-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_10552349-10693891

-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_24-snap.2274-T1
Valid prediction for GlimmerHMM_glimmerT_53371-T1
Valid prediction for GlimmerHMM_glimmerT_53382-T1
Valid prediction for CodingQuarry_transcript_37445-T1
Valid prediction for snap_scaffold_24-snap.2266-T1
Couldn't classify 51941, 52009
Sorry, prediction pasa_asmbl_32579.p1 fails validation.
(CCG)	 CC	51941-52009	GT	AGG
(GAA)	 AG	52342-52508	GT	AAG
(AGC)	 AG	52756-52872	GT	ATG
(GTA)	 AG	53154-53305	GT	AGG
(AAA)	 AG	53410-53735	CC	AAC
-recovered pasa_asmbl_32579.p1, terminal, 53410, 53735
-recovered pasa_asmbl_32579.p1, internal, 52342, 52508
-recovered pasa_asmbl_32579.p1, internal, 52756, 52872
-recovered pasa_asmbl_32579.p1, internal, 53154, 53305
Valid prediction for CodingQuarry_transcript_37446-T1
Valid prediction for snap_scaffold_24-snap.2278-T1
Valid prediction for snap_scaffold_24-snap.2275-T1
Couldn't classify 115701, 115794
Sorry, prediction pasa_asmbl_32584.p1 fails validation.
(AGG)	 CC	115701-115794	GT	TGG
(TAC)	 AG	115918-116074	GT	CTG
(GAG)	 AG	116406-116621	GT	TCG
(AAT)	 AG	116790-116933	GT	CAG
(GAT)	 AG	117087-117200	GT	CTG
(CAT)	 AG	117335-117509	GT	AGG
(GTG)	 AG	117847-117943	GT	AGG
(GTG)	 AG	118187-118485	GG	GAG
add_exon() Sorry, pasa_asmbl_32584.p1 117847-117943-terminal-3 is invalid.
-recovered pasa_asmbl_32584.p1, terminal, 117847, 117943
-recovered pasa_asmbl_32584.p1, terminal, 118187, 118485
-recovered pasa_asmbl_32584.p1, internal, 115918, 116074
-recovered pasa_asmbl_32584.p1, internal, 116406, 116621
-recovered pasa_asmbl_32584.p1, internal, 116790, 116933
-recovered pasa_asmbl_32584.p1, internal, 117087, 117200
-recovered pasa_asmbl_32584.p1, internal, 117335, 117509
-recovered pasa_asmbl_32584.p1, internal, 117847, 117943
Valid prediction for GlimmerHMM_glimmerT_53375-T1
Valid prediction for snap_scaffold_24-snap.2285-T1
Valid prediction for snap_scaffold_24-snap.2286-T1
Valid prediction for snap_scaffold_24-snap.2290-T1
Valid prediction for GlimmerHMM_glimmerT_53391-T1
Valid prediction for snap_scaffold_24-snap.2268-T1
Valid prediction for GlimmerHMM_glimmerT_53386-T1
Valid prediction for GlimmerHMM_glimmerT_53373-T1
Valid prediction for snap_scaffold_24-snap.2284-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.2292-T1
Valid prediction for snap_scaffold_24-snap.2264-T1
Valid prediction for GlimmerHMM_glimmerT_53377-T1
Valid prediction for snap_scaffold_24-snap.2271-T1
Valid prediction for snap_scaffold_24-snap.2269-T1
Valid prediction for GlimmerHMM_glimmerT_53392-T1
Valid prediction for GlimmerHMM_glimmerT_53372-T1
Valid prediction for snap_scaffold_24-snap.2277-T1
Valid prediction for snap_scaffold_24-snap.2272-T1
Valid prediction for snap_scaffold_24-snap.2279-T1
Valid prediction for GlimmerHMM_glimmerT_53378-T1
Valid prediction for snap_scaffold_24-snap.2287-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_24-snap.2267-T1
Valid prediction for GlimmerHMM_glimmerT_53374-T1
Couldn't classify 97010, 97147
Sorry, prediction pasa_asmbl_33212.p2 fails validation.
(GTC)	 CC	97010-97147	GT	GGG
(GAA)	 AG	97326-97416	GT	AGG
(ACC)	 AG	97513-97640	GT	GTG
(TGG)	 AG	98224-98298	GC	GAG
-recovered pasa_asmbl_33212.p2, terminal, 98224, 98298
-recovered pasa_asmbl_33212.p2, internal, 97326, 97416
-recovered pasa_asmbl_33212.p2, internal, 97513, 97640
-recovered pasa_asmbl_33212.p2, internal, 98224, 98298
Valid prediction for CodingQuarry_transcript_37444-T1
Valid prediction for snap_scaffold_24-snap.2273-T1
Valid prediction for snap_scaffold_24-snap.2288-T1
Valid prediction for snap_scaffold_24-snap.2282-T1
Valid prediction for GlimmerHMM_glimmerT_53396-T1
Valid prediction for snap_scaffold_24-snap.2283-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53394-T1
Valid prediction for snap_scaffold_24-snap.2276-T1
Valid prediction for GlimmerHMM_glimmerT_53387-T1
Valid prediction for GlimmerHMM_glimmerT_53380-T1
Valid prediction for snap_scaffold_24-snap.2289-T1
Valid prediction for snap_scaffold_24-snap.2291-T1
Couldn't classify 112864, 113049
Couldn't classify 113323, 113538
Sorry, prediction pasa_asmbl_33206.p1 fails validation.
(GAG)	 TC	112864-113049	GT	AGG
(AGC)	 AG	113323-113538	AA	GGA
Valid prediction for snap_scaffold_24-snap.2263-T1
Valid prediction for GlimmerHMM_glimmerT_53395-T1
Couldn't classify 109526, 109639
Couldn't classify 110038, 110241
Sorry, prediction pasa_asmbl_33208.p1 fails validation.
(CGG)	 AG	109526-109639	GT	TGG
(AAG)	 AG	110038-110241	CA	TCC
-recovered pasa_asmbl_33208.p1, internal, 109526, 109639
Valid prediction for snap_scaffold_24-snap.2280-T1
Valid prediction for GlimmerHMM_glimmerT_53388-T1
Valid prediction for GlimmerHMM_glimmerT_53385-T1
Valid prediction for snap_scaffold_24-snap.2281-T1
Valid prediction for snap_scaffold_24-snap.2265-T1
Valid prediction for snap_scaffold_24-snap.2270-T1
Valid prediction for snap_scaffold_24-snap.2293-T1
Valid prediction for GlimmerHMM_glimmerT_53376-T1
Valid prediction for GlimmerHMM_glimmerT_53390-T1
Valid prediction for GlimmerHMM_glimmerT_53384-T1
Valid prediction for GlimmerHMM_glimmerT_53383-T1
Valid prediction for GlimmerHMM_glimmerT_53393-T1
Valid prediction for GlimmerHMM_glimmerT_53381-T1
Valid prediction for GlimmerHMM_glimmerT_53379-T1
Valid prediction for GlimmerHMM_glimmerT_53389-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8764, rend_intergenic: 6369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11694, rend_intergenic: 10010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17321, rend_intergenic: 11728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21669, rend_intergenic: 19028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39322, rend_intergenic: 30811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71309, rend_intergenic: 61393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92228, rend_intergenic: 76277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127979, rend_intergenic: 123572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 141543
-exon list size: 252


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.8    
3.1    
3.5    
3.9    
4.3    
4.7    
5.1    
5.5    
5.9    
6.3    
6.7    
7.1    
7.5    
7.9    
8.3    
8.7    
9.1    
9.4    
9.8    
10.2    
10.6    
11.0    
11.4    
11.8    
12.2    
12.6    
13.0    
13.4    
13.8    
14.2    
14.6    
15.0    
15.4    
15.7    
16.1    
16.5    
16.9    
17.3    
17.7    
18.1    
18.5    
18.9    
19.3    
19.7    
20.1    
20.5    
20.9    
21.3    
21.7    
22.0    
22.4    
22.8    
23.2    
23.6    
24.0    
24.4    
24.8    
25.2    
25.6    
26.0    
26.4    
26.8    
27.2    
27.6    
28.0    
28.3    
28.7    
29.1    
29.5    
29.9    
30.3    
30.7    
31.1    
31.5    
31.9    
32.3    
32.7    
33.1    
33.5    
33.9    
34.3    
34.6    
35.0    
35.4    
35.8    
36.2    
36.6    
37.0    
37.4    
37.8    
38.2    
38.6    
39.0    
39.4    
39.8    
40.2    
40.6    
40.9    
41.3    
41.7    
42.1    
42.5    
42.9    
43.3    
43.7    
44.1    
44.5    
44.9    
45.3    
45.7    
46.1    
46.5    
46.9    
47.2    
47.6    
48.0    
48.4    
48.8    
49.2    
49.6    
50.0    
50.4    
50.8    
51.2    
51.6    
52.0    
52.4    
52.8    
53.1    
53.5    
53.9    
54.3    
54.7    
55.1    
55.5    
55.9    
56.3    
56.7    
57.1    
57.5    
57.9    
58.3    
58.7    
59.1    
59.4    
59.8    
60.2    
60.6    
61.0    
61.4    
61.8    
62.2    
62.6    
63.0    
63.4    
63.8    
64.2    
64.6    
65.0    
65.4    
65.7    
66.1    
66.5    
66.9    
67.3    
67.7    
68.1    
68.5    
68.9    
69.3    
69.7    
70.1    
70.5    
70.9    
71.3    
71.7    
72.0    
72.4    
72.8    
73.2    
73.6    
74.0    
74.4    
74.8    
75.2    
75.6    
76.0    
76.4    
76.8    
77.2    
77.6    
78.0    
78.3    
78.7    
79.1    
79.5    
79.9    
80.3    
80.7    
81.1    
81.5    
81.9    
82.3    
82.7    
83.1    
83.5    
83.9    
84.3    
84.6    
85.0    
85.4    
85.8    
86.2    
86.6    
87.0    
87.4    
87.8    
88.2    
88.6    
89.0    
89.4    
89.8    
90.2    
90.6    
90.9    
91.3    
91.7    
92.1    
92.5    
92.9    
93.3    
93.7    
94.1    
94.5    
94.9    
95.3    
95.7    
96.1    
96.5    
96.9    
97.2    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 8764, rend_intergenic: 6369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11694, rend_intergenic: 10010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17321, rend_intergenic: 11728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21669, rend_intergenic: 19028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39322, rend_intergenic: 30811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71309, rend_intergenic: 61393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92228, rend_intergenic: 76277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127979, rend_intergenic: 123572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 128911 - 141543
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 129394 - 141543
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 130493 - 141543
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

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