-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_7297566-7449570

-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: +)Couldn't classify 114819, 114939
Sorry, prediction pasa_asmbl_30181.p1 fails validation.
(GTG)	 AG	114819-114939	GT	CGG
(GTA)	 AG	115289-115424	GT	ATG
(AGC)	 AG	115742-115847	AG	GAA
-recovered pasa_asmbl_30181.p1, terminal, 115742, 115847
-recovered pasa_asmbl_30181.p1, internal, 114819, 114939
-recovered pasa_asmbl_30181.p1, internal, 115289, 115424
Valid prediction for snap_scaffold_22-snap.1455-T1
Valid prediction for snap_scaffold_22-snap.1435-T1
Valid prediction for CodingQuarry_transcript_34209-T1
Valid prediction for HiQ_model.g33187.t1
Valid prediction for GlimmerHMM_glimmerT_49728-T1
Valid prediction for GlimmerHMM_glimmerT_49732-T1
Valid prediction for snap_scaffold_22-snap.1445-T1
Valid prediction for GlimmerHMM_glimmerT_49730-T1
Valid prediction for pasa_asmbl_30174.p1
Valid prediction for Augustus_model.g33174.t1
Valid prediction for HiQ_model.g33179.t1
Valid prediction for snap_scaffold_22-snap.1456-T1
Valid prediction for snap_scaffold_22-snap.1458-T1
Valid prediction for CodingQuarry_transcript_34205-T1
Valid prediction for snap_scaffold_22-snap.1463-T1
Valid prediction for GlimmerHMM_glimmerT_49731-T1
Valid prediction for snap_scaffold_22-snap.1454-T1
Couldn't classify 36601, 36646
Couldn't classify 41204, 41272
Sorry, prediction pasa_asmbl_30171.p1 fails validation.
(TGG)	 TG	36601-36646	GT	AGG
(CCT)	 AG	37219-37268	GT	AGG
(GTG)	 AG	37473-37533	GT	AGG
(TGT)	 AG	37999-38093	GT	AGG
(GTA)	 AG	38232-38418	GT	TGG
(AAC)	 AG	39012-39109	GT	AGG
(CTG)	 AG	39288-39369	GT	AGG
(TGT)	 AG	39454-39548	GT	AGG
(GTG)	 AG	41204-41272	CA	TGC
-recovered pasa_asmbl_30171.p1, internal, 37219, 37268
-recovered pasa_asmbl_30171.p1, internal, 37473, 37533
-recovered pasa_asmbl_30171.p1, internal, 37999, 38093
-recovered pasa_asmbl_30171.p1, internal, 38232, 38418
-recovered pasa_asmbl_30171.p1, internal, 39012, 39109
-recovered pasa_asmbl_30171.p1, internal, 39288, 39369
-recovered pasa_asmbl_30171.p1, internal, 39454, 39548
Valid prediction for CodingQuarry_transcript_34206-T1
Valid prediction for CodingQuarry_transcript_34204-T1
Valid prediction for GlimmerHMM_glimmerT_49724-T1
Valid prediction for snap_scaffold_22-snap.1432-T1
Valid prediction for snap_scaffold_22-snap.1438-T1
Valid prediction for GlimmerHMM_glimmerT_49729-T1
Valid prediction for pasa_asmbl_30184.p1
Valid prediction for snap_scaffold_22-snap.1453-T1
Valid prediction for GlimmerHMM_glimmerT_49738-T1
Valid prediction for snap_scaffold_22-snap.1447-T1
Couldn't classify 93943, 94045
Couldn't classify 94638, 94790
Sorry, prediction pasa_asmbl_30461.p1 fails validation.
(AAC)	 GG	93943-94045	GT	TGG
(GAA)	 AG	94353-94441	GT	AGG
(GTG)	 AG	94638-94790	GG	AGG
-recovered pasa_asmbl_30461.p1, internal, 94353, 94441
Couldn't classify 106642, 106731
Couldn't classify 107778, 107830
Sorry, prediction pasa_asmbl_30179.p1 fails validation.
(GAG)	 TG	106642-106731	GT	AGG
(GCT)	 AG	107046-107270	GT	AGG
(GAC)	 AG	107377-107434	GC	AGG
(CGG)	 AG	107539-107682	GT	AGG
(ATG)	 AG	107778-107830	AG	TGA
-recovered pasa_asmbl_30179.p1, internal, 107046, 107270
-recovered pasa_asmbl_30179.p1, internal, 107377, 107434
-recovered pasa_asmbl_30179.p1, internal, 107539, 107682
Valid prediction for snap_scaffold_22-snap.1449-T1
Valid prediction for snap_scaffold_22-snap.1439-T1
Valid prediction for GlimmerHMM_glimmerT_49734-T1
Couldn't classify 108037, 108112
Sorry, prediction pasa_asmbl_30180.p1 fails validation.
(GGC)	 AA	108037-108112	GT	AGG
(GTA)	 AG	108466-108648	GT	AGG
(CTC)	 AG	108746-109399	GT	AGG
(ACT)	 AG	109812-109951	GT	AGG
(ATG)	 AG	110167-110347	GT	CGG
(CCA)	 AG	110576-110877	CG	AGC
-recovered pasa_asmbl_30180.p1, initial, 110167, 110347
-recovered pasa_asmbl_30180.p1, terminal, 110576, 110877
-recovered pasa_asmbl_30180.p1, internal, 108466, 108648
-recovered pasa_asmbl_30180.p1, internal, 108746, 109399
-recovered pasa_asmbl_30180.p1, internal, 109812, 109951
-recovered pasa_asmbl_30180.p1, internal, 110167, 110347
Valid prediction for GlimmerHMM_glimmerT_49725-T1
Valid prediction for HiQ_model.g33176.t1
Valid prediction for GlimmerHMM_glimmerT_49737-T1
Valid prediction for Augustus_model.g33185.t1
Valid prediction for Augustus_model.g33171.t1
Valid prediction for GlimmerHMM_glimmerT_49721-T1
Valid prediction for GlimmerHMM_glimmerT_49717-T1
Couldn't classify 89457, 89631
Couldn't classify 92337, 92510
Sorry, prediction pasa_asmbl_30176.p1 fails validation.
(AGG)	 CC	89457-89631	GT	GGG
(AGT)	 AG	90322-90510	GT	CGG
(GGA)	 AG	90840-91088	GT	AGG
(CGG)	 AG	91215-91333	GT	AGG
(TTT)	 AG	91601-91708	GT	TGG
(ATG)	 AG	92337-92510	TG	CCT
-recovered pasa_asmbl_30176.p1, internal, 90322, 90510
-recovered pasa_asmbl_30176.p1, internal, 90840, 91088
-recovered pasa_asmbl_30176.p1, internal, 91215, 91333
-recovered pasa_asmbl_30176.p1, internal, 91601, 91708
Valid prediction for snap_scaffold_22-snap.1442-T1
Valid prediction for snap_scaffold_22-snap.1441-T1
Valid prediction for GlimmerHMM_glimmerT_49735-T1
Valid prediction for Augustus_model.g33182.t1
Valid prediction for GlimmerHMM_glimmerT_49727-T1
Couldn't classify 94932, 95196
Sorry, prediction pasa_asmbl_30177.p1 fails validation.
(AGC)	 TG	94932-95196	GT	GAG
(CTG)	 AG	95637-95797	GT	AGG
(GTG)	 AG	96017-96153	GT	AGG
(CCT)	 AG	96763-96904	GG	GAG
-recovered pasa_asmbl_30177.p1, terminal, 96763, 96904
-recovered pasa_asmbl_30177.p1, internal, 95637, 95797
-recovered pasa_asmbl_30177.p1, internal, 96017, 96153
Valid prediction for Augustus_model.g33184.t1
Valid prediction for Augustus_model.g33180.t1
Valid prediction for Augustus_model.g33175.t1
Valid prediction for GlimmerHMM_glimmerT_49718-T1
Couldn't classify 136061, 136168
Sorry, prediction pasa_asmbl_30182.p1 fails validation.
(AGG)	 AC	136061-136168	GT	GGG
(GGT)	 AG	136423-136562	GT	GGG
(ACG)	 AG	137240-137351	CG	GAC
-recovered pasa_asmbl_30182.p1, terminal, 137240, 137351
-recovered pasa_asmbl_30182.p1, internal, 136423, 136562
Valid prediction for CodingQuarry_transcript_34208-T1
Couldn't classify 105095, 105418
Sorry, prediction pasa_asmbl_30178.p1 fails validation.
(CCA)	 AG	105095-105418	CC	GGC
Valid prediction for Augustus_model.g33172.t1
Valid prediction for pasa_asmbl_30172.p1
Valid prediction for GlimmerHMM_glimmerT_49720-T1
Valid prediction for Augustus_model.g33181.t1
Valid prediction for snap_scaffold_22-snap.1434-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 GlimmerHMM_glimmerT_49726-T1
Valid prediction for snap_scaffold_22-snap.1446-T1
Valid prediction for Augustus_model.g33178.t1
Couldn't classify 71520, 72167
Sorry, prediction pasa_asmbl_29392.p1 fails validation.
(TGG)	 GA	71520-72167	CA	CGC
Valid prediction for Augustus_model.g33173.t1
Valid prediction for GlimmerHMM_glimmerT_49719-T1
Valid prediction for snap_scaffold_22-snap.1443-T1
Valid prediction for snap_scaffold_22-snap.1436-T1
Valid prediction for CodingQuarry_transcript_34207-T1
Couldn't classify 70125, 70793
Sorry, prediction pasa_asmbl_29394.p1 fails validation.
(GAG)	 CG	70125-70793	CG	TCC
Valid prediction for GlimmerHMM_glimmerT_49716-T1
Valid prediction for pasa_asmbl_29399.p1
Valid prediction for snap_scaffold_22-snap.1450-T1
Couldn't classify 73836, 74186
Sorry, prediction pasa_asmbl_29389.p1 fails validation.
(CAC)	 CC	73836-74186	AG	AGA
Valid prediction for pasa_asmbl_29395.p1
Couldn't classify 72225, 72764
Sorry, prediction pasa_asmbl_29391.p1 fails validation.
(GAG)	 AC	72225-72764	GA	AAG
Valid prediction for snap_scaffold_22-snap.1460-T1
Valid prediction for snap_scaffold_22-snap.1462-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_22-snap.1433-T1
Valid prediction for snap_scaffold_22-snap.1444-T1
Valid prediction for snap_scaffold_22-snap.1457-T1
Valid prediction for snap_scaffold_22-snap.1459-T1
Valid prediction for snap_scaffold_22-snap.1451-T1
Couldn't classify 70926, 71414
Sorry, prediction pasa_asmbl_29393.p2 fails validation.
(GAG)	 CC	70926-71414	GA	GGG
Valid prediction for snap_scaffold_22-snap.1448-T1
Valid prediction for GlimmerHMM_glimmerT_49722-T1
Valid prediction for snap_scaffold_22-snap.1431-T1
Valid prediction for GlimmerHMM_glimmerT_49736-T1
Valid prediction for snap_scaffold_22-snap.1461-T1
Valid prediction for snap_scaffold_22-snap.1437-T1
Valid prediction for snap_scaffold_22-snap.1440-T1
Valid prediction for snap_scaffold_22-snap.1464-T1
Valid prediction for snap_scaffold_22-snap.1452-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49733-T1
Valid prediction for Augustus_model.g33177.t1
Valid prediction for GlimmerHMM_glimmerT_49723-T1
Valid prediction for HiQ_model.g33186.t1
Valid prediction for HiQ_model.g33183.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20940, rend_intergenic: 15794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26527, rend_intergenic: 24880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31493, rend_intergenic: 27291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44628, rend_intergenic: 37220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50330, rend_intergenic: 47748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65096, rend_intergenic: 59446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72150, rend_intergenic: 70214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84492, rend_intergenic: 79974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97653, rend_intergenic: 84677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139245, rend_intergenic: 124622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148687, rend_intergenic: 144263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 152005
-exon list size: 341


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.7    
2.0    
2.3    
2.6    
2.9    
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3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 20940, rend_intergenic: 15794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26527, rend_intergenic: 24880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31493, rend_intergenic: 27291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44628, rend_intergenic: 37220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50330, rend_intergenic: 47748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65096, rend_intergenic: 59446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72150, rend_intergenic: 70214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84492, rend_intergenic: 79974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97653, rend_intergenic: 84677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139245, rend_intergenic: 124622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148687, rend_intergenic: 144263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support