-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_1389611-1673351

-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_187-T1
Valid prediction for GlimmerHMM_glimmerT_191-T1
Valid prediction for snap_scaffold_1-snap.269-T1
Valid prediction for snap_scaffold_1-snap.285-T1
Valid prediction for snap_scaffold_1-snap.257-T1
Valid prediction for HiQ_model.g165.t1
Valid prediction for GlimmerHMM_glimmerT_196-T1
Valid prediction for GlimmerHMM_glimmerT_186-T1
Valid prediction for Augustus_model.g159.t1
Valid prediction for GlimmerHMM_glimmerT_201-T1
Couldn't classify 174295, 174689
Sorry, prediction pasa_asmbl_1494.p1 fails validation.
(CGC)	 GT	174295-174689	GT	TGG
(GAT)	 AG	175190-175317	GT	GGG
(ATG)	 AG	175507-175595	GC	AGG
(CCC)	 AG	175759-176388	TG	AGT
add_exon() Sorry, pasa_asmbl_1494.p1 175507-175595-initial-1 is invalid.
-recovered pasa_asmbl_1494.p1, initial, 175507, 175595
-recovered pasa_asmbl_1494.p1, terminal, 175759, 176388
-recovered pasa_asmbl_1494.p1, internal, 175190, 175317
-recovered pasa_asmbl_1494.p1, internal, 175507, 175595
Valid prediction for CodingQuarry_transcript_2534-T1
Valid prediction for Augustus_model.g169.t1
Valid prediction for snap_scaffold_1-snap.279-T1
Valid prediction for snap_scaffold_1-snap.265-T1
Valid prediction for Augustus_model.g161.t1
Valid prediction for snap_scaffold_1-snap.255-T1
Valid prediction for Augustus_model.g160.t1
Valid prediction for pasa_asmbl_1485.p1
Valid prediction for GlimmerHMM_glimmerT_184-T1
Valid prediction for snap_scaffold_1-snap.272-T1
Valid prediction for snap_scaffold_1-snap.273-T1
Valid prediction for snap_scaffold_1-snap.253-T1
Valid prediction for snap_scaffold_1-snap.267-T1
Valid prediction for Augustus_model.g158.t1
Valid prediction for CodingQuarry_transcript_2533-T1
Couldn't classify 167764, 167955
Couldn't classify 169309, 169428
Sorry, prediction pasa_asmbl_1490.p1 fails validation.
(AGG)	 CC	167764-167955	GT	AGG
(GAG)	 AG	168373-168456	GT	GCG
(ACA)	 AG	168946-169170	GT	CTG
(GAG)	 AG	169309-169428	CC	GCC
-recovered pasa_asmbl_1490.p1, internal, 168373, 168456
-recovered pasa_asmbl_1490.p1, internal, 168946, 169170
Valid prediction for snap_scaffold_1-snap.264-T1
Valid prediction for Augustus_model.g148.t1
Valid prediction for snap_scaffold_1-snap.252-T1
Valid prediction for GlimmerHMM_glimmerT_210-T1
Valid prediction for HiQ_model.g151.t1
Couldn't classify 137581, 137741
Sorry, prediction pasa_asmbl_1483.p1 fails validation.
(GGA)	 AG	137581-137741	GT	AGG
(TCT)	 AG	138043-138190	GT	GGG
(GAC)	 AG	138331-138395	GT	AGG
(GTA)	 AG	138532-138607	GT	GGG
(AAT)	 AG	138877-138951	GT	AGG
(ATC)	 AG	139182-139286	CA	GAC
-recovered pasa_asmbl_1483.p1, terminal, 139182, 139286
-recovered pasa_asmbl_1483.p1, internal, 137581, 137741
-recovered pasa_asmbl_1483.p1, internal, 138043, 138190
-recovered pasa_asmbl_1483.p1, internal, 138331, 138395
-recovered pasa_asmbl_1483.p1, internal, 138532, 138607
-recovered pasa_asmbl_1483.p1, internal, 138877, 138951
Valid prediction for Augustus_model.g156.t1
Valid prediction for HiQ_model.g149.t1
Valid prediction for GlimmerHMM_glimmerT_203-T1
Valid prediction for GlimmerHMM_glimmerT_209-T1
Valid prediction for GlimmerHMM_glimmerT_212-T1
Valid prediction for Augustus_model.g157.t1
Valid prediction for GlimmerHMM_glimmerT_200-T1
Valid prediction for GlimmerHMM_glimmerT_189-T1
Valid prediction for CodingQuarry_transcript_2527-T1
Valid prediction for GlimmerHMM_glimmerT_194-T1
Valid prediction for snap_scaffold_1-snap.287-T1
Valid prediction for snap_scaffold_1-snap.270-T1
Valid prediction for CodingQuarry_transcript_2529-T1
Valid prediction for pasa_asmbl_1480.p1
Couldn't classify 228431, 228469
Couldn't classify 228723, 228783
Sorry, prediction CodingQuarry_transcript_2536-T1 fails validation.
(ATG)	 AG	221851-221904	GT	AGG
(CAT)	 AG	224392-224467	GT	AGG
(GGG)	 AG	224672-224732	GT	AGG
(GAA)	 AG	224939-225061	GT	AAG
(TGT)	 AG	225299-225372	GT	AGG
(GAT)	 AG	225980-226050	GT	AGG
(GAC)	 AG	226136-226210	GT	AGG
(TCT)	 AG	226433-226499	GT	TGG
(AAG)	 AG	226916-227001	GT	CTG
(GAT)	 AG	227357-227433	GT	GGG
(TCA)	 AG	228431-228469	GA	GTG
(TTT)	 GA	228723-228783	GA	AAG
-recovered CodingQuarry_transcript_2536-T1, initial, 221851, 221904
-recovered CodingQuarry_transcript_2536-T1, internal, 221851, 221904
-recovered CodingQuarry_transcript_2536-T1, internal, 224392, 224467
-recovered CodingQuarry_transcript_2536-T1, internal, 224672, 224732
-recovered CodingQuarry_transcript_2536-T1, internal, 224939, 225061
-recovered CodingQuarry_transcript_2536-T1, internal, 225299, 225372
-recovered CodingQuarry_transcript_2536-T1, internal, 225980, 226050
-recovered CodingQuarry_transcript_2536-T1, internal, 226136, 226210
-recovered CodingQuarry_transcript_2536-T1, internal, 226433, 226499
-recovered CodingQuarry_transcript_2536-T1, internal, 226916, 227001
-recovered CodingQuarry_transcript_2536-T1, internal, 227357, 227433
Valid prediction for GlimmerHMM_glimmerT_197-T1
Couldn't classify 164087, 164278
Couldn't classify 167063, 167180
Sorry, prediction pasa_asmbl_1489.p1 fails validation.
(GTG)	 CA	164087-164278	GT	AGG
(GCC)	 AG	165315-165353	GT	AGG
(AAC)	 AG	165465-165767	GT	AGG
(TTA)	 AG	166016-166164	GT	AAG
(GCC)	 AG	167063-167180	GT	AGG
-recovered pasa_asmbl_1489.p1, internal, 165315, 165353
-recovered pasa_asmbl_1489.p1, internal, 165465, 165767
-recovered pasa_asmbl_1489.p1, internal, 166016, 166164
-recovered pasa_asmbl_1489.p1, internal, 167063, 167180
Valid prediction for snap_scaffold_1-snap.263-T1
Valid prediction for pasa_asmbl_1481.p1
Valid prediction for GlimmerHMM_glimmerT_204-T1
Valid prediction for GlimmerHMM_glimmerT_199-T1
Valid prediction for snap_scaffold_1-snap.284-T1
Valid prediction for snap_scaffold_1-snap.283-T1
Valid prediction for pasa_asmbl_1499.p1
Valid prediction for snap_scaffold_1-snap.261-T1
Valid prediction for Augustus_model.g166.t1
Valid prediction for snap_scaffold_1-snap.277-T1
Valid prediction for snap_scaffold_1-snap.286-T1
Valid prediction for snap_scaffold_1-snap.280-T1
Valid prediction for Augustus_model.g146.t1
Valid prediction for snap_scaffold_1-snap.259-T1
Valid prediction for GlimmerHMM_glimmerT_206-T1
Valid prediction for CodingQuarry_transcript_2530-T1
Valid prediction for snap_scaffold_1-snap.275-T1
Valid prediction for snap_scaffold_1-snap.289-T1
Valid prediction for snap_scaffold_1-snap.249-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_1-snap.281-T1
Valid prediction for CodingQuarry_transcript_2528-T1
Valid prediction for pasa_asmbl_77.p1
Valid prediction for HiQ_model.g155.t1
Valid prediction for GlimmerHMM_glimmerT_185-T1
Valid prediction for pasa_asmbl_64.p1
Valid prediction for HiQ_model.g153.t1
Valid prediction for snap_scaffold_1-snap.276-T1
Valid prediction for GlimmerHMM_glimmerT_188-T1
Couldn't classify 248074, 248249
Sorry, prediction pasa_asmbl_66.p1 fails validation.
(CTT)	 CC	248074-248249	GT	GGG
(AAA)	 AG	248385-248496	GT	AGG
(CCC)	 AG	248649-248750	GT	TGG
(TCC)	 AG	248859-248909	GT	AGG
(CAA)	 AG	249234-249293	GT	AGG
(GCC)	 AG	250478-250561	GT	AGG
(CTG)	 AG	250799-250909	GT	AGG
(ATG)	 AG	251569-251670	GC	AGG
(TTG)	 AG	251800-251900	GT	AGG
(GCA)	 AG	252237-252385	GT	CTG
(ACC)	 AG	252565-252654	GT	AGG
(GCA)	 AG	253040-253158	TG	AAT
-recovered pasa_asmbl_66.p1, initial, 251569, 251670
-recovered pasa_asmbl_66.p1, terminal, 253040, 253158
-recovered pasa_asmbl_66.p1, internal, 248385, 248496
-recovered pasa_asmbl_66.p1, internal, 248649, 248750
-recovered pasa_asmbl_66.p1, internal, 248859, 248909
-recovered pasa_asmbl_66.p1, internal, 249234, 249293
-recovered pasa_asmbl_66.p1, internal, 250478, 250561
-recovered pasa_asmbl_66.p1, internal, 250799, 250909
-recovered pasa_asmbl_66.p1, internal, 251569, 251670
-recovered pasa_asmbl_66.p1, internal, 251800, 251900
-recovered pasa_asmbl_66.p1, internal, 252237, 252385
-recovered pasa_asmbl_66.p1, internal, 252565, 252654
Valid prediction for GlimmerHMM_glimmerT_198-T1
Valid prediction for GlimmerHMM_glimmerT_202-T1
Valid prediction for Augustus_model.g163.t1
Valid prediction for snap_scaffold_1-snap.251-T1
Valid prediction for GlimmerHMM_glimmerT_211-T1
Valid prediction for Augustus_model.g154.t1
Valid prediction for CodingQuarry_transcript_2532-T1
Valid prediction for snap_scaffold_1-snap.268-T1
Valid prediction for snap_scaffold_1-snap.260-T1
Valid prediction for GlimmerHMM_glimmerT_207-T1
Valid prediction for Augustus_model.g168.t1
Valid prediction for GlimmerHMM_glimmerT_208-T1
Couldn't classify 66846, 67250
Sorry, prediction pasa_asmbl_80.p1 fails validation.
(ATG)	 AG	66846-67250	GG	GCG
Valid prediction for GlimmerHMM_glimmerT_205-T1
Valid prediction for snap_scaffold_1-snap.288-T1
Valid prediction for GlimmerHMM_glimmerT_192-T1
Valid prediction for snap_scaffold_1-snap.266-T1
Valid prediction for snap_scaffold_1-snap.250-T1
Valid prediction for pasa_asmbl_69.p1
Valid prediction for CodingQuarry_transcript_2531-T1
Valid prediction for snap_scaffold_1-snap.274-T1
Valid prediction for pasa_asmbl_72.p1
Valid prediction for snap_scaffold_1-snap.278-T1
Valid prediction for snap_scaffold_1-snap.254-T1
Valid prediction for GlimmerHMM_glimmerT_193-T1
Valid prediction for HiQ_model.g152.t1
Valid prediction for Augustus_model.g164.t1
Valid prediction for GlimmerHMM_glimmerT_195-T1
Valid prediction for HiQ_model.g150.t1
Valid prediction for Augustus_model.g162.t1
Valid prediction for snap_scaffold_1-snap.282-T1
Valid prediction for Augustus_model.g167.t1
Valid prediction for snap_scaffold_1-snap.262-T1
Valid prediction for GlimmerHMM_glimmerT_213-T1
Valid prediction for GlimmerHMM_glimmerT_190-T1
Valid prediction for Augustus_model.g147.t1
Valid prediction for snap_scaffold_1-snap.256-T1
Valid prediction for snap_scaffold_1-snap.271-T1
Valid prediction for snap_scaffold_1-snap.258-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 51712, rend_intergenic: 47556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104792, rend_intergenic: 102993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133921, rend_intergenic: 130506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140083, rend_intergenic: 134575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166168, rend_intergenic: 159668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172214, rend_intergenic: 167694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173279, rend_intergenic: 172528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 283741
-exon list size: 394


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.0    
3.3    
3.5    
3.8    
4.0    
4.3    
4.5    
4.8    
5.1    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.8    
8.1    
8.3    
8.6    
8.8    
9.1    
9.3    
9.6    
9.8    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.6    
11.9    
12.1    
12.4    
12.6    
12.9    
13.1    
13.4    
13.6    
13.9    
14.1    
14.4    
14.6    
14.9    
15.2    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.7    
22.0    
22.2    
22.5    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.8    
28.0    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.9    
62.1    
62.4    
62.6    
62.9    
63.1    
63.4    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.2    
65.4    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.7    
72.0    
72.2    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.1    
87.4    
87.6    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.5    
95.7    
96.0    
96.2    
96.5    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 51712, rend_intergenic: 47556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104792, rend_intergenic: 102993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133921, rend_intergenic: 130506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140083, rend_intergenic: 134575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166168, rend_intergenic: 159668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172214, rend_intergenic: 167694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173279, rend_intergenic: 172528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support