-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_5538593-5724664

-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_21-snap.1108-T1
Valid prediction for GlimmerHMM_glimmerT_47731-T1
Couldn't classify 7925, 8018
Couldn't classify 8243, 8335
Couldn't classify 11029, 11029
Sorry, prediction pasa_asmbl_28577.p1 fails validation.
(ATG)	 GC	7091-7176	GT	GGG
(GCC)	 AG	7925-8018	AT	ACA
(ACA)	 AC	8243-8335	GT	CTG
(GCG)	 AG	8461-8518	GT	TGG
(GTG)	 AG	8614-8665	GT	AAG
(AGA)	 AG	9272-9426	GT	AGG
(GCA)	 AG	9591-9681	GT	AGG
(CGT)	 AG	9806-9871	GT	AAG
(ATG)	 AG	9963-10089	GT	AGG
(GTG)	 AG	10180-10306	GT	AGG
(GAG)	 AG	10477-10521	GT	AGG
(GGA)	 AG	10641-10705	GT	AAG
(GTA)	 AG	10820-10887	GT	TGG
(ACA)	 AG	11029-11029	CA	GAC
-recovered pasa_asmbl_28577.p1, initial, 7091, 7176
add_exon() Sorry, pasa_asmbl_28577.p1 9963-10089-initial-1 is invalid.
-recovered pasa_asmbl_28577.p1, initial, 9963, 10089
-recovered pasa_asmbl_28577.p1, internal, 8461, 8518
-recovered pasa_asmbl_28577.p1, internal, 8614, 8665
-recovered pasa_asmbl_28577.p1, internal, 9272, 9426
-recovered pasa_asmbl_28577.p1, internal, 9591, 9681
-recovered pasa_asmbl_28577.p1, internal, 9806, 9871
-recovered pasa_asmbl_28577.p1, internal, 9963, 10089
-recovered pasa_asmbl_28577.p1, internal, 10180, 10306
-recovered pasa_asmbl_28577.p1, internal, 10477, 10521
-recovered pasa_asmbl_28577.p1, internal, 10641, 10705
-recovered pasa_asmbl_28577.p1, internal, 10820, 10887
Valid prediction for Augustus_model.g31830.t1
Valid prediction for GlimmerHMM_glimmerT_47701-T1
Valid prediction for HiQ_model.g31816.t1
Couldn't classify 7925, 8018
Couldn't classify 8243, 8335
Couldn't classify 11029, 11029
Sorry, prediction CodingQuarry_transcript_32545-T1 fails validation.
(ATG)	 AA	7166-7176	GT	GGG
(GCC)	 AG	7925-8018	AT	ACA
(ACA)	 AC	8243-8335	GT	CTG
(GCG)	 AG	8461-8518	GT	TGG
(GTG)	 AG	8614-8665	GT	AAG
(AGA)	 AG	9272-9426	GT	AGG
(GCA)	 AG	9591-9681	GT	AGG
(CGT)	 AG	9806-9871	GT	AAG
(ATG)	 AG	9963-10089	GT	AGG
(GTG)	 AG	10180-10306	GT	AGG
(GAG)	 AG	10477-10521	GT	AGG
(GGA)	 AG	10641-10705	GT	AAG
(GTA)	 AG	10820-10887	GT	TGG
(ACA)	 AG	11029-11029	CA	GAC
-recovered CodingQuarry_transcript_32545-T1, initial, 7166, 7176
add_exon() Sorry, CodingQuarry_transcript_32545-T1 9963-10089-initial-1 is invalid.
-recovered CodingQuarry_transcript_32545-T1, initial, 9963, 10089
-recovered CodingQuarry_transcript_32545-T1, internal, 8461, 8518
-recovered CodingQuarry_transcript_32545-T1, internal, 8614, 8665
-recovered CodingQuarry_transcript_32545-T1, internal, 9272, 9426
-recovered CodingQuarry_transcript_32545-T1, internal, 9591, 9681
-recovered CodingQuarry_transcript_32545-T1, internal, 9806, 9871
-recovered CodingQuarry_transcript_32545-T1, internal, 9963, 10089
-recovered CodingQuarry_transcript_32545-T1, internal, 10180, 10306
-recovered CodingQuarry_transcript_32545-T1, internal, 10477, 10521
-recovered CodingQuarry_transcript_32545-T1, internal, 10641, 10705
-recovered CodingQuarry_transcript_32545-T1, internal, 10820, 10887
Valid prediction for snap_scaffold_21-snap.1130-T1
Valid prediction for Augustus_model.g31818.t1
Valid prediction for GlimmerHMM_glimmerT_47724-T1
Valid prediction for Augustus_model.g31828.t1
Valid prediction for snap_scaffold_21-snap.1132-T1
Valid prediction for Augustus_model.g31831.t1
Couldn't classify 63542, 63868
Couldn't classify 65593, 65675
Sorry, prediction pasa_asmbl_28584.p1 fails validation.
(CCT)	 GC	63542-63868	GT	AGG
(GGA)	 AG	65155-65272	GT	AGG
(AGA)	 AG	65593-65675	GG	CCG
-recovered pasa_asmbl_28584.p1, internal, 65155, 65272
Valid prediction for Augustus_model.g31833.t1
Valid prediction for snap_scaffold_21-snap.1126-T1
Valid prediction for snap_scaffold_21-snap.1131-T1
Valid prediction for snap_scaffold_21-snap.1134-T1
Valid prediction for GlimmerHMM_glimmerT_47730-T1
Valid prediction for snap_scaffold_21-snap.1118-T1
Valid prediction for Augustus_model.g31817.t1
Valid prediction for GlimmerHMM_glimmerT_47717-T1
Valid prediction for CodingQuarry_transcript_32546-T1
Valid prediction for snap_scaffold_21-snap.1139-T1
Valid prediction for Augustus_model.g31826.t1
Valid prediction for Augustus_model.g31834.t1
Valid prediction for snap_scaffold_21-snap.1129-T1
Valid prediction for GlimmerHMM_glimmerT_47712-T1
Valid prediction for snap_scaffold_21-snap.1120-T1
Valid prediction for GlimmerHMM_glimmerT_47713-T1
Valid prediction for snap_scaffold_21-snap.1111-T1
Valid prediction for GlimmerHMM_glimmerT_47727-T1
Valid prediction for GlimmerHMM_glimmerT_47709-T1
Valid prediction for snap_scaffold_21-snap.1127-T1
Valid prediction for pasa_asmbl_28581.p1
Valid prediction for GlimmerHMM_glimmerT_47729-T1
Valid prediction for GlimmerHMM_glimmerT_47720-T1
Valid prediction for Augustus_model.g31819.t1
Valid prediction for GlimmerHMM_glimmerT_47723-T1
Valid prediction for Augustus_model.g31822.t1
Valid prediction for snap_scaffold_21-snap.1133-T1
Valid prediction for snap_scaffold_21-snap.1128-T1
Valid prediction for GlimmerHMM_glimmerT_47705-T1
Valid prediction for GlimmerHMM_glimmerT_47734-T1
Valid prediction for GlimmerHMM_glimmerT_47703-T1
Valid prediction for HiQ_model.g31815.t1
Valid prediction for GlimmerHMM_glimmerT_47725-T1
Valid prediction for snap_scaffold_21-snap.1114-T1
Valid prediction for snap_scaffold_21-snap.1122-T1
Valid prediction for GlimmerHMM_glimmerT_47718-T1
Valid prediction for snap_scaffold_21-snap.1124-T1
Valid prediction for snap_scaffold_21-snap.1115-T1
Valid prediction for GlimmerHMM_glimmerT_47706-T1
Valid prediction for snap_scaffold_21-snap.1103-T1
Valid prediction for Augustus_model.g31835.t1
Valid prediction for snap_scaffold_21-snap.1102-T1
Valid prediction for GlimmerHMM_glimmerT_47710-T1
Valid prediction for snap_scaffold_21-snap.1104-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_27682.p1
Valid prediction for snap_scaffold_21-snap.1110-T1
Valid prediction for snap_scaffold_21-snap.1106-T1
Valid prediction for Augustus_model.g31839.t1
Valid prediction for HiQ_model.g31824.t1
Valid prediction for snap_scaffold_21-snap.1117-T1
Valid prediction for snap_scaffold_21-snap.1135-T1
Valid prediction for GlimmerHMM_glimmerT_47702-T1
Valid prediction for snap_scaffold_21-snap.1125-T1
Couldn't classify 91984, 92039
Sorry, prediction pasa_asmbl_27685.p1 fails validation.
(GAC)	 AC	91984-92039	GT	CGG
(GAC)	 AG	92169-92373	GT	AGG
(AAA)	 AG	92646-92747	GT	TGG
(AGA)	 AG	92845-92916	GT	AAG
(GTG)	 AG	93022-93228	GT	GAG
-recovered pasa_asmbl_27685.p1, terminal, 93022, 93228
-recovered pasa_asmbl_27685.p1, internal, 92169, 92373
-recovered pasa_asmbl_27685.p1, internal, 92646, 92747
-recovered pasa_asmbl_27685.p1, internal, 92845, 92916
-recovered pasa_asmbl_27685.p1, internal, 93022, 93228
Valid prediction for snap_scaffold_21-snap.1121-T1
Valid prediction for Augustus_model.g31829.t1
Valid prediction for GlimmerHMM_glimmerT_47700-T1
Valid prediction for GlimmerHMM_glimmerT_47711-T1
Valid prediction for GlimmerHMM_glimmerT_47714-T1
Valid prediction for Augustus_model.g31837.t1
Valid prediction for CodingQuarry_transcript_32547-T1
Valid prediction for GlimmerHMM_glimmerT_47704-T1
Valid prediction for Augustus_model.g31832.t1
Valid prediction for snap_scaffold_21-snap.1107-T1
Valid prediction for GlimmerHMM_glimmerT_47728-T1
Valid prediction for snap_scaffold_21-snap.1123-T1
Valid prediction for GlimmerHMM_glimmerT_47722-T1
Valid prediction for HiQ_model.g31820.t1
Valid prediction for snap_scaffold_21-snap.1109-T1
Valid prediction for GlimmerHMM_glimmerT_47719-T1
Valid prediction for Augustus_model.g31825.t1
Valid prediction for snap_scaffold_21-snap.1119-T1
Valid prediction for snap_scaffold_21-snap.1116-T1
Valid prediction for snap_scaffold_21-snap.1140-T1
Valid prediction for Augustus_model.g31814.t1
Valid prediction for snap_scaffold_21-snap.1137-T1
Valid prediction for snap_scaffold_21-snap.1112-T1
Valid prediction for GlimmerHMM_glimmerT_47726-T1
Valid prediction for pasa_asmbl_27677.p1
Valid prediction for GlimmerHMM_glimmerT_47735-T1
Valid prediction for pasa_asmbl_27679.p1
Valid prediction for Augustus_model.g31823.t1
Valid prediction for snap_scaffold_21-snap.1138-T1
Couldn't classify 9841, 9954
Sorry, prediction pasa_asmbl_27688.p1 fails validation.
(ATG)	 GC	7277-7373	GT	AGG
(GTC)	 AG	7638-7805	GT	TGG
(GTG)	 AG	9339-9625	GT	AGG
(GTG)	 AG	9841-9954	AA	GCA
-recovered pasa_asmbl_27688.p1, initial, 7277, 7373
-recovered pasa_asmbl_27688.p1, internal, 7638, 7805
-recovered pasa_asmbl_27688.p1, internal, 9339, 9625
Valid prediction for GlimmerHMM_glimmerT_47715-T1
Valid prediction for GlimmerHMM_glimmerT_47721-T1
Valid prediction for snap_scaffold_21-snap.1113-T1
Valid prediction for GlimmerHMM_glimmerT_47716-T1
Valid prediction for Augustus_model.g31827.t1
Couldn't classify 10228, 10296
Sorry, prediction pasa_asmbl_27687.p1 fails validation.
(CCA)	 CC	10228-10296	GT	AGG
(GTG)	 AG	11304-11479	GT	ATG
(ACA)	 AG	11686-12481	TG	AGT
-recovered pasa_asmbl_27687.p1, terminal, 11686, 12481
-recovered pasa_asmbl_27687.p1, internal, 11304, 11479
Valid prediction for snap_scaffold_21-snap.1105-T1
Valid prediction for CodingQuarry_transcript_32548-T1
Valid prediction for GlimmerHMM_glimmerT_47707-T1
Valid prediction for snap_scaffold_21-snap.1136-T1
Valid prediction for GlimmerHMM_glimmerT_47708-T1
Valid prediction for Augustus_model.g31838.t1
Valid prediction for GlimmerHMM_glimmerT_47733-T1
Valid prediction for HiQ_model.g31821.t1
Valid prediction for snap_scaffold_21-snap.1101-T1
Valid prediction for snap_scaffold_21-snap.1141-T1
Valid prediction for GlimmerHMM_glimmerT_47732-T1
Valid prediction for Augustus_model.g31836.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37615, rend_intergenic: 25890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47955, rend_intergenic: 40347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52690, rend_intergenic: 48839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63079, rend_intergenic: 59430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102686, rend_intergenic: 102372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106604, rend_intergenic: 104351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156435, rend_intergenic: 152280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186072
-exon list size: 378


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.2    
3.4    
3.7    
3.9    
4.2    
4.5    
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5.0    
5.3    
5.5    
5.8    
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6.3    
6.6    
6.8    
7.1    
7.4    
7.6    
7.9    
8.2    
8.4    
8.7    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.5    
10.8    
11.1    
11.3    
11.6    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.4    
13.7    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.4    
22.6    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.3    
26.6    
26.8    
27.1    
27.4    
27.6    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.5    
29.7    
30.0    
30.3    
30.5    
30.8    
31.1    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.5    
44.7    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.3    
55.5    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.4    
68.7    
68.9    
69.2    
69.5    
69.7    
70.0    
70.3    
70.5    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.4    
72.6    
72.9    
73.2    
73.4    
73.7    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.4    
77.6    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.3    
86.6    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.5    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.5    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 37615, rend_intergenic: 25890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47955, rend_intergenic: 40347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52690, rend_intergenic: 48839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63079, rend_intergenic: 59430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102686, rend_intergenic: 102372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106604, rend_intergenic: 104351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156435, rend_intergenic: 152280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support