-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_5697320-5835099

-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_9-snap.1214-T1
Valid prediction for snap_scaffold_9-snap.1192-T1
Valid prediction for GlimmerHMM_glimmerT_22211-T1
Valid prediction for snap_scaffold_9-snap.1197-T1
Valid prediction for snap_scaffold_9-snap.1219-T1
Valid prediction for GlimmerHMM_glimmerT_22201-T1
Valid prediction for snap_scaffold_9-snap.1201-T1
Valid prediction for GlimmerHMM_glimmerT_22219-T1
Valid prediction for Augustus_model.g14770.t1
Valid prediction for GlimmerHMM_glimmerT_22202-T1
Valid prediction for GlimmerHMM_glimmerT_22207-T1
Valid prediction for GlimmerHMM_glimmerT_22221-T1
Valid prediction for GlimmerHMM_glimmerT_22212-T1
Valid prediction for HiQ_model.g14768.t1
Couldn't classify 96927, 97288
Sorry, prediction pasa_asmbl_54068.p1 fails validation.
(AGA)	 TG	96927-97288	GT	GCG
(GAG)	 AG	97466-97710	GT	AGG
(CCA)	 AG	97801-97968	GT	GGG
(GCT)	 AG	98614-99209	TT	GAT
add_exon() Sorry, pasa_asmbl_54068.p1 97466-97710-terminal-2 is invalid.
-recovered pasa_asmbl_54068.p1, terminal, 97466, 97710
-recovered pasa_asmbl_54068.p1, terminal, 98614, 99209
-recovered pasa_asmbl_54068.p1, internal, 97466, 97710
-recovered pasa_asmbl_54068.p1, internal, 97801, 97968
Valid prediction for snap_scaffold_9-snap.1223-T1
Valid prediction for snap_scaffold_9-snap.1220-T1
Valid prediction for GlimmerHMM_glimmerT_22222-T1
Valid prediction for Augustus_model.g14771.t1
Valid prediction for GlimmerHMM_glimmerT_22220-T1
Valid prediction for snap_scaffold_9-snap.1217-T1
Valid prediction for snap_scaffold_9-snap.1222-T1
Valid prediction for GlimmerHMM_glimmerT_22214-T1
Valid prediction for snap_scaffold_9-snap.1225-T1
Valid prediction for Augustus_model.g14772.t1
Valid prediction for snap_scaffold_9-snap.1203-T1
Valid prediction for snap_scaffold_9-snap.1213-T1
Valid prediction for snap_scaffold_9-snap.1210-T1
Valid prediction for snap_scaffold_9-snap.1211-T1
Valid prediction for snap_scaffold_9-snap.1194-T1
Valid prediction for snap_scaffold_9-snap.1193-T1
Valid prediction for GlimmerHMM_glimmerT_22203-T1
Valid prediction for GlimmerHMM_glimmerT_22223-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 CodingQuarry_transcript_62188-T1
Valid prediction for snap_scaffold_9-snap.1218-T1
Valid prediction for GlimmerHMM_glimmerT_22215-T1
Valid prediction for GlimmerHMM_glimmerT_22200-T1
Valid prediction for GlimmerHMM_glimmerT_22205-T1
Valid prediction for Augustus_model.g14765.t1
Valid prediction for snap_scaffold_9-snap.1195-T1
Valid prediction for Augustus_model.g14761.t1
Couldn't classify 52215, 52409
Couldn't classify 52814, 52988
Sorry, prediction pasa_asmbl_55035.p1 fails validation.
(TCT)	 TA	52215-52409	GT	AGG
(GAC)	 AG	52569-52687	GT	AAG
(GTA)	 AG	52814-52988	AA	AGA
-recovered pasa_asmbl_55035.p1, internal, 52569, 52687
Valid prediction for Augustus_model.g14759.t1
Valid prediction for snap_scaffold_9-snap.1212-T1
Valid prediction for GlimmerHMM_glimmerT_22199-T1
Valid prediction for Augustus_model.g14760.t1
Couldn't classify 122558, 122600
Couldn't classify 126171, 126436
Sorry, prediction pasa_asmbl_55025.p1 fails validation.
(AGT)	 GC	122558-122600	GT	AGG
(GCA)	 AG	123808-123950	GT	AGG
(GGT)	 AG	124519-124646	GT	CAG
(GAA)	 AG	124919-125024	GT	AGG
(ACA)	 AG	125450-125561	GT	AGG
(ACT)	 AG	126171-126436	CC	CCC
-recovered pasa_asmbl_55025.p1, internal, 123808, 123950
-recovered pasa_asmbl_55025.p1, internal, 124519, 124646
-recovered pasa_asmbl_55025.p1, internal, 124919, 125024
-recovered pasa_asmbl_55025.p1, internal, 125450, 125561
Valid prediction for GlimmerHMM_glimmerT_22210-T1
Valid prediction for snap_scaffold_9-snap.1216-T1
Valid prediction for Augustus_model.g14766.t1
Couldn't classify 26315, 26378
Couldn't classify 32141, 32223
Sorry, prediction pasa_asmbl_55039.p1 fails validation.
(GAC)	 TG	26315-26378	GT	AGG
(GTC)	 AG	27660-27793	GT	GGG
(TGC)	 AG	29486-29586	GT	AGG
(GTC)	 AG	29735-29841	GT	AGG
(GGA)	 AG	31032-31211	GT	GGG
(ACG)	 AG	32141-32223	AA	CCA
-recovered pasa_asmbl_55039.p1, internal, 27660, 27793
-recovered pasa_asmbl_55039.p1, internal, 29486, 29586
-recovered pasa_asmbl_55039.p1, internal, 29735, 29841
-recovered pasa_asmbl_55039.p1, internal, 31032, 31211
Valid prediction for snap_scaffold_9-snap.1205-T1
Valid prediction for snap_scaffold_9-snap.1198-T1
Couldn't classify 128974, 128983
Couldn't classify 133478, 133932
Sorry, prediction pasa_asmbl_55024.p1 fails validation.
(CTC)	 GT	128974-128983	GT	AGG
(AGA)	 AG	129195-129391	GT	AGG
(AGT)	 AG	130215-130427	GT	AGG
(GGG)	 AG	130513-130655	GT	AGG
(CTC)	 AG	131606-131724	GT	AGG
(ATT)	 AG	132458-132520	GT	AGG
(GGG)	 AG	133478-133932	TT	ACT
-recovered pasa_asmbl_55024.p1, terminal, 132458, 132520
-recovered pasa_asmbl_55024.p1, internal, 129195, 129391
-recovered pasa_asmbl_55024.p1, internal, 130215, 130427
-recovered pasa_asmbl_55024.p1, internal, 130513, 130655
-recovered pasa_asmbl_55024.p1, internal, 131606, 131724
-recovered pasa_asmbl_55024.p1, internal, 132458, 132520
Valid prediction for snap_scaffold_9-snap.1206-T1
Valid prediction for snap_scaffold_9-snap.1204-T1
Valid prediction for Augustus_model.g14764.t1
Couldn't classify 133987, 134442
Sorry, prediction pasa_asmbl_55023.p1 fails validation.
(GGG)	 GC	133987-134442	GG	CAG
Valid prediction for HiQ_model.g14763.t1
Valid prediction for snap_scaffold_9-snap.1199-T1
Valid prediction for snap_scaffold_9-snap.1202-T1
Valid prediction for snap_scaffold_9-snap.1196-T1
Valid prediction for GlimmerHMM_glimmerT_22208-T1
Valid prediction for snap_scaffold_9-snap.1227-T1
Valid prediction for Augustus_model.g14769.t1
Valid prediction for GlimmerHMM_glimmerT_22198-T1
Valid prediction for CodingQuarry_transcript_62189-T1
Valid prediction for Augustus_model.g14758.t1
Valid prediction for snap_scaffold_9-snap.1215-T1
Valid prediction for snap_scaffold_9-snap.1200-T1
Valid prediction for GlimmerHMM_glimmerT_22209-T1
Valid prediction for GlimmerHMM_glimmerT_22204-T1
Valid prediction for GlimmerHMM_glimmerT_22206-T1
Valid prediction for snap_scaffold_9-snap.1208-T1
Valid prediction for snap_scaffold_9-snap.1207-T1
Valid prediction for CodingQuarry_transcript_62191-T1
Valid prediction for GlimmerHMM_glimmerT_22216-T1
Valid prediction for GlimmerHMM_glimmerT_22217-T1
Valid prediction for GlimmerHMM_glimmerT_22218-T1
Couldn't classify 54295, 54589
Couldn't classify 55804, 55838
Sorry, prediction pasa_asmbl_55034.p1 fails validation.
(GTG)	 AA	54295-54589	GT	AGG
(GGA)	 AG	54695-54852	GT	AGG
(ATG)	 AG	55036-55242	GT	AGG
(GTG)	 AG	55486-55585	GT	AGG
(ACT)	 AG	55804-55838	CA	AGC
-recovered pasa_asmbl_55034.p1, initial, 55036, 55242
-recovered pasa_asmbl_55034.p1, internal, 54695, 54852
-recovered pasa_asmbl_55034.p1, internal, 55036, 55242
-recovered pasa_asmbl_55034.p1, internal, 55486, 55585
Valid prediction for pasa_asmbl_55029.p1
Valid prediction for snap_scaffold_9-snap.1209-T1
Valid prediction for snap_scaffold_9-snap.1224-T1
Valid prediction for snap_scaffold_9-snap.1221-T1
Valid prediction for pasa_asmbl_55036.p1
Valid prediction for HiQ_model.g14762.t1
Valid prediction for snap_scaffold_9-snap.1226-T1
Couldn't classify 55908, 55986
Sorry, prediction pasa_asmbl_55033.p1 fails validation.
(CCT)	 AC	55908-55986	GT	TGG
(GAG)	 AG	56305-56426	GT	AGG
(GAG)	 AG	56565-56720	GT	GGG
(GCC)	 AG	57115-57236	GT	AGG
(GTG)	 AG	57360-57540	GT	AGG
(CTG)	 AG	58017-58103	GT	AGG
(GTG)	 AG	58731-58841	GT	AGG
(GTC)	 AG	58944-59079	GT	TGG
(GTA)	 AG	59453-59580	GT	AGG
(CAT)	 AG	59734-59835	GT	AGG
(GGA)	 AG	60348-60482	GT	AGG
(ATG)	 AG	60831-61016	CG	GAC
-recovered pasa_asmbl_55033.p1, terminal, 60831, 61016
-recovered pasa_asmbl_55033.p1, internal, 56305, 56426
-recovered pasa_asmbl_55033.p1, internal, 56565, 56720
-recovered pasa_asmbl_55033.p1, internal, 57115, 57236
-recovered pasa_asmbl_55033.p1, internal, 57360, 57540
-recovered pasa_asmbl_55033.p1, internal, 58017, 58103
-recovered pasa_asmbl_55033.p1, internal, 58731, 58841
-recovered pasa_asmbl_55033.p1, internal, 58944, 59079
-recovered pasa_asmbl_55033.p1, internal, 59453, 59580
-recovered pasa_asmbl_55033.p1, internal, 59734, 59835
-recovered pasa_asmbl_55033.p1, internal, 60348, 60482
Valid prediction for HiQ_model.g14767.t1
Valid prediction for GlimmerHMM_glimmerT_22213-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31731, rend_intergenic: 28864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32565, rend_intergenic: 31999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93494, rend_intergenic: 81373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105841, rend_intergenic: 103748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107851, rend_intergenic: 106598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111984, rend_intergenic: 109151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126844, rend_intergenic: 124262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 137780
-exon list size: 342


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
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 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 31731, rend_intergenic: 28864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32565, rend_intergenic: 31999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93494, rend_intergenic: 81373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105841, rend_intergenic: 103748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107851, rend_intergenic: 106598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111984, rend_intergenic: 109151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126844, rend_intergenic: 124262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support