-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_10203053-10352781

-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_53327-T1
Valid prediction for snap_scaffold_24-snap.2204-T1
Valid prediction for GlimmerHMM_glimmerT_53306-T1
Valid prediction for snap_scaffold_24-snap.2184-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53302-T1
Valid prediction for Augustus_model.g35490.t1
Valid prediction for Augustus_model.g35476.t1
Couldn't classify 125151, 125249
Couldn't classify 125709, 125770
Sorry, prediction pasa_asmbl_32553.p1 fails validation.
(CTC)	 TC	125151-125249	GT	AGG
(GTG)	 AG	125391-125553	GT	AGG
(AGG)	 AG	125709-125770	CT	AGC
-recovered pasa_asmbl_32553.p1, internal, 125391, 125553
Valid prediction for Augustus_model.g35477.t1
Valid prediction for snap_scaffold_24-snap.2176-T1
Valid prediction for CodingQuarry_transcript_37430-T1
Valid prediction for GlimmerHMM_glimmerT_53305-T1
Valid prediction for snap_scaffold_24-snap.2186-T1
Valid prediction for Augustus_model.g35479.t1
Valid prediction for GlimmerHMM_glimmerT_53300-T1
Valid prediction for snap_scaffold_24-snap.2175-T1
Valid prediction for snap_scaffold_24-snap.2180-T1
Valid prediction for GlimmerHMM_glimmerT_53309-T1
Valid prediction for CodingQuarry_transcript_37431-T1
Valid prediction for snap_scaffold_24-snap.2199-T1
Couldn't classify 127630, 127787
Sorry, prediction pasa_asmbl_32554.p1 fails validation.
(CAG)	 TG	127630-127787	GT	ACG
(AAC)	 AG	129596-129704	GT	TGG
(GTG)	 AG	129816-130054	GT	AGG
(GTA)	 AG	130161-130338	GT	AGG
(GAG)	 AG	130975-131208	GT	AGG
(ATG)	 AG	131312-131497	GT	AGG
(GAG)	 AG	131602-131796	GT	TGG
(ATC)	 AG	132004-132111	GT	AGG
(TCG)	 AG	132331-132537	GT	TGG
(GCC)	 AG	132631-132721	GT	AGG
(AGA)	 AG	132941-133068	GA	GAG
-recovered pasa_asmbl_32554.p1, initial, 131312, 131497
-recovered pasa_asmbl_32554.p1, terminal, 132941, 133068
-recovered pasa_asmbl_32554.p1, internal, 129596, 129704
-recovered pasa_asmbl_32554.p1, internal, 129816, 130054
-recovered pasa_asmbl_32554.p1, internal, 130161, 130338
-recovered pasa_asmbl_32554.p1, internal, 130975, 131208
-recovered pasa_asmbl_32554.p1, internal, 131312, 131497
-recovered pasa_asmbl_32554.p1, internal, 131602, 131796
-recovered pasa_asmbl_32554.p1, internal, 132004, 132111
-recovered pasa_asmbl_32554.p1, internal, 132331, 132537
-recovered pasa_asmbl_32554.p1, internal, 132631, 132721
Valid prediction for GlimmerHMM_glimmerT_53315-T1
Valid prediction for GlimmerHMM_glimmerT_53298-T1
Valid prediction for Augustus_model.g35478.t1
Valid prediction for HiQ_model.g35480.t1
Valid prediction for GlimmerHMM_glimmerT_53304-T1
Valid prediction for snap_scaffold_24-snap.2190-T1
Valid prediction for GlimmerHMM_glimmerT_53325-T1
Valid prediction for snap_scaffold_24-snap.2187-T1
Valid prediction for snap_scaffold_24-snap.2206-T1
Valid prediction for Augustus_model.g35474.t1
Valid prediction for GlimmerHMM_glimmerT_53324-T1
Valid prediction for GlimmerHMM_glimmerT_53326-T1
Valid prediction for snap_scaffold_24-snap.2211-T1
Valid prediction for Augustus_model.g35491.t1
Valid prediction for snap_scaffold_24-snap.2179-T1
Valid prediction for GlimmerHMM_glimmerT_53311-T1
Valid prediction for Augustus_model.g35475.t1
Valid prediction for GlimmerHMM_glimmerT_53301-T1
Valid prediction for GlimmerHMM_glimmerT_53319-T1
Valid prediction for snap_scaffold_24-snap.2182-T1
Valid prediction for snap_scaffold_24-snap.2208-T1
Valid prediction for GlimmerHMM_glimmerT_53307-T1
Valid prediction for snap_scaffold_24-snap.2178-T1
Valid prediction for snap_scaffold_24-snap.2200-T1
Valid prediction for snap_scaffold_24-snap.2181-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.2195-T1
Valid prediction for pasa_asmbl_32550.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 GlimmerHMM_glimmerT_53299-T1
Valid prediction for snap_scaffold_24-snap.2209-T1
Valid prediction for Augustus_model.g35484.t1
Valid prediction for GlimmerHMM_glimmerT_53313-T1
Valid prediction for pasa_asmbl_33182.p1
Valid prediction for Augustus_model.g35481.t1
Valid prediction for GlimmerHMM_glimmerT_53323-T1
Valid prediction for snap_scaffold_24-snap.2201-T1
Valid prediction for CodingQuarry_transcript_37432-T1
Valid prediction for snap_scaffold_24-snap.2198-T1
Valid prediction for GlimmerHMM_glimmerT_53318-T1
Valid prediction for GlimmerHMM_glimmerT_53303-T1
Couldn't classify 69749, 69775
Sorry, prediction pasa_asmbl_33175.p1 fails validation.
(CTC)	 GC	69749-69775	GT	ACG
(GCT)	 AG	70224-70337	GT	CGG
(GTG)	 AG	70525-70612	GT	AGG
(CGG)	 AG	70983-71149	GT	CGG
(ATG)	 AG	71365-71478	GT	CGG
(CAC)	 AG	71608-71691	GT	AGG
(TCA)	 AG	71872-72627	TC	GAT
-recovered pasa_asmbl_33175.p1, initial, 71365, 71478
-recovered pasa_asmbl_33175.p1, terminal, 71872, 72627
-recovered pasa_asmbl_33175.p1, internal, 70224, 70337
-recovered pasa_asmbl_33175.p1, internal, 70525, 70612
-recovered pasa_asmbl_33175.p1, internal, 70983, 71149
-recovered pasa_asmbl_33175.p1, internal, 71365, 71478
-recovered pasa_asmbl_33175.p1, internal, 71608, 71691
Couldn't classify 80340, 80420
Sorry, prediction pasa_asmbl_33173.p1 fails validation.
(ATG)	 CA	78528-78741	GT	CGG
(AGT)	 AG	79064-79169	GT	AGG
(GAA)	 AG	79426-79573	GT	AGG
(GTC)	 AG	79673-79720	GT	AGG
(ATC)	 AG	79871-79948	GT	AGG
(GTG)	 AG	80068-80205	GT	ATG
(AAC)	 AG	80340-80420	AA	ACA
-recovered pasa_asmbl_33173.p1, initial, 78528, 78741
-recovered pasa_asmbl_33173.p1, internal, 79064, 79169
-recovered pasa_asmbl_33173.p1, internal, 79426, 79573
-recovered pasa_asmbl_33173.p1, internal, 79673, 79720
-recovered pasa_asmbl_33173.p1, internal, 79871, 79948
-recovered pasa_asmbl_33173.p1, internal, 80068, 80205
Valid prediction for snap_scaffold_24-snap.2183-T1
Valid prediction for snap_scaffold_24-snap.2191-T1
Valid prediction for Augustus_model.g35489.t1
Valid prediction for Augustus_model.g35486.t1
Valid prediction for snap_scaffold_24-snap.2177-T1
Couldn't classify 10741, 10844
Couldn't classify 11698, 11738
Sorry, prediction pasa_asmbl_33180.p1 fails validation.
(TAC)	 CC	10741-10844	GT	AGG
(TGA)	 AG	10995-11134	GT	GGG
(GTC)	 AG	11396-11536	GT	AGG
(AGT)	 AG	11698-11738	AC	AGA
-recovered pasa_asmbl_33180.p1, internal, 10995, 11134
-recovered pasa_asmbl_33180.p1, internal, 11396, 11536
Valid prediction for GlimmerHMM_glimmerT_53328-T1
Valid prediction for GlimmerHMM_glimmerT_53314-T1
Valid prediction for GlimmerHMM_glimmerT_53320-T1
Valid prediction for GlimmerHMM_glimmerT_53312-T1
Valid prediction for snap_scaffold_24-snap.2188-T1
Valid prediction for Augustus_model.g35488.t1
Valid prediction for GlimmerHMM_glimmerT_53329-T1
Couldn't classify 63253, 63339
Couldn't classify 63496, 63972
Sorry, prediction pasa_asmbl_33178.p1 fails validation.
(CCG)	 AG	63253-63339	GT	AGG
(GTG)	 AG	63496-63972	CG	CCC
-recovered pasa_asmbl_33178.p1, internal, 63253, 63339
Valid prediction for HiQ_model.g35483.t1
Valid prediction for GlimmerHMM_glimmerT_53316-T1
Couldn't classify 67579, 67677
Sorry, prediction pasa_asmbl_33177.p1 fails validation.
(ATG)	 CC	65946-66143	GT	AGG
(GAA)	 AG	66253-66363	GT	CGG
(CAA)	 AG	66541-66625	GT	AAG
(TGG)	 AG	66816-66982	GT	CGG
(TGG)	 AG	67123-67239	GT	CTG
(CGC)	 AG	67348-67422	GT	AGG
(AAT)	 AG	67579-67677	CA	GCC
-recovered pasa_asmbl_33177.p1, initial, 65946, 66143
-recovered pasa_asmbl_33177.p1, internal, 66253, 66363
-recovered pasa_asmbl_33177.p1, internal, 66541, 66625
-recovered pasa_asmbl_33177.p1, internal, 66816, 66982
-recovered pasa_asmbl_33177.p1, internal, 67123, 67239
-recovered pasa_asmbl_33177.p1, internal, 67348, 67422
Valid prediction for snap_scaffold_24-snap.2205-T1
Valid prediction for HiQ_model.g35493.t1
Valid prediction for snap_scaffold_24-snap.2197-T1
Valid prediction for GlimmerHMM_glimmerT_53322-T1
Valid prediction for GlimmerHMM_glimmerT_53308-T1
Valid prediction for Augustus_model.g35492.t1
Valid prediction for GlimmerHMM_glimmerT_53317-T1
Valid prediction for snap_scaffold_24-snap.2192-T1
Valid prediction for Augustus_model.g35485.t1
Valid prediction for snap_scaffold_24-snap.2203-T1
Valid prediction for snap_scaffold_24-snap.2202-T1
Valid prediction for snap_scaffold_24-snap.2196-T1
Valid prediction for snap_scaffold_24-snap.2207-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g35482.t1
Valid prediction for GlimmerHMM_glimmerT_53321-T1
Valid prediction for snap_scaffold_24-snap.2185-T1
Couldn't classify 12453, 12554
Sorry, prediction pasa_asmbl_33179.p1 fails validation.
(TAC)	 CC	12453-12554	GT	AGG
(AAA)	 AG	12629-12779	GT	CTG
(CTT)	 AG	13341-13553	GT	GGG
(GTC)	 AG	13670-13877	GT	AGG
(CCC)	 AG	13999-14135	GT	GGG
(GCC)	 AG	14225-14353	GT	TGG
(GTG)	 AG	14483-14589	GT	AGG
(GAC)	 AG	14687-14906	GT	CGG
(CAA)	 AG	15059-15198	GT	AGG
(CTG)	 AG	15498-15660	GT	GGG
(GCA)	 AG	15820-15845	TG	GAT
-recovered pasa_asmbl_33179.p1, terminal, 15820, 15845
-recovered pasa_asmbl_33179.p1, internal, 12629, 12779
-recovered pasa_asmbl_33179.p1, internal, 13341, 13553
-recovered pasa_asmbl_33179.p1, internal, 13670, 13877
-recovered pasa_asmbl_33179.p1, internal, 13999, 14135
-recovered pasa_asmbl_33179.p1, internal, 14225, 14353
-recovered pasa_asmbl_33179.p1, internal, 14483, 14589
-recovered pasa_asmbl_33179.p1, internal, 14687, 14906
-recovered pasa_asmbl_33179.p1, internal, 15059, 15198
-recovered pasa_asmbl_33179.p1, internal, 15498, 15660
Valid prediction for snap_scaffold_24-snap.2194-T1
Valid prediction for GlimmerHMM_glimmerT_53330-T1
Valid prediction for snap_scaffold_24-snap.2193-T1
Valid prediction for GlimmerHMM_glimmerT_53310-T1
Valid prediction for snap_scaffold_24-snap.2210-T1
Valid prediction for Augustus_model.g35487.t1
Valid prediction for snap_scaffold_24-snap.2189-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17731, rend_intergenic: 10527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37878, rend_intergenic: 25212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39847, rend_intergenic: 38161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41368, rend_intergenic: 40329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54535, rend_intergenic: 41436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61379, rend_intergenic: 56198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88351, rend_intergenic: 85740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97192, rend_intergenic: 93005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118017, rend_intergenic: 97279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122660, rend_intergenic: 119325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133068, rend_intergenic: 124937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139840, rend_intergenic: 133872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146342, rend_intergenic: 142070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 149729
-exon list size: 469


building trellis

0.2    
0.4    
0.6    
0.8    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.0    
4.2    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 17731, rend_intergenic: 10527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37878, rend_intergenic: 25212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39847, rend_intergenic: 38161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41368, rend_intergenic: 40329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54535, rend_intergenic: 41436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61379, rend_intergenic: 56198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88351, rend_intergenic: 85740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97192, rend_intergenic: 93005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118017, rend_intergenic: 97279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122660, rend_intergenic: 119325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133068, rend_intergenic: 124937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139840, rend_intergenic: 133872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146342, rend_intergenic: 142070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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