-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_6147029-6355898

-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 HiQ_model.g14827.t1
Valid prediction for CodingQuarry_transcript_62197-T1
Valid prediction for GlimmerHMM_glimmerT_22291-T1
Valid prediction for GlimmerHMM_glimmerT_22311-T1
Valid prediction for GlimmerHMM_glimmerT_22302-T1
Valid prediction for Augustus_model.g14832.t1
Valid prediction for GlimmerHMM_glimmerT_22292-T1
Valid prediction for GlimmerHMM_glimmerT_22309-T1
Valid prediction for Augustus_model.g14828.t1
Valid prediction for snap_scaffold_9-snap.1303-T1
Valid prediction for snap_scaffold_9-snap.1329-T1
Valid prediction for snap_scaffold_9-snap.1331-T1
Valid prediction for GlimmerHMM_glimmerT_22300-T1
Valid prediction for GlimmerHMM_glimmerT_22286-T1
Valid prediction for GlimmerHMM_glimmerT_22296-T1
Valid prediction for GlimmerHMM_glimmerT_22289-T1
Valid prediction for snap_scaffold_9-snap.1307-T1
Valid prediction for Augustus_model.g14815.t1
Valid prediction for Augustus_model.g14825.t1
Valid prediction for snap_scaffold_9-snap.1324-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1314-T1
Valid prediction for snap_scaffold_9-snap.1321-T1
Valid prediction for Augustus_model.g14820.t1
Valid prediction for GlimmerHMM_glimmerT_22307-T1
Couldn't classify 148306, 148503
Sorry, prediction pasa_asmbl_54088.p1 fails validation.
(TGG)	 GC	148306-148503	GT	AGG
(AAC)	 AG	148921-149047	GT	AGG
(AAT)	 AG	149298-149381	GT	GGG
(ATG)	 AG	149541-149569	AA	GAA
-recovered pasa_asmbl_54088.p1, terminal, 149541, 149569
-recovered pasa_asmbl_54088.p1, internal, 148921, 149047
-recovered pasa_asmbl_54088.p1, internal, 149298, 149381
Valid prediction for snap_scaffold_9-snap.1311-T1
Valid prediction for CodingQuarry_transcript_62195-T1
Valid prediction for Augustus_model.g14818.t1
Valid prediction for Augustus_model.g14831.t1
Valid prediction for snap_scaffold_9-snap.1305-T1
Valid prediction for CodingQuarry_transcript_62201-T1
Couldn't classify 9463, 9564
Sorry, prediction pasa_asmbl_54078.p1 fails validation.
(ATG)	 AG	1760-1858	GT	AGG
(GCG)	 AG	3192-3313	GT	ATG
(ATA)	 AG	5864-5932	GT	AGG
(GTA)	 AG	6524-6680	GT	AGG
(CAC)	 AG	9463-9564	TG	CGT
-recovered pasa_asmbl_54078.p1, initial, 1760, 1858
-recovered pasa_asmbl_54078.p1, internal, 1760, 1858
-recovered pasa_asmbl_54078.p1, internal, 3192, 3313
-recovered pasa_asmbl_54078.p1, internal, 5864, 5932
-recovered pasa_asmbl_54078.p1, internal, 6524, 6680
Valid prediction for Augustus_model.g14821.t1
Valid prediction for GlimmerHMM_glimmerT_22295-T1
Valid prediction for Augustus_model.g14823.t1
Valid prediction for pasa_asmbl_54079.p1
Valid prediction for GlimmerHMM_glimmerT_22308-T1
Valid prediction for CodingQuarry_transcript_62198-T1
Couldn't classify 146876, 147142
Sorry, prediction pasa_asmbl_54087.p1 fails validation.
(ATG)	 CC	144952-145147	GT	AGG
(CCA)	 AG	145353-145829	GT	AGG
(GCC)	 AG	145967-146206	GT	AGG
(ATG)	 AG	146335-146444	GT	AGG
(AAT)	 AG	146676-146762	GT	AGG
(GAC)	 AG	146876-147142	GG	AAG
-recovered pasa_asmbl_54087.p1, initial, 144952, 145147
add_exon() Sorry, pasa_asmbl_54087.p1 146335-146444-initial-1 is invalid.
-recovered pasa_asmbl_54087.p1, initial, 146335, 146444
-recovered pasa_asmbl_54087.p1, internal, 145353, 145829
-recovered pasa_asmbl_54087.p1, internal, 145967, 146206
-recovered pasa_asmbl_54087.p1, internal, 146335, 146444
-recovered pasa_asmbl_54087.p1, internal, 146676, 146762
Valid prediction for GlimmerHMM_glimmerT_22306-T1
Valid prediction for snap_scaffold_9-snap.1325-T1
Valid prediction for snap_scaffold_9-snap.1318-T1
Valid prediction for Augustus_model.g14822.t1
Valid prediction for snap_scaffold_9-snap.1328-T1
Valid prediction for snap_scaffold_9-snap.1315-T1
Valid prediction for snap_scaffold_9-snap.1317-T1
Valid prediction for snap_scaffold_9-snap.1304-T1
Valid prediction for snap_scaffold_9-snap.1326-T1
Valid prediction for HiQ_model.g14829.t1
Valid prediction for GlimmerHMM_glimmerT_22287-T1
Valid prediction for pasa_asmbl_54084.p1

-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_9-snap.1306-T1
Valid prediction for Augustus_model.g14824.t1
Valid prediction for snap_scaffold_9-snap.1330-T1
Valid prediction for GlimmerHMM_glimmerT_22304-T1
Valid prediction for snap_scaffold_9-snap.1323-T1
Valid prediction for GlimmerHMM_glimmerT_22312-T1
Valid prediction for Augustus_model.g14817.t1
Valid prediction for Augustus_model.g14816.t1
Valid prediction for GlimmerHMM_glimmerT_22294-T1
Valid prediction for GlimmerHMM_glimmerT_22297-T1
Valid prediction for snap_scaffold_9-snap.1319-T1
Valid prediction for snap_scaffold_9-snap.1301-T1
Valid prediction for pasa_asmbl_55051.p1
Valid prediction for snap_scaffold_9-snap.1316-T1
Valid prediction for GlimmerHMM_glimmerT_22301-T1
Valid prediction for snap_scaffold_9-snap.1310-T1
Valid prediction for snap_scaffold_9-snap.1302-T1
Valid prediction for snap_scaffold_9-snap.1322-T1
Valid prediction for Augustus_model.g14833.t1
Valid prediction for snap_scaffold_9-snap.1327-T1
Valid prediction for GlimmerHMM_glimmerT_22293-T1
Valid prediction for GlimmerHMM_glimmerT_22299-T1
Valid prediction for snap_scaffold_9-snap.1312-T1
Valid prediction for Augustus_model.g14819.t1
Valid prediction for snap_scaffold_9-snap.1320-T1
Valid prediction for Augustus_model.g14830.t1
Valid prediction for HiQ_model.g14826.t1
Valid prediction for GlimmerHMM_glimmerT_22310-T1
Valid prediction for snap_scaffold_9-snap.1334-T1
Valid prediction for snap_scaffold_9-snap.1300-T1
Valid prediction for snap_scaffold_9-snap.1308-T1
Couldn't classify 116217, 116324
Couldn't classify 116367, 116516
Sorry, prediction CodingQuarry_transcript_62196-T1 fails validation.
(ATG)	 GT	116217-116324	AT	TCA
(ATC)	 TC	116367-116516	CC	AAC
Valid prediction for snap_scaffold_9-snap.1332-T1
Valid prediction for GlimmerHMM_glimmerT_22290-T1
Valid prediction for snap_scaffold_9-snap.1333-T1
Valid prediction for GlimmerHMM_glimmerT_22305-T1
Valid prediction for GlimmerHMM_glimmerT_22303-T1
Valid prediction for GlimmerHMM_glimmerT_22298-T1
Valid prediction for snap_scaffold_9-snap.1309-T1
Valid prediction for CodingQuarry_transcript_62200-T1
Couldn't classify 110920, 111600
Sorry, prediction pasa_asmbl_55050.p1 fails validation.
(CTC)	 AC	110920-111600	GC	CGG
Valid prediction for snap_scaffold_9-snap.1313-T1
Couldn't classify 67417, 67468
Couldn't classify 67553, 67633
Sorry, prediction CodingQuarry_transcript_62199-T1 fails validation.
(ATG)	 AA	66597-66599	GT	TGG
(TCA)	 AG	67013-67109	GT	GAG
(TGA)	 AG	67284-67333	GC	AGG
(GAC)	 AG	67417-67468	AT	ATA
(TCA)	 AT	67553-67633	GT	TGG
(GAT)	 AG	67780-67853	GT	AGG
(GTT)	 AG	67966-68037	GG	GAG
-recovered CodingQuarry_transcript_62199-T1, initial, 66597, 66599
add_exon() Sorry, CodingQuarry_transcript_62199-T1 67013-67109-terminal-3 is invalid.
-recovered CodingQuarry_transcript_62199-T1, terminal, 67013, 67109
-recovered CodingQuarry_transcript_62199-T1, terminal, 67966, 68037
-recovered CodingQuarry_transcript_62199-T1, internal, 67013, 67109
-recovered CodingQuarry_transcript_62199-T1, internal, 67284, 67333
-recovered CodingQuarry_transcript_62199-T1, internal, 67780, 67853
Valid prediction for GlimmerHMM_glimmerT_22288-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17312, rend_intergenic: 10350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49738, rend_intergenic: 35376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78851, rend_intergenic: 52732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86359, rend_intergenic: 83191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91885, rend_intergenic: 86791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95388, rend_intergenic: 92355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113358, rend_intergenic: 108730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120217, rend_intergenic: 114159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130546, rend_intergenic: 127778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149471, rend_intergenic: 146950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208870
-exon list size: 381


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.9    
3.1    
3.4    
3.7    
3.9    
4.2    
4.4    
4.7    
5.0    
5.2    
5.5    
5.7    
6.0    
6.3    
6.5    
6.8    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
17.0    
17.2    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.1    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.7    
21.9    
22.2    
22.5    
22.7    
23.0    
23.2    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.2    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.1    
31.3    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.6    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.4    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.4    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.7    
68.9    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.8    
71.0    
71.3    
71.5    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.8    
77.0    
77.3    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.8    
83.0    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.2    
86.4    
86.7    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.7    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 17312, rend_intergenic: 10350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49738, rend_intergenic: 35376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78851, rend_intergenic: 52732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86359, rend_intergenic: 83191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91885, rend_intergenic: 86791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95388, rend_intergenic: 92355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113358, rend_intergenic: 108730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120217, rend_intergenic: 114159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130546, rend_intergenic: 127778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149471, rend_intergenic: 146950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support