-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_9670331-9888103

-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.2098-T1
Valid prediction for snap_scaffold_6-snap.2100-T1
Valid prediction for HiQ_model.g10180.t1
Valid prediction for snap_scaffold_6-snap.2111-T1
Valid prediction for snap_scaffold_6-snap.2120-T1
Valid prediction for snap_scaffold_6-snap.2106-T1
Valid prediction for Augustus_model.g10179.t1
Valid prediction for GlimmerHMM_glimmerT_15313-T1
Valid prediction for CodingQuarry_transcript_55172-T1
Valid prediction for GlimmerHMM_glimmerT_15311-T1
Valid prediction for snap_scaffold_6-snap.2116-T1
Valid prediction for GlimmerHMM_glimmerT_15316-T1
Valid prediction for GlimmerHMM_glimmerT_15310-T1
Valid prediction for Augustus_model.g10175.t1
Valid prediction for GlimmerHMM_glimmerT_15293-T1
Valid prediction for GlimmerHMM_glimmerT_15302-T1
Valid prediction for snap_scaffold_6-snap.2105-T1
Valid prediction for GlimmerHMM_glimmerT_15305-T1
Valid prediction for GlimmerHMM_glimmerT_15317-T1
Couldn't classify 99594, 99748
Sorry, prediction pasa_asmbl_47239.p1 fails validation.
(ACC)	 AG	99594-99748	GT	AGG
(GAT)	 AG	99898-99987	GT	GTG
(GAT)	 AG	100093-100230	GT	AGG
(ACA)	 AG	100341-100430	GT	AGG
(GTA)	 AG	100586-100698	GT	AGG
(GGA)	 AG	101651-101731	GT	GGG
(GAG)	 AG	102431-102570	GA	AAG
-recovered pasa_asmbl_47239.p1, terminal, 100341, 100430
-recovered pasa_asmbl_47239.p1, terminal, 102431, 102570
-recovered pasa_asmbl_47239.p1, internal, 99594, 99748
-recovered pasa_asmbl_47239.p1, internal, 99898, 99987
-recovered pasa_asmbl_47239.p1, internal, 100093, 100230
-recovered pasa_asmbl_47239.p1, internal, 100341, 100430
-recovered pasa_asmbl_47239.p1, internal, 100586, 100698
-recovered pasa_asmbl_47239.p1, internal, 101651, 101731
Valid prediction for snap_scaffold_6-snap.2124-T1
Valid prediction for Augustus_model.g10159.t1
Valid prediction for snap_scaffold_6-snap.2117-T1
Valid prediction for snap_scaffold_6-snap.2128-T1
Valid prediction for Augustus_model.g10168.t1
Valid prediction for snap_scaffold_6-snap.2107-T1
Valid prediction for CodingQuarry_transcript_55175-T1
Valid prediction for GlimmerHMM_glimmerT_15301-T1
Valid prediction for CodingQuarry_transcript_55176-T1
Valid prediction for snap_scaffold_6-snap.2121-T1
Valid prediction for GlimmerHMM_glimmerT_15295-T1
Valid prediction for GlimmerHMM_glimmerT_15315-T1
Valid prediction for snap_scaffold_6-snap.2118-T1
Valid prediction for Augustus_model.g10176.t1
Valid prediction for GlimmerHMM_glimmerT_15304-T1
Valid prediction for pasa_asmbl_47241.p1
Valid prediction for CodingQuarry_transcript_55177-T1
Valid prediction for pasa_asmbl_47243.p1
Couldn't classify 85620, 85698
Couldn't classify 86465, 86628
Sorry, prediction pasa_asmbl_47236.p1 fails validation.
(CAC)	 CT	85620-85698	GT	TGG
(CTC)	 AG	85953-86119	GT	CGG
(GTG)	 AG	86252-86351	GT	AGG
(GAG)	 AG	86465-86628	AA	CCA
add_exon() Sorry, pasa_asmbl_47236.p1 86252-86351-terminal-3 is invalid.
-recovered pasa_asmbl_47236.p1, terminal, 86252, 86351
-recovered pasa_asmbl_47236.p1, internal, 85953, 86119
-recovered pasa_asmbl_47236.p1, internal, 86252, 86351
Valid prediction for snap_scaffold_6-snap.2113-T1
Valid prediction for GlimmerHMM_glimmerT_15314-T1
Valid prediction for Augustus_model.g10158.t1
Valid prediction for GlimmerHMM_glimmerT_15298-T1
Valid prediction for GlimmerHMM_glimmerT_15312-T1
Couldn't classify 108716, 108821
Sorry, prediction pasa_asmbl_47240.p1 fails validation.
(AAC)	 CG	108716-108821	GT	GGG
(CTA)	 AG	109249-109943	GC	GAG
-recovered pasa_asmbl_47240.p1, terminal, 109249, 109943
-recovered pasa_asmbl_47240.p1, internal, 109249, 109943
Valid prediction for HiQ_model.g10173.t1
Valid prediction for HiQ_model.g10170.t1
Valid prediction for Augustus_model.g10177.t1
Valid prediction for snap_scaffold_6-snap.2114-T1
Valid prediction for snap_scaffold_6-snap.2108-T1
Valid prediction for Augustus_model.g10174.t1
Valid prediction for snap_scaffold_6-snap.2119-T1
Valid prediction for snap_scaffold_6-snap.2090-T1
Valid prediction for snap_scaffold_6-snap.2122-T1
Valid prediction for pasa_asmbl_47244.p1
Valid prediction for snap_scaffold_6-snap.2115-T1
Valid prediction for GlimmerHMM_glimmerT_15306-T1
Valid prediction for HiQ_model.g10178.t1
Valid prediction for snap_scaffold_6-snap.2112-T1
Valid prediction for Augustus_model.g10171.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.2094-T1
Valid prediction for snap_scaffold_6-snap.2101-T1
Valid prediction for Augustus_model.g10161.t1
Valid prediction for snap_scaffold_6-snap.2084-T1
Valid prediction for Augustus_model.g10182.t1
Valid prediction for snap_scaffold_6-snap.2091-T1
Valid prediction for GlimmerHMM_glimmerT_15303-T1
Couldn't classify 189573, 189593
Couldn't classify 190908, 190957
Sorry, prediction pasa_asmbl_48631.p1 fails validation.
(GGG)	 AG	189573-189593	GT	AGG
(GTG)	 AG	189719-190382	GT	TGG
(CAG)	 AG	190491-190661	GT	AGG
(GTA)	 AG	190908-190957	GC	GCG
-recovered pasa_asmbl_48631.p1, internal, 189573, 189593
-recovered pasa_asmbl_48631.p1, internal, 189719, 190382
-recovered pasa_asmbl_48631.p1, internal, 190491, 190661
-recovered pasa_asmbl_48631.p1, internal, 190908, 190957
Couldn't classify 161128, 161350
Couldn't classify 161764, 162044
Sorry, prediction pasa_asmbl_48636.p1 fails validation.
(TTG)	 AC	161128-161350	GT	TGG
(TTC)	 AG	161522-161563	GT	TGG
(GTG)	 AG	161764-162044	GT	CGG
-recovered pasa_asmbl_48636.p1, internal, 161522, 161563
-recovered pasa_asmbl_48636.p1, internal, 161764, 162044
Valid prediction for GlimmerHMM_glimmerT_15307-T1
Valid prediction for snap_scaffold_6-snap.2110-T1
Valid prediction for Augustus_model.g10172.t1
Valid prediction for snap_scaffold_6-snap.2093-T1
Valid prediction for GlimmerHMM_glimmerT_15294-T1
Valid prediction for snap_scaffold_6-snap.2109-T1
Valid prediction for snap_scaffold_6-snap.2097-T1
Valid prediction for Augustus_model.g10162.t1
Valid prediction for snap_scaffold_6-snap.2087-T1
Valid prediction for snap_scaffold_6-snap.2123-T1
Valid prediction for snap_scaffold_6-snap.2085-T1
Valid prediction for Augustus_model.g10164.t1
Valid prediction for snap_scaffold_6-snap.2099-T1
Valid prediction for GlimmerHMM_glimmerT_15300-T1
Couldn't classify 127001, 127057
Sorry, prediction pasa_asmbl_48637.p1 fails validation.
(GTA)	 TA	127001-127057	GT	GAG
(AGG)	 AG	127564-127665	GT	CCG
(GGA)	 AG	127753-127824	GT	CGG
(ATT)	 AG	128089-128185	GT	CGG
(GCG)	 AG	128392-128579	GT	GGG
(GGT)	 AG	128734-128839	GT	TGG
(AGG)	 AG	129324-129550	AC	GAA
-recovered pasa_asmbl_48637.p1, terminal, 129324, 129550
-recovered pasa_asmbl_48637.p1, internal, 127564, 127665
-recovered pasa_asmbl_48637.p1, internal, 127753, 127824
-recovered pasa_asmbl_48637.p1, internal, 128089, 128185
-recovered pasa_asmbl_48637.p1, internal, 128392, 128579
-recovered pasa_asmbl_48637.p1, internal, 128734, 128839
Valid prediction for snap_scaffold_6-snap.2127-T1
Valid prediction for GlimmerHMM_glimmerT_15299-T1
Valid prediction for CodingQuarry_transcript_55171-T1
Valid prediction for Augustus_model.g10165.t1
Couldn't classify 30619, 30725
Sorry, prediction pasa_asmbl_49423.p1 fails validation.
(GAT)	 AG	30619-30725	GT	AGG
(TCA)	 AG	30987-31128	GT	AGG
(GTC)	 AG	31352-31424	GT	AGG
(GCT)	 AG	34022-34113	GT	TGG
(GCA)	 AG	35515-35611	GT	AGG
(ATT)	 AG	35734-35861	GT	CTG
(ACA)	 AG	36429-36521	GT	AGG
(GTT)	 AG	37042-37107	GT	AGG
(ATC)	 AG	37285-37473	GT	AGG
(GAG)	 AG	37595-37711	GT	AGG
(AAT)	 AG	37830-37879	GT	GGG
(GAG)	 AG	38021-38148	GT	AGG
(AGT)	 AG	38460-38517	GT	GAG
(GTC)	 AG	38715-38772	AC	AGA
-recovered pasa_asmbl_49423.p1, terminal, 38715, 38772
-recovered pasa_asmbl_49423.p1, internal, 30619, 30725
-recovered pasa_asmbl_49423.p1, internal, 30987, 31128
-recovered pasa_asmbl_49423.p1, internal, 31352, 31424
-recovered pasa_asmbl_49423.p1, internal, 34022, 34113
-recovered pasa_asmbl_49423.p1, internal, 35515, 35611
-recovered pasa_asmbl_49423.p1, internal, 35734, 35861
-recovered pasa_asmbl_49423.p1, internal, 36429, 36521
-recovered pasa_asmbl_49423.p1, internal, 37042, 37107
-recovered pasa_asmbl_49423.p1, internal, 37285, 37473
-recovered pasa_asmbl_49423.p1, internal, 37595, 37711
-recovered pasa_asmbl_49423.p1, internal, 37830, 37879
-recovered pasa_asmbl_49423.p1, internal, 38021, 38148
-recovered pasa_asmbl_49423.p1, internal, 38460, 38517
Valid prediction for GlimmerHMM_glimmerT_15318-T1
Valid prediction for GlimmerHMM_glimmerT_15296-T1
Valid prediction for HiQ_model.g10169.t1
Valid prediction for Augustus_model.g10163.t1
Valid prediction for GlimmerHMM_glimmerT_15297-T1
Valid prediction for snap_scaffold_6-snap.2086-T1
Valid prediction for GlimmerHMM_glimmerT_15308-T1
Valid prediction for snap_scaffold_6-snap.2089-T1
Valid prediction for Augustus_model.g10166.t1
Couldn't classify 191003, 191013
Sorry, prediction pasa_asmbl_48630.p1 fails validation.
(TTC)	 CC	191003-191013	GT	AGG
(GAA)	 AG	191215-191312	GT	ATG
(TCT)	 AG	191947-192251	TG	AGT
-recovered pasa_asmbl_48630.p1, terminal, 191947, 192251
-recovered pasa_asmbl_48630.p1, internal, 191215, 191312
Valid prediction for snap_scaffold_6-snap.2103-T1
Valid prediction for snap_scaffold_6-snap.2088-T1
Valid prediction for snap_scaffold_6-snap.2095-T1
Valid prediction for Augustus_model.g10160.t1
Valid prediction for snap_scaffold_6-snap.2125-T1
Valid prediction for GlimmerHMM_glimmerT_15309-T1
Valid prediction for snap_scaffold_6-snap.2126-T1
Valid prediction for snap_scaffold_6-snap.2092-T1
Valid prediction for CodingQuarry_transcript_55173-T1
Valid prediction for Augustus_model.g10167.t1
Valid prediction for snap_scaffold_6-snap.2102-T1
Valid prediction for pasa_asmbl_48638.p1
Valid prediction for snap_scaffold_6-snap.2096-T1
Valid prediction for snap_scaffold_6-snap.2104-T1
Couldn't classify 172781, 173042
Sorry, prediction pasa_asmbl_48634.p1 fails validation.
(CAA)	 CG	172781-173042	GT	AGG
(TCG)	 AG	174180-174536	GT	TGG
(ATT)	 AG	174909-175217	GT	CGG
(GAG)	 AG	175559-175953	AG	AGA
-recovered pasa_asmbl_48634.p1, terminal, 175559, 175953
-recovered pasa_asmbl_48634.p1, internal, 174180, 174536
-recovered pasa_asmbl_48634.p1, internal, 174909, 175217
Valid prediction for HiQ_model.g10181.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 102570, rend_intergenic: 97670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130076, rend_intergenic: 124104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184802, rend_intergenic: 180630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187221, rend_intergenic: 185997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217773
-exon list size: 421


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.7    
1.9    
2.1    
2.4    
2.6    
2.8    
3.1    
3.3    
3.5    
3.8    
4.0    
4.3    
4.5    
4.7    
5.0    
5.2    
5.4    
5.7    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.3    
7.6    
7.8    
8.0    
8.3    
8.5    
8.7    
9.0    
9.2    
9.5    
9.7    
9.9    
10.2    
10.4    
10.6    
10.9    
11.1    
11.3    
11.6    
11.8    
12.1    
12.3    
12.5    
12.8    
13.0    
13.2    
13.5    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.1    
15.4    
15.6    
15.8    
16.1    
16.3    
16.5    
16.8    
17.0    
17.3    
17.5    
17.7    
18.0    
18.2    
18.4    
18.7    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.0    
21.3    
21.5    
21.7    
22.0    
22.2    
22.5    
22.7    
22.9    
23.2    
23.4    
23.6    
23.9    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.4    
27.7    
27.9    
28.1    
28.4    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
31.0    
31.2    
31.4    
31.7    
31.9    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.9    
37.1    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.4    
41.6    
41.8    
42.1    
42.3    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
44.0    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.2    
48.5    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.5    
51.8    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.0    
56.3    
56.5    
56.7    
57.0    
57.2    
57.4    
57.7    
57.9    
58.2    
58.4    
58.6    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.2    
61.5    
61.7    
61.9    
62.2    
62.4    
62.6    
62.9    
63.1    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.8    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.1    
68.3    
68.6    
68.8    
69.0    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.6    
71.9    
72.1    
72.3    
72.6    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.5    
77.8    
78.0    
78.3    
78.5    
78.7    
79.0    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.3    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
83.9    
84.2    
84.4    
84.6    
84.9    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.5    
87.7    
87.9    
88.2    
88.4    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.3    
94.6    
94.8    
95.0    
95.3    
95.5    
95.7    
96.0    
96.2    
96.5    
96.7    
96.9    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 102570, rend_intergenic: 97670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130076, rend_intergenic: 124104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184802, rend_intergenic: 180630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187221, rend_intergenic: 185997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support