-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_17737175-17913039

-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_3-snap.3479-T1
Valid prediction for snap_scaffold_3-snap.3493-T1
Valid prediction for HiQ_model.g5438.t1
Couldn't classify 103391, 103414
Sorry, prediction pasa_asmbl_40703.p1 fails validation.
(ATG)	 CC	102697-103002	GT	AGG
(TGG)	 AG	103391-103414	AC	CTA
-recovered pasa_asmbl_40703.p1, initial, 102697, 103002
Valid prediction for GlimmerHMM_glimmerT_8248-T1
Valid prediction for snap_scaffold_3-snap.3481-T1
Valid prediction for snap_scaffold_3-snap.3461-T1
Valid prediction for Augustus_model.g5444.t1
Valid prediction for snap_scaffold_3-snap.3452-T1
Couldn't classify 128335, 128461
Sorry, prediction pasa_asmbl_40712.p1 fails validation.
(ATG)	 AA	125811-125825	GT	AGG
(GCA)	 AG	125927-126018	GT	GGG
(GAA)	 AG	127603-127746	GT	AGG
(CAA)	 AG	128335-128461	CG	CAC
-recovered pasa_asmbl_40712.p1, initial, 125811, 125825
-recovered pasa_asmbl_40712.p1, internal, 125927, 126018
-recovered pasa_asmbl_40712.p1, internal, 127603, 127746
Valid prediction for snap_scaffold_3-snap.3472-T1
Valid prediction for GlimmerHMM_glimmerT_8266-T1
Valid prediction for GlimmerHMM_glimmerT_8272-T1
Valid prediction for snap_scaffold_3-snap.3484-T1
Valid prediction for Augustus_model.g5429.t1
Valid prediction for snap_scaffold_3-snap.3456-T1
Valid prediction for snap_scaffold_3-snap.3459-T1
Valid prediction for snap_scaffold_3-snap.3492-T1
Couldn't classify 47823, 47906
Couldn't classify 50715, 50775
Sorry, prediction pasa_asmbl_40696.p1 fails validation.
(TGT)	 AC	47823-47906	GT	AGG
(TTA)	 AG	48991-49134	GT	AGG
(GAG)	 AG	50114-50292	GT	GTG
(TCC)	 AG	50715-50775	AC	TCA
-recovered pasa_asmbl_40696.p1, internal, 48991, 49134
-recovered pasa_asmbl_40696.p1, internal, 50114, 50292
Valid prediction for Augustus_model.g5434.t1
Valid prediction for CodingQuarry_transcript_46455-T1
Valid prediction for CodingQuarry_transcript_46462-T1
Valid prediction for HiQ_model.g5443.t1
Valid prediction for snap_scaffold_3-snap.3465-T1
Valid prediction for GlimmerHMM_glimmerT_8259-T1
Valid prediction for pasa_asmbl_40692.p1
Valid prediction for pasa_asmbl_40717.p1
Valid prediction for GlimmerHMM_glimmerT_8264-T1
Valid prediction for snap_scaffold_3-snap.3478-T1
Valid prediction for Augustus_model.g5445.t1
Valid prediction for snap_scaffold_3-snap.3491-T1
Couldn't classify 170869, 171603
Sorry, prediction pasa_asmbl_40716.p1 fails validation.
(ATG)	 AA	170006-170074	GT	AGG
(GAC)	 AG	170244-170333	GT	TGG
(ACA)	 AG	170869-171603	GC	ACG
-recovered pasa_asmbl_40716.p1, initial, 170006, 170074
-recovered pasa_asmbl_40716.p1, internal, 170244, 170333
-recovered pasa_asmbl_40716.p1, internal, 170869, 171603
Valid prediction for CodingQuarry_transcript_46459-T1
Valid prediction for GlimmerHMM_glimmerT_8258-T1
Couldn't classify 113478, 113559
Couldn't classify 113877, 113935
Sorry, prediction CodingQuarry_transcript_46461-T1 fails validation.
(ATG)	 CC	112868-112939	GT	AAG
(GTA)	 AG	113243-113337	GT	AGG
(ATT)	 AG	113478-113559	CG	GCC
(TTT)	 GG	113877-113935	GT	AAG
(GTA)	 AG	114024-114072	GT	AGG
(GTC)	 AG	114228-114348	GT	AGG
(GTC)	 AG	115259-115365	GT	AGG
(GCG)	 AG	115755-115840	GT	AGG
(GAA)	 AG	116029-116857	GT	GAG
-recovered CodingQuarry_transcript_46461-T1, initial, 112868, 112939
-recovered CodingQuarry_transcript_46461-T1, terminal, 116029, 116857
-recovered CodingQuarry_transcript_46461-T1, internal, 113243, 113337
-recovered CodingQuarry_transcript_46461-T1, internal, 114024, 114072
-recovered CodingQuarry_transcript_46461-T1, internal, 114228, 114348
-recovered CodingQuarry_transcript_46461-T1, internal, 115259, 115365
-recovered CodingQuarry_transcript_46461-T1, internal, 115755, 115840
-recovered CodingQuarry_transcript_46461-T1, internal, 116029, 116857
Valid prediction for snap_scaffold_3-snap.3471-T1
Valid prediction for GlimmerHMM_glimmerT_8251-T1
Valid prediction for snap_scaffold_3-snap.3448-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8260-T1
Valid prediction for Augustus_model.g5441.t1
Couldn't classify 116029, 116146
Sorry, prediction pasa_asmbl_40709.p1 fails validation.
(ATG)	 CC	112868-112939	GT	AAG
(GTA)	 AG	113243-113337	GT	AGG
(ATT)	 AG	113478-113551	GT	AGG
(AAG)	 AG	113684-113697	GT	AGG
(GAT)	 AG	113883-113935	GT	AAG
(GTA)	 AG	114024-114072	GT	AGG
(GTC)	 AG	114228-114348	GT	AGG
(GTC)	 AG	115259-115365	GT	AGG
(GCG)	 AG	115755-115840	GT	AGG
(GAA)	 AG	116029-116146	TC	CCT
-recovered pasa_asmbl_40709.p1, initial, 112868, 112939
-recovered pasa_asmbl_40709.p1, internal, 113243, 113337
-recovered pasa_asmbl_40709.p1, internal, 113478, 113551
-recovered pasa_asmbl_40709.p1, internal, 113684, 113697
-recovered pasa_asmbl_40709.p1, internal, 113883, 113935
-recovered pasa_asmbl_40709.p1, internal, 114024, 114072
-recovered pasa_asmbl_40709.p1, internal, 114228, 114348
-recovered pasa_asmbl_40709.p1, internal, 115259, 115365
-recovered pasa_asmbl_40709.p1, internal, 115755, 115840
Valid prediction for GlimmerHMM_glimmerT_8249-T1
Valid prediction for GlimmerHMM_glimmerT_8252-T1
Valid prediction for snap_scaffold_3-snap.3486-T1
Valid prediction for snap_scaffold_3-snap.3475-T1
Couldn't classify 116126, 116857
Sorry, prediction pasa_asmbl_40711.p1 fails validation.
(AGC)	 GC	116126-116857	GT	GAG
Valid prediction for GlimmerHMM_glimmerT_8265-T1
Valid prediction for Augustus_model.g5437.t1
Valid prediction for CodingQuarry_transcript_46457-T1
Valid prediction for snap_scaffold_3-snap.3458-T1
Valid prediction for HiQ_model.g5439.t1
Valid prediction for snap_scaffold_3-snap.3450-T1
Valid prediction for snap_scaffold_3-snap.3483-T1
Valid prediction for snap_scaffold_3-snap.3462-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8262-T1
Valid prediction for snap_scaffold_3-snap.3473-T1
Valid prediction for snap_scaffold_3-snap.3488-T1
Valid prediction for Augustus_model.g5433.t1
Couldn't classify 103465, 103790
Sorry, prediction pasa_asmbl_40704.p1 fails validation.
(GTC)	 TG	103465-103790	GT	CTG
(GTT)	 AG	104387-104555	GT	TGG
(GTC)	 AG	104662-104817	GT	TGG
(GTT)	 AG	105330-105413	GT	AAG
(TTT)	 AG	105533-105653	GT	AGG
(GGT)	 AG	105803-105887	GT	GGG
(GCT)	 AG	106052-106142	GT	AGG
(ATG)	 AG	106585-106786	GC	AGG
(ATT)	 AG	106974-107063	GT	AGG
(GTC)	 AG	107545-107675	GT	CTG
(AAC)	 AG	107789-107884	GT	AGG
(GGT)	 AG	107980-108044	GT	AGG
(GTT)	 AG	108127-108264	GT	AGG
(GTG)	 AG	108667-108865	GG	AGG
-recovered pasa_asmbl_40704.p1, initial, 106585, 106786
-recovered pasa_asmbl_40704.p1, terminal, 108667, 108865
-recovered pasa_asmbl_40704.p1, internal, 104387, 104555
-recovered pasa_asmbl_40704.p1, internal, 104662, 104817
-recovered pasa_asmbl_40704.p1, internal, 105330, 105413
-recovered pasa_asmbl_40704.p1, internal, 105533, 105653
-recovered pasa_asmbl_40704.p1, internal, 105803, 105887
-recovered pasa_asmbl_40704.p1, internal, 106052, 106142
-recovered pasa_asmbl_40704.p1, internal, 106585, 106786
-recovered pasa_asmbl_40704.p1, internal, 106974, 107063
-recovered pasa_asmbl_40704.p1, internal, 107545, 107675
-recovered pasa_asmbl_40704.p1, internal, 107789, 107884
-recovered pasa_asmbl_40704.p1, internal, 107980, 108044
-recovered pasa_asmbl_40704.p1, internal, 108127, 108264
Valid prediction for GlimmerHMM_glimmerT_8254-T1
Valid prediction for GlimmerHMM_glimmerT_8271-T1
Valid prediction for snap_scaffold_3-snap.3476-T1
Valid prediction for GlimmerHMM_glimmerT_8270-T1
Valid prediction for GlimmerHMM_glimmerT_8245-T1
Valid prediction for Augustus_model.g5447.t1
Valid prediction for snap_scaffold_3-snap.3457-T1
Couldn't classify 157201, 157340
Sorry, prediction pasa_asmbl_40713.p1 fails validation.
(TTG)	 GG	157201-157340	GT	AGG
(TGT)	 AG	157941-158037	GT	GAG
(AAA)	 AG	160533-160655	GT	AGG
(GAA)	 AG	161399-161448	GT	CTG
(GCA)	 AG	164225-164264	TG	AGT
-recovered pasa_asmbl_40713.p1, terminal, 164225, 164264
-recovered pasa_asmbl_40713.p1, internal, 157941, 158037
-recovered pasa_asmbl_40713.p1, internal, 160533, 160655
-recovered pasa_asmbl_40713.p1, internal, 161399, 161448
Valid prediction for pasa_asmbl_40698.p1
Valid prediction for CodingQuarry_transcript_46458-T1
Valid prediction for GlimmerHMM_glimmerT_8268-T1
Valid prediction for snap_scaffold_3-snap.3463-T1
Valid prediction for HiQ_model.g5432.t1
Valid prediction for Augustus_model.g5448.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_3-snap.3468-T1
Valid prediction for HiQ_model.g5440.t1
Valid prediction for snap_scaffold_3-snap.3449-T1
Valid prediction for snap_scaffold_3-snap.3466-T1
Valid prediction for GlimmerHMM_glimmerT_8255-T1
Valid prediction for GlimmerHMM_glimmerT_8243-T1
Valid prediction for snap_scaffold_3-snap.3490-T1
Valid prediction for snap_scaffold_3-snap.3480-T1
Valid prediction for GlimmerHMM_glimmerT_8247-T1
Valid prediction for snap_scaffold_3-snap.3460-T1
Valid prediction for pasa_asmbl_39576.p1
Valid prediction for GlimmerHMM_glimmerT_8250-T1
Valid prediction for snap_scaffold_3-snap.3489-T1
Valid prediction for GlimmerHMM_glimmerT_8242-T1
Valid prediction for snap_scaffold_3-snap.3485-T1
Valid prediction for GlimmerHMM_glimmerT_8269-T1
Valid prediction for GlimmerHMM_glimmerT_8261-T1
Valid prediction for snap_scaffold_3-snap.3470-T1
Valid prediction for GlimmerHMM_glimmerT_8256-T1
Valid prediction for GlimmerHMM_glimmerT_8246-T1
Valid prediction for snap_scaffold_3-snap.3455-T1
Valid prediction for Augustus_model.g5446.t1
Valid prediction for Augustus_model.g5435.t1
Valid prediction for snap_scaffold_3-snap.3451-T1
Valid prediction for snap_scaffold_3-snap.3477-T1
Valid prediction for snap_scaffold_3-snap.3474-T1
Valid prediction for GlimmerHMM_glimmerT_8244-T1
Valid prediction for Augustus_model.g5431.t1
Valid prediction for snap_scaffold_3-snap.3469-T1
Valid prediction for snap_scaffold_3-snap.3482-T1
Valid prediction for CodingQuarry_transcript_46460-T1
Valid prediction for Augustus_model.g5436.t1
Valid prediction for snap_scaffold_3-snap.3464-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8267-T1
Valid prediction for snap_scaffold_3-snap.3453-T1
Valid prediction for Augustus_model.g5430.t1
Valid prediction for GlimmerHMM_glimmerT_8263-T1
Valid prediction for HiQ_model.g5442.t1
Valid prediction for snap_scaffold_3-snap.3467-T1
Valid prediction for GlimmerHMM_glimmerT_8257-T1
Valid prediction for snap_scaffold_3-snap.3454-T1
Valid prediction for snap_scaffold_3-snap.3487-T1
Valid prediction for GlimmerHMM_glimmerT_8253-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8704, rend_intergenic: 6491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59368, rend_intergenic: 57668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88190, rend_intergenic: 85586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99227, rend_intergenic: 96510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139909, rend_intergenic: 138144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153878, rend_intergenic: 152100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158288, rend_intergenic: 156733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175865
-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    
3.2    
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 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 8704, rend_intergenic: 6491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59368, rend_intergenic: 57668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88190, rend_intergenic: 85586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99227, rend_intergenic: 96510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139909, rend_intergenic: 138144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153878, rend_intergenic: 152100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158288, rend_intergenic: 156733  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