-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_333510-565061

-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 GlimmerHMM_glimmerT_54972-T1
Valid prediction for GlimmerHMM_glimmerT_54964-T1
Valid prediction for GlimmerHMM_glimmerT_54959-T1
Valid prediction for HiQ_model.g36463.t1
Valid prediction for Augustus_model.g36460.t1
Valid prediction for Augustus_model.g36464.t1
Valid prediction for snap_scaffold_26-snap.101-T1
Valid prediction for Augustus_model.g36457.t1
Valid prediction for GlimmerHMM_glimmerT_54982-T1
Valid prediction for GlimmerHMM_glimmerT_54969-T1
Valid prediction for snap_scaffold_26-snap.96-T1
Valid prediction for snap_scaffold_26-snap.89-T1
Couldn't classify 52174, 53022
Sorry, prediction pasa_asmbl_34675.p1 fails validation.
(ATG)	 AG	52174-53022	GA	AAG
Valid prediction for snap_scaffold_26-snap.94-T1
Valid prediction for GlimmerHMM_glimmerT_54957-T1
Valid prediction for snap_scaffold_26-snap.98-T1
Valid prediction for GlimmerHMM_glimmerT_54963-T1
Valid prediction for GlimmerHMM_glimmerT_54970-T1
Valid prediction for GlimmerHMM_glimmerT_54973-T1
Couldn't classify 88882, 89164
Sorry, prediction pasa_asmbl_34680.p1 fails validation.
(TAT)	 GC	88882-89164	GT	AGG
(GTC)	 AG	90505-90595	GT	AAG
(TTT)	 AG	91023-91098	GT	AGG
(TCC)	 AG	91479-91571	GT	CGG
(GTG)	 AG	92072-92148	GT	AGG
(AGA)	 AG	92299-92365	GT	AGG
(GCA)	 AG	92893-92955	GT	AGG
(AGA)	 AG	93158-93245	GT	TGG
(GCT)	 AG	93757-93987	GT	AGG
(CTG)	 AG	94261-94399	GT	GAG
(GCA)	 AG	95946-96108	GT	TGG
(TAC)	 AG	96229-96326	GT	TCG
(CCA)	 AG	97107-97179	CA	AGC
-recovered pasa_asmbl_34680.p1, terminal, 97107, 97179
-recovered pasa_asmbl_34680.p1, internal, 90505, 90595
-recovered pasa_asmbl_34680.p1, internal, 91023, 91098
-recovered pasa_asmbl_34680.p1, internal, 91479, 91571
-recovered pasa_asmbl_34680.p1, internal, 92072, 92148
-recovered pasa_asmbl_34680.p1, internal, 92299, 92365
-recovered pasa_asmbl_34680.p1, internal, 92893, 92955
-recovered pasa_asmbl_34680.p1, internal, 93158, 93245
-recovered pasa_asmbl_34680.p1, internal, 93757, 93987
-recovered pasa_asmbl_34680.p1, internal, 94261, 94399
-recovered pasa_asmbl_34680.p1, internal, 95946, 96108
-recovered pasa_asmbl_34680.p1, internal, 96229, 96326
Valid prediction for Augustus_model.g36466.t1
Couldn't classify 119646, 119799
Sorry, prediction pasa_asmbl_34689.p1 fails validation.
(CTG)	 GT	119646-119799	GT	AGG
(GGT)	 AG	120163-120251	GT	TGG
(GGT)	 AG	120356-120469	CC	GAC
-recovered pasa_asmbl_34689.p1, terminal, 120356, 120469
-recovered pasa_asmbl_34689.p1, internal, 120163, 120251
Valid prediction for Augustus_model.g36465.t1
Valid prediction for Augustus_model.g36461.t1
Couldn't classify 53260, 53880
Sorry, prediction pasa_asmbl_34676.p1 fails validation.
(CCA)	 AA	53260-53880	AA	AAA
Valid prediction for snap_scaffold_26-snap.104-T1
Valid prediction for snap_scaffold_26-snap.73-T1
Valid prediction for GlimmerHMM_glimmerT_54966-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.100-T1
Valid prediction for snap_scaffold_26-snap.86-T1
Valid prediction for GlimmerHMM_glimmerT_54977-T1
Valid prediction for snap_scaffold_26-snap.83-T1
Sorry, intron length (8) is less than minimum required (10)
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_54967-T1
Valid prediction for snap_scaffold_26-snap.108-T1
Valid prediction for snap_scaffold_26-snap.91-T1
Valid prediction for GlimmerHMM_glimmerT_54958-T1
Valid prediction for snap_scaffold_26-snap.111-T1
Valid prediction for GlimmerHMM_glimmerT_54979-T1
Valid prediction for snap_scaffold_26-snap.109-T1
Valid prediction for GlimmerHMM_glimmerT_54968-T1
Valid prediction for snap_scaffold_26-snap.90-T1
Valid prediction for Augustus_model.g36459.t1
Valid prediction for snap_scaffold_26-snap.81-T1
Valid prediction for Augustus_model.g36456.t1
Couldn't classify 51034, 51108
Couldn't classify 51220, 51783
Sorry, prediction pasa_asmbl_34674.p1 fails validation.
(CCT)	 GT	51034-51108	GT	AGG
(GAA)	 AG	51220-51783	GA	ACG
Valid prediction for pasa_asmbl_35337.p1
Valid prediction for GlimmerHMM_glimmerT_54962-T1
Valid prediction for GlimmerHMM_glimmerT_54981-T1
Valid prediction for snap_scaffold_26-snap.92-T1
Valid prediction for snap_scaffold_26-snap.87-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g36462.t1
Valid prediction for snap_scaffold_26-snap.106-T1
Valid prediction for snap_scaffold_26-snap.103-T1
Valid prediction for snap_scaffold_26-snap.76-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 GlimmerHMM_glimmerT_54975-T1
Valid prediction for GlimmerHMM_glimmerT_54956-T1
Valid prediction for GlimmerHMM_glimmerT_54960-T1
Valid prediction for snap_scaffold_26-snap.79-T1
Valid prediction for snap_scaffold_26-snap.102-T1
Valid prediction for Augustus_model.g36467.t1
Valid prediction for Augustus_model.g36468.t1
Valid prediction for snap_scaffold_26-snap.82-T1
Valid prediction for snap_scaffold_26-snap.74-T1
Valid prediction for GlimmerHMM_glimmerT_54976-T1
Valid prediction for snap_scaffold_26-snap.97-T1
Valid prediction for GlimmerHMM_glimmerT_54965-T1
Valid prediction for GlimmerHMM_glimmerT_54955-T1
Valid prediction for GlimmerHMM_glimmerT_54980-T1
Valid prediction for GlimmerHMM_glimmerT_54984-T1
Valid prediction for snap_scaffold_26-snap.107-T1
Valid prediction for snap_scaffold_26-snap.110-T1
Valid prediction for snap_scaffold_26-snap.72-T1
Valid prediction for snap_scaffold_26-snap.77-T1
Valid prediction for snap_scaffold_26-snap.88-T1
Valid prediction for GlimmerHMM_glimmerT_54974-T1
Valid prediction for GlimmerHMM_glimmerT_54971-T1
Valid prediction for snap_scaffold_26-snap.85-T1
Valid prediction for GlimmerHMM_glimmerT_54978-T1
Valid prediction for snap_scaffold_26-snap.84-T1
Valid prediction for snap_scaffold_26-snap.93-T1
Valid prediction for snap_scaffold_26-snap.75-T1
Valid prediction for GlimmerHMM_glimmerT_54983-T1
Valid prediction for snap_scaffold_26-snap.105-T1
Valid prediction for snap_scaffold_26-snap.99-T1
Valid prediction for snap_scaffold_26-snap.80-T1
Valid prediction for snap_scaffold_26-snap.95-T1
Valid prediction for snap_scaffold_26-snap.78-T1
Valid prediction for Augustus_model.g36458.t1
Valid prediction for GlimmerHMM_glimmerT_54961-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11418, rend_intergenic: 9793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35297, rend_intergenic: 17149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56136, rend_intergenic: 50688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67787, rend_intergenic: 65880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72255, rend_intergenic: 68805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77604, rend_intergenic: 75005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94403, rend_intergenic: 92851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98092, rend_intergenic: 96465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113343, rend_intergenic: 110540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114089, rend_intergenic: 113671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117243, rend_intergenic: 115380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128570, rend_intergenic: 117914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149250, rend_intergenic: 128597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158129, rend_intergenic: 149779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172679, rend_intergenic: 159955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173490, rend_intergenic: 172762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176858, rend_intergenic: 173525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205452, rend_intergenic: 177041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216320, rend_intergenic: 215348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231552
-exon list size: 390


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.8    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 11418, rend_intergenic: 9793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35297, rend_intergenic: 17149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56136, rend_intergenic: 50688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67787, rend_intergenic: 65880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72255, rend_intergenic: 68805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77604, rend_intergenic: 75005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94403, rend_intergenic: 92851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98092, rend_intergenic: 96465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113343, rend_intergenic: 110540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114089, rend_intergenic: 113671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117243, rend_intergenic: 115380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128570, rend_intergenic: 117914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149250, rend_intergenic: 128597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158129, rend_intergenic: 149779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172679, rend_intergenic: 159955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173490, rend_intergenic: 172762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176858, rend_intergenic: 173525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205452, rend_intergenic: 177041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216320, rend_intergenic: 215348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support