-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_16529103-16707824

-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_6-snap.3534-T1
Valid prediction for snap_scaffold_6-snap.3502-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_55382-T1
Valid prediction for snap_scaffold_6-snap.3523-T1
Valid prediction for GlimmerHMM_glimmerT_16306-T1
Valid prediction for snap_scaffold_6-snap.3532-T1
Valid prediction for snap_scaffold_6-snap.3541-T1
Valid prediction for GlimmerHMM_glimmerT_16294-T1
Valid prediction for GlimmerHMM_glimmerT_16305-T1
Valid prediction for snap_scaffold_6-snap.3533-T1
Valid prediction for snap_scaffold_6-snap.3517-T1
Valid prediction for snap_scaffold_6-snap.3543-T1
Valid prediction for HiQ_model.g10927.t1
Valid prediction for snap_scaffold_6-snap.3522-T1
Valid prediction for Augustus_model.g10934.t1
Valid prediction for pasa_asmbl_47712.p1
Valid prediction for CodingQuarry_transcript_55380-T1
Valid prediction for pasa_asmbl_47710.p1
Valid prediction for GlimmerHMM_glimmerT_16308-T1
Valid prediction for CodingQuarry_transcript_55383-T1
Valid prediction for GlimmerHMM_glimmerT_16299-T1
Valid prediction for GlimmerHMM_glimmerT_16286-T1
Couldn't classify 76033, 76341
Couldn't classify 76998, 77078
Sorry, prediction CodingQuarry_transcript_55381-T1 fails validation.
(ATG)	 AC	75430-75699	GT	AGG
(ATC)	 AG	76033-76341	AT	CGA
(ACA)	 AC	76998-77078	CC	GAC
-recovered CodingQuarry_transcript_55381-T1, initial, 75430, 75699
Valid prediction for GlimmerHMM_glimmerT_16284-T1
Valid prediction for GlimmerHMM_glimmerT_16301-T1
Valid prediction for Augustus_model.g10928.t1
Valid prediction for snap_scaffold_6-snap.3509-T1
Valid prediction for snap_scaffold_6-snap.3536-T1
Valid prediction for Augustus_model.g10935.t1
Valid prediction for snap_scaffold_6-snap.3529-T1
Valid prediction for GlimmerHMM_glimmerT_16295-T1
Valid prediction for snap_scaffold_6-snap.3527-T1
Valid prediction for GlimmerHMM_glimmerT_16285-T1
Valid prediction for snap_scaffold_6-snap.3512-T1
Valid prediction for snap_scaffold_6-snap.3519-T1
Valid prediction for snap_scaffold_6-snap.3501-T1
Valid prediction for Augustus_model.g10929.t1
Valid prediction for snap_scaffold_6-snap.3505-T1
Valid prediction for GlimmerHMM_glimmerT_16312-T1
Valid prediction for Augustus_model.g10922.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_6-snap.3524-T1
Valid prediction for Augustus_model.g10923.t1
Valid prediction for GlimmerHMM_glimmerT_16313-T1
Valid prediction for GlimmerHMM_glimmerT_16281-T1
Valid prediction for Augustus_model.g10924.t1
Valid prediction for GlimmerHMM_glimmerT_16297-T1
Valid prediction for Augustus_model.g10920.t1
Valid prediction for GlimmerHMM_glimmerT_16283-T1
Valid prediction for GlimmerHMM_glimmerT_16290-T1
Valid prediction for snap_scaffold_6-snap.3520-T1
Valid prediction for GlimmerHMM_glimmerT_16300-T1
Valid prediction for Augustus_model.g10932.t1
Valid prediction for GlimmerHMM_glimmerT_16311-T1
Valid prediction for snap_scaffold_6-snap.3514-T1
Valid prediction for GlimmerHMM_glimmerT_16310-T1
Valid prediction for snap_scaffold_6-snap.3540-T1
Valid prediction for Augustus_model.g10937.t1
Valid prediction for GlimmerHMM_glimmerT_16302-T1
Valid prediction for snap_scaffold_6-snap.3507-T1
Valid prediction for snap_scaffold_6-snap.3515-T1
Valid prediction for Augustus_model.g10931.t1
Valid prediction for snap_scaffold_6-snap.3530-T1
Valid prediction for Augustus_model.g10925.t1
Valid prediction for GlimmerHMM_glimmerT_16291-T1
Valid prediction for snap_scaffold_6-snap.3521-T1
Valid prediction for HiQ_model.g10930.t1
Valid prediction for GlimmerHMM_glimmerT_16292-T1
Valid prediction for snap_scaffold_6-snap.3537-T1
Couldn't classify 107450, 107515
Sorry, prediction pasa_asmbl_49144.p1 fails validation.
(CCG)	 AG	107450-107515	GT	TGG
(GAA)	 AG	109079-109147	GT	AGG
(TAC)	 AG	109294-109378	GT	CAG
(ATG)	 AG	110498-110589	GT	AGG
(CTT)	 AG	110731-110786	GT	AGG
(GAA)	 AG	111326-111403	GT	GGG
(GGT)	 AG	111666-111717	GT	GGG
(GCG)	 AG	112756-112794	GT	AGG
(GTT)	 AG	113802-113849	CA	AAC
add_exon() Sorry, pasa_asmbl_49144.p1 110498-110589-initial-1 is invalid.
-recovered pasa_asmbl_49144.p1, initial, 110498, 110589
-recovered pasa_asmbl_49144.p1, terminal, 113802, 113849
-recovered pasa_asmbl_49144.p1, internal, 107450, 107515
-recovered pasa_asmbl_49144.p1, internal, 109079, 109147
-recovered pasa_asmbl_49144.p1, internal, 109294, 109378
-recovered pasa_asmbl_49144.p1, internal, 110498, 110589
-recovered pasa_asmbl_49144.p1, internal, 110731, 110786
-recovered pasa_asmbl_49144.p1, internal, 111326, 111403
-recovered pasa_asmbl_49144.p1, internal, 111666, 111717
-recovered pasa_asmbl_49144.p1, internal, 112756, 112794
Valid prediction for snap_scaffold_6-snap.3503-T1
Valid prediction for snap_scaffold_6-snap.3525-T1
Valid prediction for snap_scaffold_6-snap.3538-T1
Valid prediction for snap_scaffold_6-snap.3516-T1
Valid prediction for GlimmerHMM_glimmerT_16287-T1
Valid prediction for GlimmerHMM_glimmerT_16282-T1
Valid prediction for GlimmerHMM_glimmerT_16307-T1
Valid prediction for snap_scaffold_6-snap.3518-T1
Valid prediction for GlimmerHMM_glimmerT_16298-T1
Valid prediction for snap_scaffold_6-snap.3528-T1
Valid prediction for snap_scaffold_6-snap.3542-T1
Valid prediction for snap_scaffold_6-snap.3531-T1
Valid prediction for snap_scaffold_6-snap.3504-T1
Valid prediction for snap_scaffold_6-snap.3511-T1
Valid prediction for HiQ_model.g10926.t1
Valid prediction for GlimmerHMM_glimmerT_16303-T1
Valid prediction for CodingQuarry_transcript_55385-T1
Valid prediction for GlimmerHMM_glimmerT_16288-T1
Valid prediction for snap_scaffold_6-snap.3526-T1
Valid prediction for Augustus_model.g10936.t1
Valid prediction for GlimmerHMM_glimmerT_16304-T1
Valid prediction for GlimmerHMM_glimmerT_16309-T1
Valid prediction for GlimmerHMM_glimmerT_16289-T1
Valid prediction for snap_scaffold_6-snap.3506-T1
Valid prediction for snap_scaffold_6-snap.3535-T1
Valid prediction for pasa_asmbl_49150.p1
Valid prediction for snap_scaffold_6-snap.3510-T1
Valid prediction for Augustus_model.g10933.t1
Valid prediction for snap_scaffold_6-snap.3508-T1
Valid prediction for Augustus_model.g10921.t1
Valid prediction for snap_scaffold_6-snap.3513-T1
Valid prediction for GlimmerHMM_glimmerT_16293-T1
Valid prediction for snap_scaffold_6-snap.3539-T1
Valid prediction for GlimmerHMM_glimmerT_16296-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6597, rend_intergenic: 2982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15655, rend_intergenic: 9790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21891, rend_intergenic: 18364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25285, rend_intergenic: 21925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37050, rend_intergenic: 26013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39823, rend_intergenic: 37058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55844, rend_intergenic: 52752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86487, rend_intergenic: 76014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92784, rend_intergenic: 88891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100589, rend_intergenic: 98864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102314, rend_intergenic: 100598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120558, rend_intergenic: 105961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137987, rend_intergenic: 125740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141066, rend_intergenic: 140157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159517, rend_intergenic: 141564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164641, rend_intergenic: 159916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177107, rend_intergenic: 169687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178722
-exon list size: 349


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
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    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
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    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
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    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 6597, rend_intergenic: 2982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15655, rend_intergenic: 9790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21891, rend_intergenic: 18364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25285, rend_intergenic: 21925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37050, rend_intergenic: 26013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39823, rend_intergenic: 37058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55844, rend_intergenic: 52752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86487, rend_intergenic: 76014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92784, rend_intergenic: 88891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100589, rend_intergenic: 98864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102314, rend_intergenic: 100598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120558, rend_intergenic: 105961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137987, rend_intergenic: 125740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141066, rend_intergenic: 140157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159517, rend_intergenic: 141564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164641, rend_intergenic: 159916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177107, rend_intergenic: 169687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support