-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_5907459-6108043

-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_6-snap.1362-T1
Valid prediction for Augustus_model.g9761.t1
Couldn't classify 11653, 12132
Sorry, prediction pasa_asmbl_46981.p1 fails validation.
(GGC)	 CT	11653-12132	AC	AGA
Couldn't classify 4436, 4529
Couldn't classify 5189, 5278
Sorry, prediction pasa_asmbl_47881.p2 fails validation.
(ATT)	 AG	4436-4529	GT	CGG
(CTC)	 AG	4705-4838	GT	AGG
(ATT)	 AG	5189-5278	CA	GAC
-recovered pasa_asmbl_47881.p2, internal, 4436, 4529
-recovered pasa_asmbl_47881.p2, internal, 4705, 4838
Couldn't classify 21218, 21248
Sorry, prediction pasa_asmbl_46982.p1 fails validation.
(TCT)	 CC	21218-21248	GT	AGG
(GAC)	 AG	22205-22288	GT	AGG
(GTG)	 AG	22749-22877	GT	GGG
(TGC)	 AG	23085-23198	GT	AGG
(GCT)	 AG	23641-23723	CG	GAC
-recovered pasa_asmbl_46982.p1, terminal, 23641, 23723
-recovered pasa_asmbl_46982.p1, internal, 22205, 22288
-recovered pasa_asmbl_46982.p1, internal, 22749, 22877
-recovered pasa_asmbl_46982.p1, internal, 23085, 23198
Valid prediction for snap_scaffold_6-snap.1373-T1
Valid prediction for snap_scaffold_6-snap.1348-T1
Valid prediction for GlimmerHMM_glimmerT_14737-T1
Valid prediction for GlimmerHMM_glimmerT_14720-T1
Valid prediction for GlimmerHMM_glimmerT_14736-T1
Couldn't classify 196121, 196268
Sorry, prediction pasa_asmbl_47903.p1 fails validation.
(GGG)	 GG	196121-196268	GT	CCG
(ATA)	 AG	196573-196655	GT	AGG
(GAG)	 AG	196766-196843	GT	GAG
(TAT)	 AG	196959-197024	GT	AGG
(GTG)	 AG	197175-197240	GT	CAG
(GAA)	 AG	197429-197517	GT	AGG
(ACT)	 AG	197722-197848	AA	AGA
-recovered pasa_asmbl_47903.p1, terminal, 197722, 197848
-recovered pasa_asmbl_47903.p1, internal, 196573, 196655
-recovered pasa_asmbl_47903.p1, internal, 196766, 196843
-recovered pasa_asmbl_47903.p1, internal, 196959, 197024
-recovered pasa_asmbl_47903.p1, internal, 197175, 197240
-recovered pasa_asmbl_47903.p1, internal, 197429, 197517
Valid prediction for snap_scaffold_6-snap.1370-T1
Valid prediction for GlimmerHMM_glimmerT_14743-T1
Valid prediction for Augustus_model.g9763.t1
Couldn't classify 181978, 182049
Couldn't classify 182288, 182521
Sorry, prediction pasa_asmbl_47967.p2 fails validation.
(TCA)	 GA	181978-182049	GT	AGG
(GTG)	 AG	182288-182521	GA	TGG
Couldn't classify 3533, 3646
Couldn't classify 4120, 4176
Sorry, prediction pasa_asmbl_47950.p1 fails validation.
(AAG)	 GC	3533-3646	GT	AGG
(GTG)	 AG	3777-4013	GT	AGG
(GTG)	 AG	4120-4176	CA	GTC
-recovered pasa_asmbl_47950.p1, internal, 3777, 4013
Valid prediction for HiQ_model.g9766.t1
Valid prediction for snap_scaffold_6-snap.1342-T1
Valid prediction for Augustus_model.g9768.t1
Valid prediction for GlimmerHMM_glimmerT_14742-T1
Valid prediction for GlimmerHMM_glimmerT_14732-T1
Valid prediction for snap_scaffold_6-snap.1367-T1
Valid prediction for CodingQuarry_transcript_55071-T1
Couldn't classify 2101, 2169
Couldn't classify 2499, 2675
Sorry, prediction pasa_asmbl_47894.p1 fails validation.
(CTG)	 TC	2101-2169	GT	AGG
(GAC)	 AG	2272-2352	GT	AGG
(GGT)	 AG	2499-2675	CT	TGC
-recovered pasa_asmbl_47894.p1, internal, 2272, 2352
Valid prediction for snap_scaffold_6-snap.1346-T1
Valid prediction for GlimmerHMM_glimmerT_14731-T1
Valid prediction for snap_scaffold_6-snap.1338-T1
Valid prediction for Augustus_model.g9767.t1
Valid prediction for snap_scaffold_6-snap.1371-T1
Valid prediction for snap_scaffold_6-snap.1368-T1
Valid prediction for Augustus_model.g9764.t1
Valid prediction for snap_scaffold_6-snap.1345-T1
Valid prediction for snap_scaffold_6-snap.1347-T1
Valid prediction for snap_scaffold_6-snap.1365-T1
Valid prediction for HiQ_model.g9750.t1
Valid prediction for snap_scaffold_6-snap.1334-T1
Valid prediction for Augustus_model.g9765.t1
Valid prediction for snap_scaffold_6-snap.1355-T1
Valid prediction for GlimmerHMM_glimmerT_14738-T1
Valid prediction for snap_scaffold_6-snap.1366-T1
Valid prediction for GlimmerHMM_glimmerT_14726-T1
Valid prediction for GlimmerHMM_glimmerT_14730-T1
Valid prediction for GlimmerHMM_glimmerT_14741-T1
Valid prediction for CodingQuarry_transcript_55064-T1
Valid prediction for GlimmerHMM_glimmerT_14727-T1
Valid prediction for GlimmerHMM_glimmerT_14733-T1
Valid prediction for snap_scaffold_6-snap.1364-T1
Couldn't classify 168500, 168594
Sorry, prediction pasa_asmbl_46991.p1 fails validation.
(GAA)	 AG	168500-168594	GT	CTG
(TAC)	 AG	168834-168907	GT	AGG
(GTG)	 AG	169027-169097	GT	GAG
(AAA)	 AG	169229-169408	GT	AGG
(AAG)	 AG	169799-170020	GT	ATG
(GCG)	 AG	170211-170303	GT	TGG
(GGA)	 AG	170440-170603	GT	AGG
(GGA)	 AG	170993-171155	GC	GAG
-recovered pasa_asmbl_46991.p1, terminal, 170993, 171155
-recovered pasa_asmbl_46991.p1, internal, 168500, 168594
-recovered pasa_asmbl_46991.p1, internal, 168834, 168907
-recovered pasa_asmbl_46991.p1, internal, 169027, 169097
-recovered pasa_asmbl_46991.p1, internal, 169229, 169408
-recovered pasa_asmbl_46991.p1, internal, 169799, 170020
-recovered pasa_asmbl_46991.p1, internal, 170211, 170303
-recovered pasa_asmbl_46991.p1, internal, 170440, 170603
-recovered pasa_asmbl_46991.p1, internal, 170993, 171155
Valid prediction for Augustus_model.g9757.t1
Valid prediction for GlimmerHMM_glimmerT_14739-T1
Valid prediction for GlimmerHMM_glimmerT_14721-T1
Valid prediction for GlimmerHMM_glimmerT_14735-T1
Valid prediction for snap_scaffold_6-snap.1350-T1
Valid prediction for CodingQuarry_transcript_55069-T1
Valid prediction for snap_scaffold_6-snap.1344-T1
Valid prediction for GlimmerHMM_glimmerT_14734-T1
Valid prediction for snap_scaffold_6-snap.1358-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 pasa_asmbl_48444.p1
Valid prediction for HiQ_model.g9752.t1
Valid prediction for GlimmerHMM_glimmerT_14719-T1
Valid prediction for snap_scaffold_6-snap.1333-T1
Valid prediction for Augustus_model.g9755.t1
Valid prediction for HiQ_model.g9758.t1
Valid prediction for Augustus_model.g9759.t1
Valid prediction for snap_scaffold_6-snap.1340-T1
Valid prediction for snap_scaffold_6-snap.1353-T1
Valid prediction for Augustus_model.g9749.t1
Couldn't classify 162887, 162955
Couldn't classify 163853, 163885
Sorry, prediction pasa_asmbl_48442.p1 fails validation.
(CTG)	 AT	162887-162955	GT	AGG
(CTG)	 AG	163202-163274	GT	GCG
(ATG)	 AG	163468-163622	GT	AGG
(ATG)	 AG	163853-163885	CC	AGC
add_exon() Sorry, pasa_asmbl_48442.p1 163468-163622-initial-1 is invalid.
-recovered pasa_asmbl_48442.p1, initial, 163468, 163622
-recovered pasa_asmbl_48442.p1, internal, 163202, 163274
-recovered pasa_asmbl_48442.p1, internal, 163468, 163622
Valid prediction for snap_scaffold_6-snap.1361-T1
Valid prediction for HiQ_model.g9760.t1
Valid prediction for snap_scaffold_6-snap.1369-T1
Valid prediction for snap_scaffold_6-snap.1335-T1
Valid prediction for Augustus_model.g9756.t1
Valid prediction for GlimmerHMM_glimmerT_14725-T1
Valid prediction for snap_scaffold_6-snap.1357-T1
Valid prediction for CodingQuarry_transcript_55067-T1
Couldn't classify 86267, 86473
Sorry, prediction pasa_asmbl_48449.p1 fails validation.
(GCG)	 CT	86267-86473	GT	GGG
(ATA)	 AG	87371-87608	GT	AGG
(GAC)	 AG	87753-87889	GT	GGG
(GGT)	 AG	88101-88307	AA	AAA
-recovered pasa_asmbl_48449.p1, terminal, 88101, 88307
-recovered pasa_asmbl_48449.p1, internal, 87371, 87608
-recovered pasa_asmbl_48449.p1, internal, 87753, 87889
Valid prediction for Augustus_model.g9751.t1
Valid prediction for snap_scaffold_6-snap.1363-T1
Couldn't classify 95862, 95967
Couldn't classify 96488, 96546
Sorry, prediction pasa_asmbl_48448.p1 fails validation.
(CCC)	 CC	95862-95967	GT	GAG
(ACG)	 AG	96164-96340	GT	CGG
(TGC)	 AG	96488-96546	GA	CCG
-recovered pasa_asmbl_48448.p1, internal, 96164, 96340
Couldn't classify 172087, 172256
Sorry, prediction pasa_asmbl_48439.p1 fails validation.
(ATG)	 AG	168001-168007	GT	AAG
(AAA)	 AG	168252-168295	GT	CAG
(CAA)	 AG	168984-169082	GT	GGG
(AAT)	 AG	170029-170109	GT	AGG
(GTA)	 AG	170595-170726	GT	AGG
(ATC)	 AG	170858-171029	GT	TGG
(ACT)	 AG	171158-171330	GT	AGG
(AGA)	 AG	171429-171530	GT	GGG
(CTG)	 AG	171667-171952	GT	AGG
(ATG)	 AG	172087-172256	GC	CCG
-recovered pasa_asmbl_48439.p1, initial, 168001, 168007
-recovered pasa_asmbl_48439.p1, initial, 172087, 172256
-recovered pasa_asmbl_48439.p1, internal, 168001, 168007
-recovered pasa_asmbl_48439.p1, internal, 168252, 168295
-recovered pasa_asmbl_48439.p1, internal, 168984, 169082
-recovered pasa_asmbl_48439.p1, internal, 170029, 170109
-recovered pasa_asmbl_48439.p1, internal, 170595, 170726
-recovered pasa_asmbl_48439.p1, internal, 170858, 171029
-recovered pasa_asmbl_48439.p1, internal, 171158, 171330
-recovered pasa_asmbl_48439.p1, internal, 171429, 171530
-recovered pasa_asmbl_48439.p1, internal, 171667, 171952
-recovered pasa_asmbl_48439.p1, internal, 172087, 172256
Valid prediction for Augustus_model.g9753.t1
Valid prediction for GlimmerHMM_glimmerT_14729-T1
Valid prediction for GlimmerHMM_glimmerT_14724-T1
Valid prediction for pasa_asmbl_48437.p1
Valid prediction for snap_scaffold_6-snap.1351-T1
Valid prediction for snap_scaffold_6-snap.1339-T1
Valid prediction for CodingQuarry_transcript_55063-T1
Valid prediction for Augustus_model.g9754.t1
Valid prediction for snap_scaffold_6-snap.1337-T1
Valid prediction for Augustus_model.g9762.t1
Valid prediction for snap_scaffold_6-snap.1332-T1
Valid prediction for snap_scaffold_6-snap.1349-T1
Valid prediction for snap_scaffold_6-snap.1343-T1
Couldn't classify 96937, 97049
Sorry, prediction pasa_asmbl_48446.p1 fails validation.
(GGA)	 AA	96937-97049	GT	AGG
(CTC)	 AG	97282-97518	GT	AGG
(TGT)	 AG	97625-97707	GT	TGG
(GGA)	 AG	98166-98238	GT	AGG
(GCA)	 AG	98495-98591	GT	AGG
(CCG)	 AG	98871-99044	GG	GAG
-recovered pasa_asmbl_48446.p1, terminal, 98871, 99044
-recovered pasa_asmbl_48446.p1, internal, 97282, 97518
-recovered pasa_asmbl_48446.p1, internal, 97625, 97707
-recovered pasa_asmbl_48446.p1, internal, 98166, 98238
-recovered pasa_asmbl_48446.p1, internal, 98495, 98591
Valid prediction for CodingQuarry_transcript_55068-T1
Valid prediction for GlimmerHMM_glimmerT_14728-T1
Valid prediction for GlimmerHMM_glimmerT_14740-T1
Valid prediction for snap_scaffold_6-snap.1360-T1
Valid prediction for snap_scaffold_6-snap.1352-T1
Valid prediction for snap_scaffold_6-snap.1356-T1
Valid prediction for snap_scaffold_6-snap.1372-T1
Valid prediction for snap_scaffold_6-snap.1354-T1
Valid prediction for GlimmerHMM_glimmerT_14723-T1
Valid prediction for snap_scaffold_6-snap.1336-T1
Valid prediction for GlimmerHMM_glimmerT_14722-T1
Valid prediction for snap_scaffold_6-snap.1359-T1
Valid prediction for snap_scaffold_6-snap.1341-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 63501, rend_intergenic: 60734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121304, rend_intergenic: 119916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135495, rend_intergenic: 132151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148299, rend_intergenic: 146185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180960, rend_intergenic: 176993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200585
-exon list size: 344


building trellis

0.3    
0.6    
0.9    
1.2    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
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    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
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    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.8    
99.1    
99.4    
99.7    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 63501, rend_intergenic: 60734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121304, rend_intergenic: 119916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135495, rend_intergenic: 132151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148299, rend_intergenic: 146185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180960, rend_intergenic: 176993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support