-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_1-156590

-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_26-snap.32-T1
Valid prediction for GlimmerHMM_glimmerT_54914-T1
Valid prediction for snap_scaffold_26-snap.21-T1
Valid prediction for snap_scaffold_26-snap.29-T1
Valid prediction for snap_scaffold_26-snap.14-T1
Valid prediction for GlimmerHMM_glimmerT_54911-T1
Valid prediction for GlimmerHMM_glimmerT_54900-T1
Valid prediction for snap_scaffold_26-snap.37-T1
Valid prediction for GlimmerHMM_glimmerT_54901-T1
Couldn't classify 27137, 27280
Couldn't classify 29238, 29242
Sorry, prediction pasa_asmbl_34668.p1 fails validation.
(GTC)	 AT	27137-27280	GT	AGG
(GTG)	 AG	28263-28397	GT	AGG
(ATT)	 AG	28772-28892	GT	AGG
(ACC)	 AG	29238-29242	GT	TGG
-recovered pasa_asmbl_34668.p1, internal, 28263, 28397
-recovered pasa_asmbl_34668.p1, internal, 28772, 28892
-recovered pasa_asmbl_34668.p1, internal, 29238, 29242
Couldn't classify 31996, 32183
Sorry, prediction pasa_asmbl_34670.p1 fails validation.
(CAG)	 CC	31996-32183	GT	AGG
(CCT)	 AG	32451-32612	GT	TGG
(GAT)	 AG	32749-32889	GT	AAG
(GTT)	 AG	33173-33254	GT	AGG
(GTG)	 AG	33358-33582	GG	AAG
-recovered pasa_asmbl_34670.p1, terminal, 33358, 33582
-recovered pasa_asmbl_34670.p1, internal, 32451, 32612
-recovered pasa_asmbl_34670.p1, internal, 32749, 32889
-recovered pasa_asmbl_34670.p1, internal, 33173, 33254
Valid prediction for GlimmerHMM_glimmerT_54921-T1
Valid prediction for GlimmerHMM_glimmerT_54917-T1
Valid prediction for GlimmerHMM_glimmerT_54913-T1
Valid prediction for Augustus_model.g36442.t1
Valid prediction for pasa_asmbl_35300.p1
Valid prediction for GlimmerHMM_glimmerT_54906-T1
Valid prediction for snap_scaffold_26-snap.16-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g36429.t1
Valid prediction for snap_scaffold_26-snap.35-T1
Valid prediction for snap_scaffold_26-snap.36-T1
Couldn't classify 28877, 28892
Couldn't classify 31654, 31738
Sorry, prediction pasa_asmbl_34669.p1 fails validation.
(CCT)	 AC	28877-28892	GT	AGG
(ACC)	 AG	29238-29392	GT	AGG
(TGG)	 AG	29729-29842	GT	TGG
(AAT)	 AG	29982-30113	GT	AGG
(GGG)	 AG	30191-30322	GT	ATG
(ATC)	 AG	30405-30479	GT	CTG
(AAG)	 AG	30601-30758	GT	GGG
(CTT)	 AG	30938-31017	GT	TGG
(CTG)	 AG	31094-31277	GT	AGG
(CGT)	 AG	31654-31738	CT	GAC
-recovered pasa_asmbl_34669.p1, internal, 29238, 29392
-recovered pasa_asmbl_34669.p1, internal, 29729, 29842
-recovered pasa_asmbl_34669.p1, internal, 29982, 30113
-recovered pasa_asmbl_34669.p1, internal, 30191, 30322
-recovered pasa_asmbl_34669.p1, internal, 30405, 30479
-recovered pasa_asmbl_34669.p1, internal, 30601, 30758
-recovered pasa_asmbl_34669.p1, internal, 30938, 31017
-recovered pasa_asmbl_34669.p1, internal, 31094, 31277
Valid prediction for snap_scaffold_26-snap.17-T1
Valid prediction for snap_scaffold_26-snap.26-T1
Couldn't classify 118307, 118430
Sorry, prediction pasa_asmbl_34671.p1 fails validation.
(ATG)	 AA	117193-117284	GT	AAG
(TAA)	 AG	117477-117526	GT	AGG
(GCA)	 AG	117852-117957	GT	AAG
(AGA)	 AG	118307-118430	GT	AGG
-recovered pasa_asmbl_34671.p1, initial, 117193, 117284
add_exon() Sorry, pasa_asmbl_34671.p1 117852-117957-terminal-3 is invalid.
-recovered pasa_asmbl_34671.p1, terminal, 117852, 117957
-recovered pasa_asmbl_34671.p1, internal, 117477, 117526
-recovered pasa_asmbl_34671.p1, internal, 117852, 117957
-recovered pasa_asmbl_34671.p1, internal, 118307, 118430
Valid prediction for snap_scaffold_26-snap.12-T1
Valid prediction for HiQ_model.g36436.t1
Valid prediction for GlimmerHMM_glimmerT_54909-T1
Valid prediction for Augustus_model.g36437.t1
Valid prediction for snap_scaffold_26-snap.10-T1
Valid prediction for GlimmerHMM_glimmerT_54922-T1
Valid prediction for CodingQuarry_transcript_40238-T1
Valid prediction for GlimmerHMM_glimmerT_54927-T1
Valid prediction for snap_scaffold_26-snap.8-T1
Valid prediction for GlimmerHMM_glimmerT_54915-T1
Valid prediction for Augustus_model.g36440.t1
Valid prediction for snap_scaffold_26-snap.6-T1
Valid prediction for snap_scaffold_26-snap.28-T1
Valid prediction for snap_scaffold_26-snap.19-T1
Valid prediction for Augustus_model.g36433.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_54923-T1
Valid prediction for snap_scaffold_26-snap.33-T1
Valid prediction for Augustus_model.g36439.t1
Valid prediction for GlimmerHMM_glimmerT_54907-T1
Couldn't classify 10056, 10139
Couldn't classify 11731, 11832
Sorry, prediction pasa_asmbl_35375.p1 fails validation.
(GGT)	 AA	10056-10139	GT	AGG
(GGG)	 AG	10346-10492	GT	GCG
(TCC)	 AG	11731-11832	CC	AGC
-recovered pasa_asmbl_35375.p1, internal, 10346, 10492
Valid prediction for snap_scaffold_26-snap.7-T1
Valid prediction for HiQ_model.g36438.t1
Valid prediction for snap_scaffold_26-snap.18-T1
Valid prediction for pasa_asmbl_35365.p1
Valid prediction for GlimmerHMM_glimmerT_54899-T1
Valid prediction for GlimmerHMM_glimmerT_54925-T1
Valid prediction for GlimmerHMM_glimmerT_54918-T1
Valid prediction for snap_scaffold_26-snap.30-T1
Valid prediction for GlimmerHMM_glimmerT_54926-T1
Valid prediction for snap_scaffold_26-snap.9-T1
Valid prediction for GlimmerHMM_glimmerT_54905-T1
Valid prediction for CodingQuarry_transcript_40234-T1
Valid prediction for snap_scaffold_26-snap.22-T1
Valid prediction for GlimmerHMM_glimmerT_54912-T1
Valid prediction for snap_scaffold_26-snap.5-T1
Valid prediction for CodingQuarry_transcript_40235-T1
Valid prediction for GlimmerHMM_glimmerT_54902-T1
Valid prediction for CodingQuarry_transcript_40237-T1
Valid prediction for HiQ_model.g36430.t1
Valid prediction for snap_scaffold_26-snap.2-T1
Valid prediction for snap_scaffold_26-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_54903-T1
Valid prediction for Augustus_model.g36432.t1
Valid prediction for snap_scaffold_26-snap.27-T1
Couldn't classify 150666, 150824
Sorry, prediction pasa_asmbl_35361.p1 fails validation.
(GGG)	 CA	150666-150824	GT	GGG
(AGT)	 AG	152159-152217	GT	AGG
(TCG)	 AG	152306-152402	GT	AGG
(GAG)	 AG	152672-152830	GT	TGG
(GGA)	 AG	152989-153057	GT	TGG
(ACC)	 AG	153781-153986	GT	CGG
(ATT)	 AG	154078-154231	AG	GAA
-recovered pasa_asmbl_35361.p1, terminal, 154078, 154231
-recovered pasa_asmbl_35361.p1, internal, 152159, 152217
-recovered pasa_asmbl_35361.p1, internal, 152306, 152402
-recovered pasa_asmbl_35361.p1, internal, 152672, 152830
-recovered pasa_asmbl_35361.p1, internal, 152989, 153057
-recovered pasa_asmbl_35361.p1, internal, 153781, 153986
Valid prediction for snap_scaffold_26-snap.24-T1
Valid prediction for snap_scaffold_26-snap.34-T1
Valid prediction for GlimmerHMM_glimmerT_54920-T1
Valid prediction for snap_scaffold_26-snap.13-T1
Valid prediction for GlimmerHMM_glimmerT_54910-T1
Valid prediction for snap_scaffold_26-snap.20-T1
Couldn't classify 150243, 150599
Sorry, prediction pasa_asmbl_35362.p1 fails validation.
(CCA)	 CG	150243-150599	GG	GAG
Valid prediction for Augustus_model.g36435.t1
Valid prediction for Augustus_model.g36441.t1
Valid prediction for Augustus_model.g36428.t1
Valid prediction for Augustus_model.g36434.t1
Valid prediction for snap_scaffold_26-snap.23-T1
Valid prediction for GlimmerHMM_glimmerT_54916-T1
Valid prediction for GlimmerHMM_glimmerT_54919-T1
Valid prediction for HiQ_model.g36427.t1
Couldn't classify 5593, 5694
Couldn't classify 6105, 6224
Sorry, prediction pasa_asmbl_35878.p2 fails validation.
(AGG)	 AG	5593-5694	GT	AGG
(GCT)	 AG	5938-6018	GT	AGG
(GGT)	 AG	6105-6224	CA	CCC
-recovered pasa_asmbl_35878.p2, internal, 5593, 5694
-recovered pasa_asmbl_35878.p2, internal, 5938, 6018
Valid prediction for snap_scaffold_26-snap.1-T1
Valid prediction for pasa_asmbl_35371.p1
Valid prediction for GlimmerHMM_glimmerT_54924-T1
Valid prediction for GlimmerHMM_glimmerT_54904-T1
Valid prediction for snap_scaffold_26-snap.25-T1
Valid prediction for snap_scaffold_26-snap.3-T1
Valid prediction for snap_scaffold_26-snap.31-T1
Valid prediction for snap_scaffold_26-snap.4-T1
Couldn't classify 14293, 14363
Sorry, prediction pasa_asmbl_35374.p1 fails validation.
(CCT)	 CT	14293-14363	GT	AGG
(GCT)	 AG	15131-15365	CA	GAC
-recovered pasa_asmbl_35374.p1, terminal, 15131, 15365
Valid prediction for GlimmerHMM_glimmerT_54908-T1
Valid prediction for Augustus_model.g36431.t1
Valid prediction for snap_scaffold_26-snap.15-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39940, rend_intergenic: 37277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41232, rend_intergenic: 40330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64127, rend_intergenic: 56664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72163, rend_intergenic: 70217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77701, rend_intergenic: 72235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84907, rend_intergenic: 82438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91762, rend_intergenic: 88674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127976, rend_intergenic: 124977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136189, rend_intergenic: 135287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140021, rend_intergenic: 136459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151382, rend_intergenic: 141248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156590
-exon list size: 297


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.7    
3.0    
3.3    
3.7    
4.0    
4.3    
4.7    
5.0    
5.4    
5.7    
6.0    
6.4    
6.7    
7.0    
7.4    
7.7    
8.0    
8.4    
8.7    
9.0    
9.4    
9.7    
10.0    
10.4    
10.7    
11.0    
11.4    
11.7    
12.0    
12.4    
12.7    
13.0    
13.4    
13.7    
14.0    
14.4    
14.7    
15.1    
15.4    
15.7    
16.1    
16.4    
16.7    
17.1    
17.4    
17.7    
18.1    
18.4    
18.7    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.1    
21.4    
21.7    
22.1    
22.4    
22.7    
23.1    
23.4    
23.7    
24.1    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.4    
26.8    
27.1    
27.4    
27.8    
28.1    
28.4    
28.8    
29.1    
29.4    
29.8    
30.1    
30.4    
30.8    
31.1    
31.4    
31.8    
32.1    
32.4    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.8    
35.1    
35.5    
35.8    
36.1    
36.5    
36.8    
37.1    
37.5    
37.8    
38.1    
38.5    
38.8    
39.1    
39.5    
39.8    
40.1    
40.5    
40.8    
41.1    
41.5    
41.8    
42.1    
42.5    
42.8    
43.1    
43.5    
43.8    
44.1    
44.5    
44.8    
45.2    
45.5    
45.8    
46.2    
46.5    
46.8    
47.2    
47.5    
47.8    
48.2    
48.5    
48.8    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.2    
51.5    
51.8    
52.2    
52.5    
52.8    
53.2    
53.5    
53.8    
54.2    
54.5    
54.8    
55.2    
55.5    
55.9    
56.2    
56.5    
56.9    
57.2    
57.5    
57.9    
58.2    
58.5    
58.9    
59.2    
59.5    
59.9    
60.2    
60.5    
60.9    
61.2    
61.5    
61.9    
62.2    
62.5    
62.9    
63.2    
63.5    
63.9    
64.2    
64.5    
64.9    
65.2    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.6    
67.9    
68.2    
68.6    
68.9    
69.2    
69.6    
69.9    
70.2    
70.6    
70.9    
71.2    
71.6    
71.9    
72.2    
72.6    
72.9    
73.2    
73.6    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
75.9    
76.3    
76.6    
76.9    
77.3    
77.6    
77.9    
78.3    
78.6    
78.9    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.3    
81.6    
81.9    
82.3    
82.6    
82.9    
83.3    
83.6    
83.9    
84.3    
84.6    
84.9    
85.3    
85.6    
86.0    
86.3    
86.6    
87.0    
87.3    
87.6    
88.0    
88.3    
88.6    
89.0    
89.3    
89.6    
90.0    
90.3    
90.6    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
93.0    
93.3    
93.6    
94.0    
94.3    
94.6    
95.0    
95.3    
95.7    
96.0    
96.3    
96.7    
97.0    
97.3    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 39940, rend_intergenic: 37277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41232, rend_intergenic: 40330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64127, rend_intergenic: 56664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72163, rend_intergenic: 70217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77701, rend_intergenic: 72235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84907, rend_intergenic: 82438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91762, rend_intergenic: 88674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127976, rend_intergenic: 124977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136189, rend_intergenic: 135287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140021, rend_intergenic: 136459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151382, rend_intergenic: 141248  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