-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_6740159-6954632

-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 GlimmerHMM_glimmerT_45323-T1
Valid prediction for CodingQuarry_transcript_25642-T1
Couldn't classify 93103, 93182
Couldn't classify 93775, 93848
Sorry, prediction pasa_asmbl_22757.p1 fails validation.
(CAG)	 TT	93103-93182	GT	AAG
(ACA)	 AG	93348-93438	GT	TGG
(CTC)	 AG	93616-93691	GT	TGG
(GCC)	 AG	93775-93848	GA	GGG
-recovered pasa_asmbl_22757.p1, internal, 93348, 93438
-recovered pasa_asmbl_22757.p1, internal, 93616, 93691
Valid prediction for GeneMark_model.79234_t
Valid prediction for GlimmerHMM_glimmerT_45316-T1
Couldn't classify 21651, 21764
Couldn't classify 22766, 22819
Sorry, prediction pasa_asmbl_22742.p1 fails validation.
(TCA)	 TT	21651-21764	GT	AGG
(TGG)	 AG	22474-22608	GT	AGG
(GGT)	 AG	22766-22819	CA	AAC
-recovered pasa_asmbl_22742.p1, internal, 22474, 22608
Valid prediction for GlimmerHMM_glimmerT_45331-T1
Valid prediction for GlimmerHMM_glimmerT_45332-T1
Valid prediction for GlimmerHMM_glimmerT_45334-T1
Valid prediction for GeneMark_model.79244_t
Valid prediction for GeneMark_model.79232_t
Valid prediction for GlimmerHMM_glimmerT_45318-T1
Valid prediction for CodingQuarry_transcript_25644-T1
Valid prediction for HiQ_model.g30228.t1
Valid prediction for GeneMark_model.79229_t
Valid prediction for GeneMark_model.79250_t
Valid prediction for snap_scaffold_19-snap.1414-T1
Valid prediction for snap_scaffold_19-snap.1402-T1
Valid prediction for Augustus_model.g30222.t1
Couldn't classify 2462, 2549
Couldn't classify 3612, 3922
Sorry, prediction pasa_asmbl_22243.p1 fails validation.
(CTC)	 AC	2462-2549	GT	AGG
(GTG)	 AG	2688-2785	GT	AGG
(GGC)	 AG	2991-3075	GT	AGG
(TAA)	 AG	3612-3922	CC	AGC
-recovered pasa_asmbl_22243.p1, internal, 2688, 2785
-recovered pasa_asmbl_22243.p1, internal, 2991, 3075
Valid prediction for GlimmerHMM_glimmerT_45325-T1
Couldn't classify 94539, 94712
Sorry, prediction pasa_asmbl_22250.p1 fails validation.
(GAC)	 AG	94539-94712	GT	AGG
(ACA)	 AG	94824-94910	GT	TGG
(ATG)	 AG	95006-95114	GT	TGG
(GTC)	 AG	95269-95364	GT	CGG
(AGT)	 AG	95452-95519	GT	AGG
(GCG)	 AG	95649-95831	TG	AAT
-recovered pasa_asmbl_22250.p1, initial, 95006, 95114
-recovered pasa_asmbl_22250.p1, terminal, 95649, 95831
-recovered pasa_asmbl_22250.p1, internal, 94539, 94712
-recovered pasa_asmbl_22250.p1, internal, 94824, 94910
-recovered pasa_asmbl_22250.p1, internal, 95006, 95114
-recovered pasa_asmbl_22250.p1, internal, 95269, 95364
-recovered pasa_asmbl_22250.p1, internal, 95452, 95519
Valid prediction for GeneMark_model.79230_t
Valid prediction for Augustus_model.g30219.t1
Valid prediction for Augustus_model.g30235.t1
Valid prediction for GlimmerHMM_glimmerT_45314-T1
Valid prediction for CodingQuarry_transcript_25643-T1
Valid prediction for snap_scaffold_19-snap.1397-T1
Valid prediction for snap_scaffold_19-snap.1391-T1
Valid prediction for GlimmerHMM_glimmerT_45339-T1
Valid prediction for snap_scaffold_19-snap.1407-T1
Valid prediction for GeneMark_model.79253_t
Valid prediction for snap_scaffold_19-snap.1394-T1
Valid prediction for GeneMark_model.79237_t
Valid prediction for GeneMark_model.79238_t
Valid prediction for snap_scaffold_19-snap.1401-T1
Couldn't classify 6203, 6283
Sorry, prediction pasa_asmbl_22730.p1 fails validation.
(ATG)	 CC	5765-5954	GC	AGG
(ATG)	 AG	6036-6127	GT	ATG
(GTG)	 AG	6203-6283	CA	CAC
-recovered pasa_asmbl_22730.p1, initial, 5765, 5954
add_exon() Sorry, pasa_asmbl_22730.p1 6036-6127-initial-1 is invalid.
-recovered pasa_asmbl_22730.p1, initial, 6036, 6127
-recovered pasa_asmbl_22730.p1, internal, 6036, 6127
Couldn't classify 6587, 6922
Sorry, prediction pasa_asmbl_22247.p1 fails validation.
(TTT)	 AG	6587-6922	AA	GGA
Valid prediction for snap_scaffold_19-snap.1400-T1
Valid prediction for pasa_asmbl_22249.p1
Valid prediction for GlimmerHMM_glimmerT_45333-T1
Valid prediction for GeneMark_model.79241_t
Valid prediction for GeneMark_model.79246_t
Valid prediction for GlimmerHMM_glimmerT_45320-T1
Valid prediction for snap_scaffold_19-snap.1413-T1
Valid prediction for GlimmerHMM_glimmerT_45328-T1
Valid prediction for snap_scaffold_19-snap.1393-T1
Valid prediction for GeneMark_model.79252_t
Valid prediction for snap_scaffold_19-snap.1398-T1
Valid prediction for GeneMark_model.79236_t
Valid prediction for snap_scaffold_19-snap.1411-T1
Valid prediction for Augustus_model.g30225.t1
Valid prediction for Augustus_model.g30232.t1
Valid prediction for GlimmerHMM_glimmerT_45317-T1
Valid prediction for GlimmerHMM_glimmerT_45335-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_19-snap.1409-T1
Valid prediction for snap_scaffold_19-snap.1412-T1
Valid prediction for GlimmerHMM_glimmerT_45327-T1
Valid prediction for snap_scaffold_19-snap.1399-T1
Valid prediction for Augustus_model.g30221.t1
Valid prediction for snap_scaffold_19-snap.1405-T1
Valid prediction for GeneMark_model.79251_t
Valid prediction for Augustus_model.g30231.t1
Valid prediction for Augustus_model.g30229.t1
Valid prediction for GlimmerHMM_glimmerT_45324-T1
Valid prediction for GeneMark_model.79242_t
Couldn't classify 127648, 127953
Sorry, prediction pasa_asmbl_21437.p1 fails validation.
(GGC)	 CC	127648-127953	AG	ACA
Valid prediction for Augustus_model.g30226.t1
Valid prediction for GlimmerHMM_glimmerT_45338-T1
Couldn't classify 128005, 128035
Couldn't classify 129850, 129900
Sorry, prediction pasa_asmbl_21436.p1 fails validation.
(AGG)	 AT	128005-128035	GT	AGG
(GTG)	 AG	129418-129686	GT	AGG
(GTC)	 AG	129850-129900	TC	AGT
-recovered pasa_asmbl_21436.p1, internal, 129418, 129686
Couldn't classify 112114, 112251
Sorry, prediction pasa_asmbl_21442.p1 fails validation.
(GGG)	 CC	112114-112251	GT	AGG
(GAC)	 AG	112481-112624	GT	AGG
(GGC)	 AG	113464-113609	GT	AGG
(AGA)	 AG	114063-114177	GT	AGG
(GTG)	 AG	114400-114538	GT	CGG
(GCC)	 AG	114922-115052	GT	CGG
(GGT)	 AG	115228-115422	TT	GAT
-recovered pasa_asmbl_21442.p1, terminal, 115228, 115422
-recovered pasa_asmbl_21442.p1, internal, 112481, 112624
-recovered pasa_asmbl_21442.p1, internal, 113464, 113609
-recovered pasa_asmbl_21442.p1, internal, 114063, 114177
-recovered pasa_asmbl_21442.p1, internal, 114400, 114538
-recovered pasa_asmbl_21442.p1, internal, 114922, 115052
Valid prediction for GeneMark_model.79245_t
Valid prediction for GlimmerHMM_glimmerT_45315-T1
Couldn't classify 105141, 105349
Couldn't classify 106800, 106843
Sorry, prediction pasa_asmbl_21444.p3 fails validation.
(GGT)	 CA	105141-105349	GT	AGG
(CAG)	 AG	106196-106305	GT	GAG
(CAA)	 AG	106800-106843	CT	CCC
-recovered pasa_asmbl_21444.p3, internal, 106196, 106305
Valid prediction for snap_scaffold_19-snap.1404-T1
Valid prediction for Augustus_model.g30236.t1
Valid prediction for snap_scaffold_19-snap.1396-T1
Valid prediction for snap_scaffold_19-snap.1410-T1
Valid prediction for GeneMark_model.79247_t
Valid prediction for GlimmerHMM_glimmerT_45322-T1
Valid prediction for GlimmerHMM_glimmerT_45330-T1
Couldn't classify 130282, 131034
Sorry, prediction pasa_asmbl_21435.p1 fails validation.
(AGG)	 CC	130282-131034	GT	AGG
(GTG)	 AG	131226-131299	GT	AAG
(AGC)	 AG	131862-131937	GT	CGG
(GTT)	 AG	132618-132689	CA	AAC
-recovered pasa_asmbl_21435.p1, terminal, 132618, 132689
-recovered pasa_asmbl_21435.p1, internal, 131226, 131299
-recovered pasa_asmbl_21435.p1, internal, 131862, 131937
Valid prediction for GlimmerHMM_glimmerT_45337-T1
Valid prediction for GlimmerHMM_glimmerT_45321-T1
Valid prediction for snap_scaffold_19-snap.1408-T1
Valid prediction for snap_scaffold_19-snap.1392-T1
Valid prediction for GeneMark_model.79240_t
Valid prediction for Augustus_model.g30220.t1
Valid prediction for GlimmerHMM_glimmerT_45336-T1
Valid prediction for GlimmerHMM_glimmerT_45326-T1
Valid prediction for Augustus_model.g30227.t1
Valid prediction for GeneMark_model.79248_t
Valid prediction for snap_scaffold_19-snap.1406-T1
Valid prediction for Augustus_model.g30223.t1
Valid prediction for GeneMark_model.79235_t
Couldn't classify 158596, 158665
Couldn't classify 159348, 159515
Sorry, prediction pasa_asmbl_21434.p1 fails validation.
(TTC)	 GC	158596-158665	GT	AGG
(AAA)	 AG	159001-159131	GT	AGG
(GTC)	 AG	159348-159515	CA	GCC
-recovered pasa_asmbl_21434.p1, internal, 159001, 159131
Valid prediction for snap_scaffold_19-snap.1395-T1
Valid prediction for GeneMark_model.79243_t
Valid prediction for Augustus_model.g30233.t1
Valid prediction for snap_scaffold_19-snap.1403-T1
Valid prediction for Augustus_model.g30230.t1
Valid prediction for GeneMark_model.79233_t
Valid prediction for GeneMark_model.79239_t
Valid prediction for Augustus_model.g30224.t1
Valid prediction for Augustus_model.g30234.t1
Valid prediction for GeneMark_model.79249_t
Valid prediction for GeneMark_model.79231_t
Valid prediction for GlimmerHMM_glimmerT_45319-T1
Valid prediction for GlimmerHMM_glimmerT_45329-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23014, rend_intergenic: 16660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214474
-exon list size: 389


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.2    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.5    
10.7    
11.0    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.8    
13.0    
13.3    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.1    
15.3    
15.6    
15.9    
16.1    
16.4    
16.6    
16.9    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.7    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
30.9    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.5    
42.7    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.3    
57.5    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.1    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
87.0    
87.2    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 23014, rend_intergenic: 16660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 159571 - 214474
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-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 159571 - 175632
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 159571 - 170186
-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 175660 - 214474
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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 175660 - 201755
-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 182417 - 201755
-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 184981 - 201755
-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
	-no exons in range 191498 - 201755

-building DP trellis

-building trellis in range 201786 - 214474
-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