-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_16900780-17090003

-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.3266-T1
Valid prediction for GlimmerHMM_glimmerT_8110-T1
Valid prediction for snap_scaffold_3-snap.3281-T1
Couldn't classify 93861, 94202
Sorry, prediction pasa_asmbl_40635.p1 fails validation.
(CTC)	 TT	93861-94202	AG	AAA
Valid prediction for snap_scaffold_3-snap.3256-T1
Valid prediction for snap_scaffold_3-snap.3287-T1
Valid prediction for snap_scaffold_3-snap.3269-T1
Valid prediction for Augustus_model.g5359.t1
Valid prediction for GlimmerHMM_glimmerT_8109-T1
Valid prediction for Augustus_model.g5353.t1
Valid prediction for snap_scaffold_3-snap.3292-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3284-T1
Valid prediction for GlimmerHMM_glimmerT_8104-T1
Valid prediction for snap_scaffold_3-snap.3258-T1
Valid prediction for snap_scaffold_3-snap.3262-T1
Valid prediction for Augustus_model.g5348.t1
Valid prediction for snap_scaffold_3-snap.3280-T1
Valid prediction for GlimmerHMM_glimmerT_8111-T1
Valid prediction for snap_scaffold_3-snap.3279-T1
Valid prediction for GlimmerHMM_glimmerT_8107-T1
Valid prediction for GlimmerHMM_glimmerT_8123-T1
Valid prediction for snap_scaffold_3-snap.3257-T1
Valid prediction for Augustus_model.g5349.t1
Valid prediction for GlimmerHMM_glimmerT_8124-T1
Valid prediction for snap_scaffold_3-snap.3289-T1
Valid prediction for GlimmerHMM_glimmerT_8117-T1
Valid prediction for snap_scaffold_3-snap.3260-T1
Valid prediction for snap_scaffold_3-snap.3261-T1
Valid prediction for snap_scaffold_3-snap.3294-T1
Valid prediction for GlimmerHMM_glimmerT_8102-T1
Valid prediction for snap_scaffold_3-snap.3290-T1
Valid prediction for snap_scaffold_3-snap.3271-T1
Valid prediction for snap_scaffold_3-snap.3285-T1
Valid prediction for GlimmerHMM_glimmerT_8120-T1
Valid prediction for GlimmerHMM_glimmerT_8122-T1
Valid prediction for snap_scaffold_3-snap.3277-T1
Valid prediction for snap_scaffold_3-snap.3267-T1
Valid prediction for Augustus_model.g5347.t1
Couldn't classify 166656, 167000
Sorry, prediction pasa_asmbl_39531.p1 fails validation.
(ATG)	 GC	166656-167000	TC	CGT
Valid prediction for snap_scaffold_3-snap.3278-T1
Valid prediction for snap_scaffold_3-snap.3264-T1
Valid prediction for snap_scaffold_3-snap.3283-T1
Valid prediction for snap_scaffold_3-snap.3286-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 Augustus_model.g5351.t1
Valid prediction for GlimmerHMM_glimmerT_8118-T1
Couldn't classify 5822, 5899
Couldn't classify 12040, 12122
Sorry, prediction pasa_asmbl_39534.p1 fails validation.
(CGG)	 TA	5822-5899	GT	AGG
(CCG)	 AG	6683-6767	GT	TGG
(AGG)	 AG	6859-7091	GT	GGG
(AGA)	 AG	7270-7325	GT	GAG
(GAG)	 AG	8071-8151	GT	AGG
(GGA)	 AG	8554-8790	GT	AGG
(CCT)	 AG	8931-9059	GT	AGG
(AGG)	 AG	9192-9360	GT	AGG
(CAA)	 AG	9523-9576	GT	TGG
(GCT)	 AG	9749-9884	GT	CGG
(CCA)	 AG	10774-10980	GT	CAG
(ATG)	 AG	11236-11298	GT	AGG
(AGA)	 AG	11506-11610	GT	AGG
(ACG)	 AG	12040-12122	AG	CCA
add_exon() Sorry, pasa_asmbl_39534.p1 11236-11298-initial-1 is invalid.
-recovered pasa_asmbl_39534.p1, initial, 11236, 11298
add_exon() Sorry, pasa_asmbl_39534.p1 7270-7325-terminal-2 is invalid.
-recovered pasa_asmbl_39534.p1, terminal, 7270, 7325
-recovered pasa_asmbl_39534.p1, internal, 6683, 6767
-recovered pasa_asmbl_39534.p1, internal, 6859, 7091
-recovered pasa_asmbl_39534.p1, internal, 7270, 7325
-recovered pasa_asmbl_39534.p1, internal, 8071, 8151
-recovered pasa_asmbl_39534.p1, internal, 8554, 8790
-recovered pasa_asmbl_39534.p1, internal, 8931, 9059
-recovered pasa_asmbl_39534.p1, internal, 9192, 9360
-recovered pasa_asmbl_39534.p1, internal, 9523, 9576
-recovered pasa_asmbl_39534.p1, internal, 9749, 9884
-recovered pasa_asmbl_39534.p1, internal, 10774, 10980
-recovered pasa_asmbl_39534.p1, internal, 11236, 11298
-recovered pasa_asmbl_39534.p1, internal, 11506, 11610
Valid prediction for snap_scaffold_3-snap.3268-T1
Valid prediction for GlimmerHMM_glimmerT_8112-T1
Valid prediction for snap_scaffold_3-snap.3276-T1
Valid prediction for HiQ_model.g5360.t1
Valid prediction for snap_scaffold_3-snap.3274-T1
Valid prediction for snap_scaffold_3-snap.3265-T1
Valid prediction for Augustus_model.g5350.t1
Valid prediction for snap_scaffold_3-snap.3295-T1
Couldn't classify 101881, 102015
Sorry, prediction pasa_asmbl_39525.p1 fails validation.
(AGT)	 TC	101881-102015	GT	AGG
(GTG)	 AG	102214-102361	GT	AGG
(CGG)	 AG	102544-102641	GG	AGG
-recovered pasa_asmbl_39525.p1, terminal, 102544, 102641
-recovered pasa_asmbl_39525.p1, internal, 102214, 102361
Valid prediction for snap_scaffold_3-snap.3263-T1
Valid prediction for GlimmerHMM_glimmerT_8119-T1
Valid prediction for GlimmerHMM_glimmerT_8116-T1
Valid prediction for HiQ_model.g5361.t1
Valid prediction for Augustus_model.g5352.t1
Valid prediction for CodingQuarry_transcript_46429-T1
Valid prediction for GlimmerHMM_glimmerT_8115-T1
Couldn't classify 90414, 90495
Couldn't classify 91484, 91591
Sorry, prediction pasa_asmbl_39530.p1 fails validation.
(GAA)	 AG	90414-90495	GT	AGG
(GGT)	 AG	90795-90976	GT	AGG
(CAC)	 AG	91106-91207	GT	CTG
(GCT)	 AG	91484-91591	AG	CCA
-recovered pasa_asmbl_39530.p1, internal, 90414, 90495
-recovered pasa_asmbl_39530.p1, internal, 90795, 90976
-recovered pasa_asmbl_39530.p1, internal, 91106, 91207
Valid prediction for snap_scaffold_3-snap.3282-T1
Valid prediction for Augustus_model.g5362.t1
Valid prediction for GlimmerHMM_glimmerT_8121-T1
Valid prediction for GlimmerHMM_glimmerT_8125-T1
Valid prediction for Augustus_model.g5355.t1
Valid prediction for GlimmerHMM_glimmerT_8106-T1
Valid prediction for GlimmerHMM_glimmerT_8105-T1
Valid prediction for GlimmerHMM_glimmerT_8114-T1
Valid prediction for snap_scaffold_3-snap.3273-T1
Valid prediction for snap_scaffold_3-snap.3270-T1
Valid prediction for GlimmerHMM_glimmerT_8113-T1
Valid prediction for GlimmerHMM_glimmerT_8108-T1
Valid prediction for Augustus_model.g5358.t1
Valid prediction for Augustus_model.g5357.t1
Valid prediction for snap_scaffold_3-snap.3272-T1
Valid prediction for GlimmerHMM_glimmerT_8126-T1
Valid prediction for snap_scaffold_3-snap.3297-T1
Valid prediction for snap_scaffold_3-snap.3291-T1
Valid prediction for pasa_asmbl_39524.p1
Valid prediction for snap_scaffold_3-snap.3293-T1
Valid prediction for Augustus_model.g5354.t1
Couldn't classify 18942, 19019
Couldn't classify 21678, 21979
Sorry, prediction pasa_asmbl_39533.p1 fails validation.
(AAA)	 AG	18942-19019	GT	GGG
(AGG)	 AG	19178-19330	GT	GCG
(GTG)	 AG	19629-19756	GT	ATG
(GAC)	 AG	19882-19983	GT	ACG
(TGA)	 AG	20599-20777	GT	AGG
(ACT)	 AG	21678-21979	AC	GGA
-recovered pasa_asmbl_39533.p1, internal, 18942, 19019
-recovered pasa_asmbl_39533.p1, internal, 19178, 19330
-recovered pasa_asmbl_39533.p1, internal, 19629, 19756
-recovered pasa_asmbl_39533.p1, internal, 19882, 19983
-recovered pasa_asmbl_39533.p1, internal, 20599, 20777
Valid prediction for snap_scaffold_3-snap.3275-T1
Valid prediction for GlimmerHMM_glimmerT_8103-T1
Valid prediction for snap_scaffold_3-snap.3259-T1
Valid prediction for Augustus_model.g5356.t1
Valid prediction for snap_scaffold_3-snap.3288-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28167, rend_intergenic: 11816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32406, rend_intergenic: 28210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47039, rend_intergenic: 35669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61957, rend_intergenic: 48390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67947, rend_intergenic: 63780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68553, rend_intergenic: 68016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84786, rend_intergenic: 68924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109347, rend_intergenic: 97623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124437, rend_intergenic: 114641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148753, rend_intergenic: 124528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151679, rend_intergenic: 151556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161685, rend_intergenic: 151805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168578, rend_intergenic: 166808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171949, rend_intergenic: 168723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172173, rend_intergenic: 172072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181226, rend_intergenic: 173391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 189224
-exon list size: 400


building trellis

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1.0    
1.2    
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3.5    
3.7    
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4.2    
4.5    
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5.2    
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6.2    
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9.2    
9.5    
9.7    
10.0    
10.2    
10.4    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.4    
64.7    
64.9    
65.2    
65.4    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 28167, rend_intergenic: 11816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32406, rend_intergenic: 28210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47039, rend_intergenic: 35669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61957, rend_intergenic: 48390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67947, rend_intergenic: 63780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68553, rend_intergenic: 68016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84786, rend_intergenic: 68924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109347, rend_intergenic: 97623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124437, rend_intergenic: 114641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148753, rend_intergenic: 124528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151679, rend_intergenic: 151556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161685, rend_intergenic: 151805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168578, rend_intergenic: 166808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171949, rend_intergenic: 168723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172173, rend_intergenic: 172072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181226, rend_intergenic: 173391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support