-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_13609060-13762102

-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_25850-T1
Valid prediction for GeneMark_model.80596_t
Valid prediction for GlimmerHMM_glimmerT_46352-T1
Couldn't classify 133216, 133407
Couldn't classify 134652, 134690
Sorry, prediction pasa_asmbl_22693.p1 fails validation.
(GCG)	 GA	133216-133407	GT	AGG
(AGA)	 AG	133655-133748	GT	CGG
(ATA)	 AG	133897-134003	GT	AGG
(GTC)	 AG	134652-134690	TA	AGT
-recovered pasa_asmbl_22693.p1, internal, 133655, 133748
-recovered pasa_asmbl_22693.p1, internal, 133897, 134003
Valid prediction for snap_scaffold_19-snap.2702-T1
Valid prediction for GeneMark_model.80612_t
Valid prediction for snap_scaffold_19-snap.2694-T1
Valid prediction for snap_scaffold_19-snap.2709-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.2706-T1
Valid prediction for GeneMark_model.80600_t
Valid prediction for GeneMark_model.80599_t
Valid prediction for GlimmerHMM_glimmerT_46353-T1
Valid prediction for GeneMark_model.80615_t
Valid prediction for GlimmerHMM_glimmerT_46343-T1
Valid prediction for snap_scaffold_19-snap.2703-T1
Valid prediction for GlimmerHMM_glimmerT_46341-T1
Valid prediction for GeneMark_model.80614_t
Valid prediction for GlimmerHMM_glimmerT_46350-T1
Valid prediction for snap_scaffold_19-snap.2699-T1
Valid prediction for CodingQuarry_transcript_25851-T1
Valid prediction for GeneMark_model.80616_t
Valid prediction for GlimmerHMM_glimmerT_46359-T1
Valid prediction for GeneMark_model.80607_t
Valid prediction for snap_scaffold_19-snap.2689-T1
Valid prediction for snap_scaffold_19-snap.2691-T1
Valid prediction for snap_scaffold_19-snap.2700-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 138080, 138157
Sorry, prediction pasa_asmbl_22695.p1 fails validation.
(TAT)	 GG	138080-138157	GT	TGG
(GCC)	 AG	138675-138769	GT	AGG
(TAT)	 AG	139225-139270	GT	AGG
(ACC)	 AG	139371-139517	GT	GGG
(GTT)	 AG	139743-139825	GT	AGG
(GGA)	 AG	139936-139975	GT	TGG
(ACT)	 AG	140066-140156	GT	GGG
(GCA)	 AG	140238-140342	GT	GGG
(TGA)	 AG	143201-143292	CC	GAC
add_exon() Sorry, pasa_asmbl_22695.p1 139743-139825-terminal-2 is invalid.
-recovered pasa_asmbl_22695.p1, terminal, 139743, 139825
-recovered pasa_asmbl_22695.p1, terminal, 143201, 143292
-recovered pasa_asmbl_22695.p1, internal, 138675, 138769
-recovered pasa_asmbl_22695.p1, internal, 139225, 139270
-recovered pasa_asmbl_22695.p1, internal, 139371, 139517
-recovered pasa_asmbl_22695.p1, internal, 139743, 139825
-recovered pasa_asmbl_22695.p1, internal, 139936, 139975
-recovered pasa_asmbl_22695.p1, internal, 140066, 140156
-recovered pasa_asmbl_22695.p1, internal, 140238, 140342
Valid prediction for snap_scaffold_19-snap.2705-T1
Valid prediction for GlimmerHMM_glimmerT_46360-T1
Valid prediction for snap_scaffold_19-snap.2687-T1
Valid prediction for GeneMark_model.80603_t
Valid prediction for GeneMark_model.80605_t
Valid prediction for snap_scaffold_19-snap.2708-T1
Valid prediction for GlimmerHMM_glimmerT_46355-T1
Valid prediction for GlimmerHMM_glimmerT_46362-T1
Valid prediction for GeneMark_model.80598_t
Valid prediction for snap_scaffold_19-snap.2692-T1
Valid prediction for GlimmerHMM_glimmerT_46346-T1
Valid prediction for snap_scaffold_19-snap.2684-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.80601_t
Valid prediction for GlimmerHMM_glimmerT_46357-T1
Valid prediction for GlimmerHMM_glimmerT_46340-T1
Valid prediction for GeneMark_model.80594_t
Valid prediction for GeneMark_model.80609_t
Couldn't classify 3233, 3571
Sorry, prediction pasa_asmbl_21885.p1 fails validation.
(TTC)	 TG	3233-3571	CA	CAC

-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 GeneMark_model.80602_t
Valid prediction for snap_scaffold_19-snap.2710-T1
Valid prediction for snap_scaffold_19-snap.2693-T1
Valid prediction for GlimmerHMM_glimmerT_46348-T1
Valid prediction for GlimmerHMM_glimmerT_46351-T1
Valid prediction for GlimmerHMM_glimmerT_46344-T1
Valid prediction for GeneMark_model.80604_t
Valid prediction for GlimmerHMM_glimmerT_46347-T1
Valid prediction for snap_scaffold_19-snap.2704-T1
Valid prediction for GlimmerHMM_glimmerT_46345-T1
Valid prediction for snap_scaffold_19-snap.2688-T1
Valid prediction for snap_scaffold_19-snap.2701-T1
Valid prediction for GeneMark_model.80613_t
Valid prediction for snap_scaffold_19-snap.2707-T1
Valid prediction for GlimmerHMM_glimmerT_46354-T1
Valid prediction for GeneMark_model.80595_t
Valid prediction for snap_scaffold_19-snap.2698-T1
Valid prediction for snap_scaffold_19-snap.2685-T1
Valid prediction for GeneMark_model.80611_t
Valid prediction for GeneMark_model.80608_t
Valid prediction for GlimmerHMM_glimmerT_46358-T1
Valid prediction for GlimmerHMM_glimmerT_46356-T1
Couldn't classify 132800, 132892
Couldn't classify 135750, 135828
Sorry, prediction pasa_asmbl_21887.p1 fails validation.
(GAT)	 TA	132800-132892	GT	CAG
(GAT)	 AG	132967-133100	GT	AGG
(ACC)	 AG	135750-135828	TG	GCT
-recovered pasa_asmbl_21887.p1, internal, 132967, 133100
Couldn't classify 544, 666
Sorry, prediction GeneMark_model.80617_t fails validation.
(AGG)	 AG	544-666	GT	GGG
(AGG)	 AG	787-941	GT	CCG
(GCC)	 AG	3672-3682	GT	AGG
(ATG)	 AG	3835-3981	GT	CGG
(CTG)	 AG	4867-4937	GT	GGG
(AGA)	 AG	4977-4991	GT	GGG
(ACG)	 AG	6001-6031	GT	AAG
(TCC)	 AG	6055-6093	AC	AAA
-recovered GeneMark_model.80617_t, initial, 3835, 3981
-recovered GeneMark_model.80617_t, terminal, 6055, 6093
-recovered GeneMark_model.80617_t, internal, 544, 666
-recovered GeneMark_model.80617_t, internal, 787, 941
-recovered GeneMark_model.80617_t, internal, 3672, 3682
-recovered GeneMark_model.80617_t, internal, 3835, 3981
-recovered GeneMark_model.80617_t, internal, 4867, 4937
-recovered GeneMark_model.80617_t, internal, 4977, 4991
-recovered GeneMark_model.80617_t, internal, 6001, 6031
Valid prediction for snap_scaffold_19-snap.2690-T1
Valid prediction for snap_scaffold_19-snap.2696-T1
Valid prediction for GlimmerHMM_glimmerT_46361-T1
Valid prediction for GeneMark_model.80606_t
Valid prediction for snap_scaffold_19-snap.2695-T1
Valid prediction for GlimmerHMM_glimmerT_46342-T1
Valid prediction for GeneMark_model.80610_t
Valid prediction for snap_scaffold_19-snap.2697-T1
Couldn't classify 114770, 114922
Sorry, prediction pasa_asmbl_21891.p1 fails validation.
(GAT)	 AG	114770-114922	GT	AGG
(GAG)	 AG	115190-115282	GT	GGG
(GGG)	 AG	116449-116697	TG	GAT
-recovered pasa_asmbl_21891.p1, terminal, 116449, 116697
-recovered pasa_asmbl_21891.p1, internal, 114770, 114922
-recovered pasa_asmbl_21891.p1, internal, 115190, 115282
Valid prediction for snap_scaffold_19-snap.2686-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_46349-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 130567, rend_intergenic: 127582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 153043
-exon list size: 269


building trellis

0.4    
0.7    
1.1    
1.5    
1.8    
2.2    
2.6    
3.0    
3.3    
3.7    
4.1    
4.4    
4.8    
5.2    
5.5    
5.9    
6.3    
6.6    
7.0    
7.4    
7.7    
8.1    
8.5    
8.9    
9.2    
9.6    
10.0    
10.3    
10.7    
11.1    
11.4    
11.8    
12.2    
12.5    
12.9    
13.3    
13.7    
14.0    
14.4    
14.8    
15.1    
15.5    
15.9    
16.2    
16.6    
17.0    
17.3    
17.7    
18.1    
18.5    
18.8    
19.2    
19.6    
19.9    
20.3    
20.7    
21.0    
21.4    
21.8    
22.1    
22.5    
22.9    
23.2    
23.6    
24.0    
24.4    
24.7    
25.1    
25.5    
25.8    
26.2    
26.6    
26.9    
27.3    
27.7    
28.0    
28.4    
28.8    
29.2    
29.5    
29.9    
30.3    
30.6    
31.0    
31.4    
31.7    
32.1    
32.5    
32.8    
33.2    
33.6    
33.9    
34.3    
34.7    
35.1    
35.4    
35.8    
36.2    
36.5    
36.9    
37.3    
37.6    
38.0    
38.4    
38.7    
39.1    
39.5    
39.9    
40.2    
40.6    
41.0    
41.3    
41.7    
42.1    
42.4    
42.8    
43.2    
43.5    
43.9    
44.3    
44.6    
45.0    
45.4    
45.8    
46.1    
46.5    
46.9    
47.2    
47.6    
48.0    
48.3    
48.7    
49.1    
49.4    
49.8    
50.2    
50.6    
50.9    
51.3    
51.7    
52.0    
52.4    
52.8    
53.1    
53.5    
53.9    
54.2    
54.6    
55.0    
55.4    
55.7    
56.1    
56.5    
56.8    
57.2    
57.6    
57.9    
58.3    
58.7    
59.0    
59.4    
59.8    
60.1    
60.5    
60.9    
61.3    
61.6    
62.0    
62.4    
62.7    
63.1    
63.5    
63.8    
64.2    
64.6    
64.9    
65.3    
65.7    
66.1    
66.4    
66.8    
67.2    
67.5    
67.9    
68.3    
68.6    
69.0    
69.4    
69.7    
70.1    
70.5    
70.8    
71.2    
71.6    
72.0    
72.3    
72.7    
73.1    
73.4    
73.8    
74.2    
74.5    
74.9    
75.3    
75.6    
76.0    
76.4    
76.8    
77.1    
77.5    
77.9    
78.2    
78.6    
79.0    
79.3    
79.7    
80.1    
80.4    
80.8    
81.2    
81.5    
81.9    
82.3    
82.7    
83.0    
83.4    
83.8    
84.1    
84.5    
84.9    
85.2    
85.6    
86.0    
86.3    
86.7    
87.1    
87.5    
87.8    
88.2    
88.6    
88.9    
89.3    
89.7    
90.0    
90.4    
90.8    
91.1    
91.5    
91.9    
92.3    
92.6    
93.0    
93.4    
93.7    
94.1    
94.5    
94.8    
95.2    
95.6    
95.9    
96.3    
96.7    
97.0    
97.4    
97.8    
98.2    
98.5    
98.9    
99.3    
99.6    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 130567, rend_intergenic: 127582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 17188
-exon list size: 24


building trellis

3.8    
7.7    
11.5    
15.4    
19.2    
23.1    
26.9    
30.8    
34.6    
38.5    
42.3    
46.2    
50.0    
53.8    
57.7    
61.5    
65.4    
69.2    
73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support