-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_11596938-11831931

-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_32439-T1
Valid prediction for snap_scaffold_13-snap.2164-T1
Valid prediction for snap_scaffold_13-snap.2173-T1
Valid prediction for GlimmerHMM_glimmerT_32432-T1
Couldn't classify 12027, 12227
Couldn't classify 16033, 16129
Sorry, prediction pasa_asmbl_11299.p1 fails validation.
(GCG)	 AG	12027-12227	GT	TGG
(ATT)	 AG	14768-14863	GT	ACG
(GAG)	 AG	15174-15514	GT	CGG
(CTC)	 AG	15839-15946	GT	AGG
(TCA)	 AG	16033-16129	AC	GGA
-recovered pasa_asmbl_11299.p1, internal, 12027, 12227
-recovered pasa_asmbl_11299.p1, internal, 14768, 14863
-recovered pasa_asmbl_11299.p1, internal, 15174, 15514
-recovered pasa_asmbl_11299.p1, internal, 15839, 15946
Valid prediction for snap_scaffold_13-snap.2182-T1
Valid prediction for GlimmerHMM_glimmerT_32423-T1
Valid prediction for GlimmerHMM_glimmerT_32438-T1
Valid prediction for Augustus_model.g21658.t1
Couldn't classify 121626, 121701
Sorry, prediction pasa_asmbl_11303.p1 fails validation.
(GAC)	 AA	121626-121701	GT	AGG
(GTG)	 AG	121787-121936	GT	AGG
(AGC)	 AG	122510-122665	GT	GGG
(GAA)	 AG	123195-123374	GT	AGG
(GAA)	 AG	123543-123619	GT	AGG
(ATC)	 AG	124316-124469	GT	AGG
(GAG)	 AG	124887-125018	GT	AGG
(GCA)	 AG	126607-126815	AG	AGA
-recovered pasa_asmbl_11303.p1, terminal, 126607, 126815
-recovered pasa_asmbl_11303.p1, internal, 121787, 121936
-recovered pasa_asmbl_11303.p1, internal, 122510, 122665
-recovered pasa_asmbl_11303.p1, internal, 123195, 123374
-recovered pasa_asmbl_11303.p1, internal, 123543, 123619
-recovered pasa_asmbl_11303.p1, internal, 124316, 124469
-recovered pasa_asmbl_11303.p1, internal, 124887, 125018
Valid prediction for GlimmerHMM_glimmerT_32428-T1
Couldn't classify 161291, 161340
Sorry, prediction pasa_asmbl_11310.p1 fails validation.
(AAC)	 AC	161291-161340	GT	AGG
(TGA)	 AG	161474-161568	GT	GAG
(TGA)	 AG	161726-161814	GT	AGG
(GAG)	 AG	161936-162023	GT	AGG
(GTG)	 AG	162123-162177	GT	AGG
(GAA)	 AG	162310-162466	GT	AGG
(GCG)	 AG	162584-162705	GT	AGG
(TGA)	 AG	162989-163202	GA	AGG
-recovered pasa_asmbl_11310.p1, terminal, 161474, 161568
-recovered pasa_asmbl_11310.p1, terminal, 162989, 163202
-recovered pasa_asmbl_11310.p1, internal, 161474, 161568
-recovered pasa_asmbl_11310.p1, internal, 161726, 161814
-recovered pasa_asmbl_11310.p1, internal, 161936, 162023
-recovered pasa_asmbl_11310.p1, internal, 162123, 162177
-recovered pasa_asmbl_11310.p1, internal, 162310, 162466
-recovered pasa_asmbl_11310.p1, internal, 162584, 162705
Valid prediction for Augustus_model.g21654.t1
Valid prediction for GlimmerHMM_glimmerT_32437-T1
Valid prediction for snap_scaffold_13-snap.2175-T1
Valid prediction for Augustus_model.g21670.t1
Valid prediction for snap_scaffold_13-snap.2190-T1
Valid prediction for Augustus_model.g21671.t1
Valid prediction for snap_scaffold_13-snap.2191-T1
Valid prediction for snap_scaffold_13-snap.2176-T1
Valid prediction for CodingQuarry_transcript_13254-T1
Valid prediction for GlimmerHMM_glimmerT_32422-T1
Valid prediction for snap_scaffold_13-snap.2168-T1
Valid prediction for pasa_asmbl_11287.p1
Valid prediction for snap_scaffold_13-snap.2171-T1
Valid prediction for snap_scaffold_13-snap.2189-T1
Valid prediction for snap_scaffold_13-snap.2179-T1
Valid prediction for GlimmerHMM_glimmerT_32436-T1
Valid prediction for snap_scaffold_13-snap.2188-T1
Valid prediction for snap_scaffold_13-snap.2199-T1
Valid prediction for GlimmerHMM_glimmerT_32430-T1
Valid prediction for snap_scaffold_13-snap.2187-T1
Valid prediction for snap_scaffold_13-snap.2194-T1
Valid prediction for Augustus_model.g21651.t1
Valid prediction for CodingQuarry_transcript_13252-T1
Valid prediction for snap_scaffold_13-snap.2186-T1
Valid prediction for Augustus_model.g21664.t1
Valid prediction for CodingQuarry_transcript_13255-T1
Valid prediction for GlimmerHMM_glimmerT_32444-T1
Valid prediction for snap_scaffold_13-snap.2185-T1
Valid prediction for GlimmerHMM_glimmerT_32443-T1
Valid prediction for snap_scaffold_13-snap.2163-T1
Valid prediction for GlimmerHMM_glimmerT_32435-T1
Valid prediction for HiQ_model.g21665.t1
Couldn't classify 153825, 153912
Sorry, prediction pasa_asmbl_11307.p1 fails validation.
(GTG)	 TA	153825-153912	GT	TGG
(AGT)	 AG	154069-155106	GT	AGG
(GTC)	 AG	155310-155816	GT	TGG
(GTT)	 AG	155944-156083	GT	AGG
(GAA)	 AG	156255-156364	GT	ACG
(GAG)	 AG	156535-156677	GT	GAG
(TTG)	 AG	156819-156838	CA	AGC
-recovered pasa_asmbl_11307.p1, terminal, 156819, 156838
-recovered pasa_asmbl_11307.p1, internal, 154069, 155106
-recovered pasa_asmbl_11307.p1, internal, 155310, 155816
-recovered pasa_asmbl_11307.p1, internal, 155944, 156083
-recovered pasa_asmbl_11307.p1, internal, 156255, 156364
-recovered pasa_asmbl_11307.p1, internal, 156535, 156677
Valid prediction for GlimmerHMM_glimmerT_32433-T1
Valid prediction for snap_scaffold_13-snap.2203-T1
Couldn't classify 16826, 16868
Sorry, prediction pasa_asmbl_11301.p1 fails validation.
(GGC)	 TA	16826-16868	GT	AGG
(GTG)	 AG	17062-17161	GT	AGG
(TGA)	 AG	17383-17567	GT	AGG
(AGA)	 AG	17704-17797	GT	AGG
(GTA)	 AG	17894-17963	GT	AGG
(GCC)	 AG	18052-18144	GT	AGG
(TCG)	 AG	18234-18313	GT	CCG
(GCC)	 AG	18438-18579	GT	TAG
(GCC)	 AG	19187-19335	GT	AAG
(GTC)	 AG	20243-20329	GT	GAG
(GAA)	 AG	20481-20633	GT	AGG
(AGA)	 AG	20955-21069	GT	ATG
(GAT)	 AG	22259-22362	GT	TCG
(GTA)	 AG	23098-23242	CC	GAC
add_exon() Sorry, pasa_asmbl_11301.p1 17704-17797-terminal-3 is invalid.
-recovered pasa_asmbl_11301.p1, terminal, 17704, 17797
-recovered pasa_asmbl_11301.p1, terminal, 23098, 23242
-recovered pasa_asmbl_11301.p1, internal, 17062, 17161
-recovered pasa_asmbl_11301.p1, internal, 17383, 17567
-recovered pasa_asmbl_11301.p1, internal, 17704, 17797
-recovered pasa_asmbl_11301.p1, internal, 17894, 17963
-recovered pasa_asmbl_11301.p1, internal, 18052, 18144
-recovered pasa_asmbl_11301.p1, internal, 18234, 18313
-recovered pasa_asmbl_11301.p1, internal, 18438, 18579
-recovered pasa_asmbl_11301.p1, internal, 19187, 19335
-recovered pasa_asmbl_11301.p1, internal, 20243, 20329
-recovered pasa_asmbl_11301.p1, internal, 20481, 20633
-recovered pasa_asmbl_11301.p1, internal, 20955, 21069
-recovered pasa_asmbl_11301.p1, internal, 22259, 22362
Couldn't classify 16148, 16159
Couldn't classify 16283, 16615
Sorry, prediction pasa_asmbl_11300.p1 fails validation.
(GAA)	 CA	16148-16159	GT	GGG
(GTA)	 AG	16283-16615	AC	TGA
Valid prediction for Augustus_model.g21655.t1
Valid prediction for Augustus_model.g21667.t1
Valid prediction for Augustus_model.g21666.t1
Valid prediction for snap_scaffold_13-snap.2192-T1
Valid prediction for snap_scaffold_13-snap.2174-T1
Couldn't classify 161145, 161218
Sorry, prediction pasa_asmbl_11308.p1 fails validation.
(ATG)	 CA	158339-158378	GT	TGG
(AGA)	 AG	159461-159545	GT	GGG
(GCC)	 AG	159853-159928	GT	CTG
(CTG)	 AG	160080-160175	GT	AGG
(GGT)	 AG	160267-160413	GT	AGG
(GCT)	 AG	160684-160774	GT	AGG
(CTA)	 AG	161145-161218	AG	CCA
-recovered pasa_asmbl_11308.p1, initial, 158339, 158378
-recovered pasa_asmbl_11308.p1, internal, 159461, 159545
-recovered pasa_asmbl_11308.p1, internal, 159853, 159928
-recovered pasa_asmbl_11308.p1, internal, 160080, 160175
-recovered pasa_asmbl_11308.p1, internal, 160267, 160413
-recovered pasa_asmbl_11308.p1, internal, 160684, 160774
Valid prediction for Augustus_model.g21662.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 GlimmerHMM_glimmerT_32426-T1
Valid prediction for GlimmerHMM_glimmerT_32442-T1
Valid prediction for snap_scaffold_13-snap.2202-T1
Valid prediction for snap_scaffold_13-snap.2183-T1
Valid prediction for GlimmerHMM_glimmerT_32427-T1
Valid prediction for pasa_asmbl_10105.p1
Valid prediction for snap_scaffold_13-snap.2169-T1
Valid prediction for snap_scaffold_13-snap.2165-T1
Valid prediction for Augustus_model.g21663.t1
Valid prediction for pasa_asmbl_10103.p1
Valid prediction for snap_scaffold_13-snap.2181-T1
Valid prediction for snap_scaffold_13-snap.2198-T1
Valid prediction for GlimmerHMM_glimmerT_32434-T1
Valid prediction for GlimmerHMM_glimmerT_32441-T1
Valid prediction for Augustus_model.g21652.t1
Valid prediction for Augustus_model.g21657.t1
Valid prediction for GlimmerHMM_glimmerT_32424-T1
Valid prediction for snap_scaffold_13-snap.2172-T1
Valid prediction for snap_scaffold_13-snap.2201-T1
Valid prediction for Augustus_model.g21660.t1
Valid prediction for snap_scaffold_13-snap.2193-T1
Valid prediction for snap_scaffold_13-snap.2167-T1
Valid prediction for snap_scaffold_13-snap.2196-T1
Valid prediction for Augustus_model.g21659.t1
Valid prediction for snap_scaffold_13-snap.2197-T1
Valid prediction for Augustus_model.g21669.t1
Valid prediction for GlimmerHMM_glimmerT_32431-T1
Valid prediction for Augustus_model.g21653.t1
Valid prediction for CodingQuarry_transcript_13256-T1
Valid prediction for GlimmerHMM_glimmerT_32425-T1
Valid prediction for snap_scaffold_13-snap.2180-T1
Valid prediction for Augustus_model.g21661.t1
Valid prediction for snap_scaffold_13-snap.2166-T1
Valid prediction for GlimmerHMM_glimmerT_32440-T1
Couldn't classify 207554, 207934
Sorry, prediction pasa_asmbl_10099.p1 fails validation.
(TCT)	 TC	207554-207934	CT	AGC
Valid prediction for GlimmerHMM_glimmerT_32429-T1
Valid prediction for snap_scaffold_13-snap.2184-T1
Valid prediction for Augustus_model.g21656.t1
Valid prediction for snap_scaffold_13-snap.2178-T1
Valid prediction for snap_scaffold_13-snap.2195-T1
Valid prediction for snap_scaffold_13-snap.2170-T1
Valid prediction for snap_scaffold_13-snap.2177-T1
Valid prediction for snap_scaffold_13-snap.2200-T1
Couldn't classify 199422, 201412
Sorry, prediction pasa_asmbl_10100.p1 fails validation.
(ATG)	 AA	197319-197476	GT	AGG
(GAA)	 AG	197864-197989	GT	CTG
(CCA)	 AG	199085-199272	GT	AAG
(GAG)	 AG	199422-201412	GG	CAG
-recovered pasa_asmbl_10100.p1, initial, 197319, 197476
-recovered pasa_asmbl_10100.p1, internal, 197864, 197989
-recovered pasa_asmbl_10100.p1, internal, 199085, 199272
Valid prediction for HiQ_model.g21668.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23561, rend_intergenic: 20410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31809, rend_intergenic: 29969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89636, rend_intergenic: 87628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95200, rend_intergenic: 92905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126815, rend_intergenic: 123181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176383, rend_intergenic: 173942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192603, rend_intergenic: 182506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227313, rend_intergenic: 214030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 234994
-exon list size: 463


building trellis

0.2    
0.4    
0.6    
0.9    
1.1    
1.3    
1.5    
1.7    
1.9    
2.2    
2.4    
2.6    
2.8    
3.0    
3.2    
3.4    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.2    
5.4    
5.6    
5.8    
6.0    
6.2    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.2    
9.5    
9.7    
9.9    
10.1    
10.3    
10.5    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
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    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.4    
19.6    
19.8    
20.0    
20.2    
20.4    
20.6    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
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    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
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    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
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    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 23561, rend_intergenic: 20410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31809, rend_intergenic: 29969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89636, rend_intergenic: 87628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95200, rend_intergenic: 92905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126815, rend_intergenic: 123181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176383, rend_intergenic: 173942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192603, rend_intergenic: 182506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227313, rend_intergenic: 214030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support