-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_598145-771452

-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_28-snap.138-T1
Valid prediction for snap_scaffold_28-snap.142-T1
Valid prediction for Augustus_model.g38407.t1
Valid prediction for Augustus_model.g38416.t1
Valid prediction for snap_scaffold_28-snap.131-T1
Valid prediction for snap_scaffold_28-snap.127-T1
Valid prediction for snap_scaffold_28-snap.128-T1
Valid prediction for GlimmerHMM_glimmerT_58017-T1
Valid prediction for Augustus_model.g38406.t1
Valid prediction for GlimmerHMM_glimmerT_58037-T1
Valid prediction for snap_scaffold_28-snap.163-T1
Valid prediction for snap_scaffold_28-snap.153-T1
Valid prediction for Augustus_model.g38410.t1
Valid prediction for Augustus_model.g38413.t1
Valid prediction for GlimmerHMM_glimmerT_58016-T1
Valid prediction for snap_scaffold_28-snap.145-T1
Valid prediction for snap_scaffold_28-snap.157-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g38412.t1
Valid prediction for GlimmerHMM_glimmerT_58035-T1
Valid prediction for GlimmerHMM_glimmerT_58034-T1
Valid prediction for snap_scaffold_28-snap.134-T1
Valid prediction for Augustus_model.g38421.t1
Valid prediction for snap_scaffold_28-snap.136-T1
Valid prediction for Augustus_model.g38417.t1
Valid prediction for snap_scaffold_28-snap.159-T1
Valid prediction for snap_scaffold_28-snap.137-T1
Valid prediction for Augustus_model.g38402.t1
Valid prediction for Augustus_model.g38401.t1
Valid prediction for snap_scaffold_28-snap.133-T1
Valid prediction for GlimmerHMM_glimmerT_58020-T1
Valid prediction for snap_scaffold_28-snap.147-T1
Valid prediction for GlimmerHMM_glimmerT_58024-T1
Valid prediction for Augustus_model.g38405.t1
Valid prediction for snap_scaffold_28-snap.162-T1
Valid prediction for snap_scaffold_28-snap.160-T1
Valid prediction for GlimmerHMM_glimmerT_58025-T1
Valid prediction for snap_scaffold_28-snap.144-T1
Valid prediction for snap_scaffold_28-snap.156-T1
Valid prediction for GlimmerHMM_glimmerT_58023-T1
Valid prediction for snap_scaffold_28-snap.151-T1
Valid prediction for snap_scaffold_28-snap.154-T1
Valid prediction for Augustus_model.g38419.t1
Valid prediction for GlimmerHMM_glimmerT_58021-T1
Valid prediction for snap_scaffold_28-snap.164-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_28-snap.161-T1
Valid prediction for snap_scaffold_28-snap.132-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_58022-T1
Valid prediction for GlimmerHMM_glimmerT_58032-T1
Valid prediction for GlimmerHMM_glimmerT_58026-T1
Valid prediction for snap_scaffold_28-snap.140-T1
Valid prediction for GlimmerHMM_glimmerT_58030-T1
Valid prediction for GlimmerHMM_glimmerT_58027-T1
Valid prediction for GlimmerHMM_glimmerT_58028-T1
Couldn't classify 167463, 167471
Couldn't classify 169798, 169812
Sorry, prediction pasa_asmbl_37924.p1 fails validation.
(GAC)	 GC	167463-167471	GC	AGG
(GTG)	 AG	167911-168032	GT	AAG
(GTA)	 AG	168183-168264	GT	GGG
(GCC)	 AG	168664-168796	GT	CAG
(GAT)	 AG	169204-169307	GT	ACG
(AAC)	 AG	169798-169812	GC	CCG
-recovered pasa_asmbl_37924.p1, internal, 167911, 168032
-recovered pasa_asmbl_37924.p1, internal, 168183, 168264
-recovered pasa_asmbl_37924.p1, internal, 168664, 168796
-recovered pasa_asmbl_37924.p1, internal, 169204, 169307
-recovered pasa_asmbl_37924.p1, internal, 169798, 169812
Valid prediction for Augustus_model.g38408.t1
Valid prediction for snap_scaffold_28-snap.148-T1
Valid prediction for snap_scaffold_28-snap.130-T1
Couldn't classify 10611, 10720
Sorry, prediction pasa_asmbl_37936.p1 fails validation.
(CAC)	 CT	10611-10720	GT	AGG
(CTC)	 AG	12887-12969	GT	TGG
(TGG)	 AG	14514-14575	GT	AGG
(AAG)	 AG	14809-14855	GT	AAG
(GGA)	 AG	15122-15236	GT	AGG
(ATC)	 AG	15346-15471	GT	AGG
(GGC)	 AG	15639-16145	GT	AGG
(GAT)	 AG	16274-16365	GT	CCG
(ATA)	 AG	16530-16636	GT	AGG
(GTA)	 AG	16812-16873	GT	AAG
add_exon() Sorry, pasa_asmbl_37936.p1 16530-16636-terminal-2 is invalid.
-recovered pasa_asmbl_37936.p1, terminal, 16530, 16636
-recovered pasa_asmbl_37936.p1, terminal, 16812, 16873
-recovered pasa_asmbl_37936.p1, internal, 12887, 12969
-recovered pasa_asmbl_37936.p1, internal, 14514, 14575
-recovered pasa_asmbl_37936.p1, internal, 14809, 14855
-recovered pasa_asmbl_37936.p1, internal, 15122, 15236
-recovered pasa_asmbl_37936.p1, internal, 15346, 15471
-recovered pasa_asmbl_37936.p1, internal, 15639, 16145
-recovered pasa_asmbl_37936.p1, internal, 16274, 16365
-recovered pasa_asmbl_37936.p1, internal, 16530, 16636
-recovered pasa_asmbl_37936.p1, internal, 16812, 16873
Couldn't classify 92255, 93103
Sorry, prediction pasa_asmbl_37928.p1 fails validation.
(CCG)	 AC	92255-93103	CC	GAC
Valid prediction for Augustus_model.g38414.t1
Valid prediction for snap_scaffold_28-snap.135-T1
Valid prediction for snap_scaffold_28-snap.155-T1
Valid prediction for GlimmerHMM_glimmerT_58031-T1
Valid prediction for Augustus_model.g38404.t1
Valid prediction for GlimmerHMM_glimmerT_58029-T1
Couldn't classify 99990, 100802
Sorry, prediction pasa_asmbl_37927.p1 fails validation.
(TCC)	 GC	99990-100802	TA	GGT
Valid prediction for Augustus_model.g38403.t1
Valid prediction for GlimmerHMM_glimmerT_58036-T1
Valid prediction for snap_scaffold_28-snap.146-T1
Valid prediction for snap_scaffold_28-snap.143-T1
Valid prediction for CodingQuarry_transcript_43518-T1
Valid prediction for Augustus_model.g38409.t1
Valid prediction for snap_scaffold_28-snap.150-T1
Valid prediction for GlimmerHMM_glimmerT_58019-T1
Valid prediction for snap_scaffold_28-snap.149-T1
Valid prediction for GlimmerHMM_glimmerT_58039-T1
Valid prediction for pasa_asmbl_37929.p2
Valid prediction for snap_scaffold_28-snap.158-T1
Valid prediction for Augustus_model.g38418.t1
Valid prediction for snap_scaffold_28-snap.141-T1
Couldn't classify 104647, 104775
Sorry, prediction pasa_asmbl_37926.p1 fails validation.
(CCC)	 TT	104647-104775	GT	TGG
(GTG)	 AG	104996-105202	GA	AGG
-recovered pasa_asmbl_37926.p1, terminal, 104996, 105202
Valid prediction for Augustus_model.g38411.t1
Valid prediction for snap_scaffold_28-snap.129-T1
Couldn't classify 31146, 31217
Couldn't classify 33110, 33203
Sorry, prediction pasa_asmbl_37930.p1 fails validation.
(AGA)	 CC	31146-31217	GT	AGG
(GAG)	 AG	32227-32372	GT	AGG
(CAT)	 AG	33110-33203	CA	GAC
-recovered pasa_asmbl_37930.p1, internal, 32227, 32372
Valid prediction for Augustus_model.g38420.t1
Valid prediction for Augustus_model.g38415.t1
Valid prediction for GlimmerHMM_glimmerT_58015-T1
Valid prediction for GlimmerHMM_glimmerT_58038-T1
Valid prediction for GlimmerHMM_glimmerT_58033-T1
Valid prediction for snap_scaffold_28-snap.152-T1
Valid prediction for snap_scaffold_28-snap.139-T1
Valid prediction for GlimmerHMM_glimmerT_58018-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20999, rend_intergenic: 18726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37249, rend_intergenic: 32434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40841, rend_intergenic: 37864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90656, rend_intergenic: 89344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102340, rend_intergenic: 95853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107937, rend_intergenic: 103724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108124, rend_intergenic: 107962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128582, rend_intergenic: 124645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131264, rend_intergenic: 129107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139672, rend_intergenic: 131857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148461, rend_intergenic: 147221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168066, rend_intergenic: 158112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173308
-exon list size: 364


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.5    
2.7    
3.0    
3.3    
3.6    
3.8    
4.1    
4.4    
4.6    
4.9    
5.2    
5.5    
5.7    
6.0    
6.3    
6.6    
6.8    
7.1    
7.4    
7.7    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
12.8    
13.1    
13.4    
13.7    
13.9    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.8    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.0    
21.3    
21.6    
21.9    
22.1    
22.4    
22.7    
23.0    
23.2    
23.5    
23.8    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.4    
43.7    
44.0    
44.3    
44.5    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.5    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.5    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.5    
55.7    
56.0    
56.3    
56.6    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.7    
63.9    
64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.9    
72.1    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.2    
76.5    
76.8    
77.0    
77.3    
77.6    
77.9    
78.1    
78.4    
78.7    
79.0    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.3    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.2    
93.4    
93.7    
94.0    
94.3    
94.5    
94.8    
95.1    
95.4    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 20999, rend_intergenic: 18726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37249, rend_intergenic: 32434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40841, rend_intergenic: 37864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90656, rend_intergenic: 89344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102340, rend_intergenic: 95853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107937, rend_intergenic: 103724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108124, rend_intergenic: 107962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128582, rend_intergenic: 124645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131264, rend_intergenic: 129107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139672, rend_intergenic: 131857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148461, rend_intergenic: 147221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168066, rend_intergenic: 158112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20085
-exon list size: 27


building trellis

3.4    
6.9    
10.3    
13.8    
17.2    
20.7    
24.1    
27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 5399 - 20085
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 5399 - 18494
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 7320 - 18494
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 7708 - 18494
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support