 138009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150005, rend_intergenic: 147985  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

-building DP trellis

-building trellis in range 155674 - 173448
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-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 156700 - 173448
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-found 1 predictions from path traversal

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