-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_13363620-13552337

-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 Augustus_model.g4960.t1
Valid prediction for snap_scaffold_3-snap.2576-T1
Valid prediction for GlimmerHMM_glimmerT_7591-T1
Valid prediction for snap_scaffold_3-snap.2593-T1
Valid prediction for GlimmerHMM_glimmerT_7583-T1
Valid prediction for Augustus_model.g4953.t1
Valid prediction for Augustus_model.g4961.t1
Valid prediction for GlimmerHMM_glimmerT_7597-T1
Valid prediction for snap_scaffold_3-snap.2579-T1
Valid prediction for Augustus_model.g4959.t1
Valid prediction for snap_scaffold_3-snap.2596-T1
Valid prediction for Augustus_model.g4968.t1
Valid prediction for GlimmerHMM_glimmerT_7585-T1
Couldn't classify 94735, 94830
Couldn't classify 101184, 101297
Sorry, prediction pasa_asmbl_40439.p1 fails validation.
(GCT)	 AT	94735-94830	GT	AGG
(GTC)	 AG	95130-95243	GT	AGG
(GTG)	 AG	95324-95418	GT	ATG
(AGC)	 AG	95707-95818	GT	AGG
(TGG)	 AG	95935-96033	GT	AGG
(GAT)	 AG	96123-96179	GT	CTG
(GAA)	 AG	96291-96391	GT	AGG
(ACG)	 AG	96681-96717	GT	AGG
(GCA)	 AG	98045-98143	GT	AGG
(CTG)	 AG	98246-98296	GT	CGG
(GGG)	 AG	98379-98465	GT	GGG
(CAA)	 AG	98994-99110	GT	AAG
(TTG)	 AG	99233-99295	GT	AGG
(GCT)	 AG	99421-99494	GT	AGG
(ACT)	 AG	99593-99674	GT	GAG
(GAG)	 AG	99813-99887	GT	AGG
(GAG)	 AG	100002-100073	GT	TGG
(GCA)	 AG	100168-100276	GT	AGG
(TTT)	 AG	100402-100484	GT	AGG
(GTG)	 AG	100568-100605	GT	CAG
(GGC)	 AG	100720-100804	GT	AGG
(ATG)	 AG	101184-101297	GT	AGG
-recovered pasa_asmbl_40439.p1, initial, 101184, 101297
add_exon() Sorry, pasa_asmbl_40439.p1 99421-99494-terminal-2 is invalid.
-recovered pasa_asmbl_40439.p1, terminal, 99421, 99494
-recovered pasa_asmbl_40439.p1, internal, 95130, 95243
-recovered pasa_asmbl_40439.p1, internal, 95324, 95418
-recovered pasa_asmbl_40439.p1, internal, 95707, 95818
-recovered pasa_asmbl_40439.p1, internal, 95935, 96033
-recovered pasa_asmbl_40439.p1, internal, 96123, 96179
-recovered pasa_asmbl_40439.p1, internal, 96291, 96391
-recovered pasa_asmbl_40439.p1, internal, 96681, 96717
-recovered pasa_asmbl_40439.p1, internal, 98045, 98143
-recovered pasa_asmbl_40439.p1, internal, 98246, 98296
-recovered pasa_asmbl_40439.p1, internal, 98379, 98465
-recovered pasa_asmbl_40439.p1, internal, 98994, 99110
-recovered pasa_asmbl_40439.p1, internal, 99233, 99295
-recovered pasa_asmbl_40439.p1, internal, 99421, 99494
-recovered pasa_asmbl_40439.p1, internal, 99593, 99674
-recovered pasa_asmbl_40439.p1, internal, 99813, 99887
-recovered pasa_asmbl_40439.p1, internal, 100002, 100073
-recovered pasa_asmbl_40439.p1, internal, 100168, 100276
-recovered pasa_asmbl_40439.p1, internal, 100402, 100484
-recovered pasa_asmbl_40439.p1, internal, 100568, 100605
-recovered pasa_asmbl_40439.p1, internal, 100720, 100804
-recovered pasa_asmbl_40439.p1, internal, 101184, 101297
Valid prediction for snap_scaffold_3-snap.2585-T1
Valid prediction for GlimmerHMM_glimmerT_7590-T1
Valid prediction for Augustus_model.g4963.t1
Valid prediction for snap_scaffold_3-snap.2589-T1
Valid prediction for snap_scaffold_3-snap.2584-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7584-T1
Valid prediction for snap_scaffold_3-snap.2600-T1
Valid prediction for GlimmerHMM_glimmerT_7589-T1
Valid prediction for Augustus_model.g4967.t1
Valid prediction for GlimmerHMM_glimmerT_7588-T1
Valid prediction for Augustus_model.g4971.t1
Valid prediction for Augustus_model.g4962.t1
Valid prediction for HiQ_model.g4964.t1
Valid prediction for GlimmerHMM_glimmerT_7596-T1
Valid prediction for snap_scaffold_3-snap.2592-T1
Valid prediction for GlimmerHMM_glimmerT_7598-T1
Valid prediction for GlimmerHMM_glimmerT_7586-T1
Valid prediction for snap_scaffold_3-snap.2597-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.g4974.t1
Valid prediction for pasa_asmbl_39259.p1
Valid prediction for Augustus_model.g4973.t1
Valid prediction for Augustus_model.g4958.t1
Valid prediction for snap_scaffold_3-snap.2586-T1
Valid prediction for snap_scaffold_3-snap.2601-T1
Valid prediction for snap_scaffold_3-snap.2577-T1
Valid prediction for GlimmerHMM_glimmerT_7582-T1
Couldn't classify 173306, 173416
Couldn't classify 174225, 174338
Sorry, prediction pasa_asmbl_39255.p1 fails validation.
(GAA)	 TT	173306-173416	GT	AGG
(ATT)	 AG	173810-173884	GT	AGG
(GCC)	 AG	174004-174135	GT	CGG
(GTG)	 AG	174225-174338	GT	AGG
-recovered pasa_asmbl_39255.p1, internal, 173810, 173884
-recovered pasa_asmbl_39255.p1, internal, 174004, 174135
-recovered pasa_asmbl_39255.p1, internal, 174225, 174338
Valid prediction for snap_scaffold_3-snap.2602-T1
Valid prediction for CodingQuarry_transcript_46327-T1
Valid prediction for CodingQuarry_transcript_46326-T1
Valid prediction for GlimmerHMM_glimmerT_7595-T1
Valid prediction for snap_scaffold_3-snap.2591-T1
Valid prediction for CodingQuarry_transcript_46324-T1
Valid prediction for GlimmerHMM_glimmerT_7594-T1
Valid prediction for snap_scaffold_3-snap.2583-T1
Valid prediction for snap_scaffold_3-snap.2587-T1
Valid prediction for Augustus_model.g4956.t1
Valid prediction for snap_scaffold_3-snap.2599-T1
Valid prediction for GlimmerHMM_glimmerT_7599-T1
Valid prediction for Augustus_model.g4955.t1
Valid prediction for Augustus_model.g4954.t1
Couldn't classify 30104, 30223
Sorry, prediction pasa_asmbl_39271.p1 fails validation.
(TAC)	 CA	30104-30223	GT	ATG
(CCA)	 AG	30897-30968	GT	AGG
(GAC)	 AG	31175-31289	GT	AGG
(GTC)	 AG	31370-31452	GC	GAG
-recovered pasa_asmbl_39271.p1, terminal, 31370, 31452
-recovered pasa_asmbl_39271.p1, internal, 30897, 30968
-recovered pasa_asmbl_39271.p1, internal, 31175, 31289
-recovered pasa_asmbl_39271.p1, internal, 31370, 31452
Valid prediction for snap_scaffold_3-snap.2581-T1
Valid prediction for CodingQuarry_transcript_46320-T1
Valid prediction for Augustus_model.g4966.t1
Valid prediction for Augustus_model.g4970.t1
Valid prediction for GlimmerHMM_glimmerT_7592-T1
Valid prediction for snap_scaffold_3-snap.2578-T1
Valid prediction for snap_scaffold_3-snap.2580-T1
Valid prediction for HiQ_model.g4975.t1
Valid prediction for Augustus_model.g4965.t1
Couldn't classify 63796, 63855
Couldn't classify 65337, 65780
Sorry, prediction pasa_asmbl_39269.p1 fails validation.
(GAG)	 AG	63796-63855	GT	AGG
(ATC)	 AG	64068-64199	GT	AGG
(CTG)	 AG	64311-64523	GT	TGG
(ATA)	 AG	64680-64763	GT	AGG
(AAT)	 AG	64924-65065	GT	TGG
(TTT)	 AG	65156-65250	GT	AGG
(ACT)	 AG	65337-65780	GA	GGG
-recovered pasa_asmbl_39269.p1, internal, 63796, 63855
-recovered pasa_asmbl_39269.p1, internal, 64068, 64199
-recovered pasa_asmbl_39269.p1, internal, 64311, 64523
-recovered pasa_asmbl_39269.p1, internal, 64680, 64763
-recovered pasa_asmbl_39269.p1, internal, 64924, 65065
-recovered pasa_asmbl_39269.p1, internal, 65156, 65250
Valid prediction for snap_scaffold_3-snap.2594-T1
Valid prediction for GlimmerHMM_glimmerT_7602-T1
Valid prediction for GlimmerHMM_glimmerT_7587-T1
Couldn't classify 98941, 99273
Sorry, prediction pasa_asmbl_39266.p1 fails validation.
(CCA)	 AC	98941-99273	CA	AGC
Couldn't classify 66063, 66647
Sorry, prediction pasa_asmbl_39268.p1 fails validation.
(GAG)	 AG	66063-66647	TG	ACT
Valid prediction for snap_scaffold_3-snap.2595-T1
Valid prediction for CodingQuarry_transcript_46325-T1
Valid prediction for Augustus_model.g4969.t1
Valid prediction for GlimmerHMM_glimmerT_7581-T1
Valid prediction for Augustus_model.g4972.t1
Valid prediction for snap_scaffold_3-snap.2598-T1
Valid prediction for snap_scaffold_3-snap.2590-T1
Valid prediction for HiQ_model.g4957.t1
Valid prediction for snap_scaffold_3-snap.2588-T1
Valid prediction for snap_scaffold_3-snap.2582-T1
Couldn't classify 166113, 166117
Couldn't classify 169470, 169596
Sorry, prediction pasa_asmbl_39256.p1 fails validation.
(TCC)	 AG	166113-166117	GT	AAG
(AGT)	 AG	166412-166546	GT	ACG
(GAC)	 AG	168906-169028	GT	TCG
(TTT)	 AG	169470-169596	GC	CTG
-recovered pasa_asmbl_39256.p1, internal, 166113, 166117
-recovered pasa_asmbl_39256.p1, internal, 166412, 166546
-recovered pasa_asmbl_39256.p1, internal, 168906, 169028
-recovered pasa_asmbl_39256.p1, internal, 169470, 169596
Valid prediction for GlimmerHMM_glimmerT_7600-T1
Valid prediction for GlimmerHMM_glimmerT_7603-T1
Valid prediction for GlimmerHMM_glimmerT_7580-T1
Valid prediction for GlimmerHMM_glimmerT_7601-T1
Valid prediction for GlimmerHMM_glimmerT_7593-T1
Valid prediction for CodingQuarry_transcript_46323-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28967, rend_intergenic: 27214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188718
-exon list size: 281


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.2    
4.6    
4.9    
5.3    
5.7    
6.0    
6.4    
6.7    
7.1    
7.4    
7.8    
8.1    
8.5    
8.8    
9.2    
9.5    
9.9    
10.2    
10.6    
11.0    
11.3    
11.7    
12.0    
12.4    
12.7    
13.1    
13.4    
13.8    
14.1    
14.5    
14.8    
15.2    
15.5    
15.9    
16.3    
16.6    
17.0    
17.3    
17.7    
18.0    
18.4    
18.7    
19.1    
19.4    
19.8    
20.1    
20.5    
20.8    
21.2    
21.6    
21.9    
22.3    
22.6    
23.0    
23.3    
23.7    
24.0    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.5    
26.9    
27.2    
27.6    
27.9    
28.3    
28.6    
29.0    
29.3    
29.7    
30.0    
30.4    
30.7    
31.1    
31.4    
31.8    
32.2    
32.5    
32.9    
33.2    
33.6    
33.9    
34.3    
34.6    
35.0    
35.3    
35.7    
36.0    
36.4    
36.7    
37.1    
37.5    
37.8    
38.2    
38.5    
38.9    
39.2    
39.6    
39.9    
40.3    
40.6    
41.0    
41.3    
41.7    
42.0    
42.4    
42.8    
43.1    
43.5    
43.8    
44.2    
44.5    
44.9    
45.2    
45.6    
45.9    
46.3    
46.6    
47.0    
47.3    
47.7    
48.1    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
51.9    
52.3    
52.7    
53.0    
53.4    
53.7    
54.1    
54.4    
54.8    
55.1    
55.5    
55.8    
56.2    
56.5    
56.9    
57.2    
57.6    
58.0    
58.3    
58.7    
59.0    
59.4    
59.7    
60.1    
60.4    
60.8    
61.1    
61.5    
61.8    
62.2    
62.5    
62.9    
63.3    
63.6    
64.0    
64.3    
64.7    
65.0    
65.4    
65.7    
66.1    
66.4    
66.8    
67.1    
67.5    
67.8    
68.2    
68.6    
68.9    
69.3    
69.6    
70.0    
70.3    
70.7    
71.0    
71.4    
71.7    
72.1    
72.4    
72.8    
73.1    
73.5    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
76.0    
76.3    
76.7    
77.0    
77.4    
77.7    
78.1    
78.4    
78.8    
79.2    
79.5    
79.9    
80.2    
80.6    
80.9    
81.3    
81.6    
82.0    
82.3    
82.7    
83.0    
83.4    
83.7    
84.1    
84.5    
84.8    
85.2    
85.5    
85.9    
86.2    
86.6    
86.9    
87.3    
87.6    
88.0    
88.3    
88.7    
89.0    
89.4    
89.8    
90.1    
90.5    
90.8    
91.2    
91.5    
91.9    
92.2    
92.6    
92.9    
93.3    
93.6    
94.0    
94.3    
94.7    
95.1    
95.4    
95.8    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 28967, rend_intergenic: 27214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support