-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_959752-1155545

-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 CodingQuarry_transcript_41776-T1
Valid prediction for snap_scaffold_27-snap.245-T1
Valid prediction for CodingQuarry_transcript_41772-T1
Valid prediction for GlimmerHMM_glimmerT_56622-T1
Valid prediction for snap_scaffold_27-snap.223-T1
Couldn't classify 21067, 21102
Sorry, prediction pasa_asmbl_35977.p1 fails validation.
(ATT)	 CC	21067-21102	GT	AGG
(GCC)	 AG	21495-21661	GT	ATG
(GTT)	 AG	21805-21889	GT	AGG
(CAA)	 AG	22804-22887	CA	AAC
-recovered pasa_asmbl_35977.p1, terminal, 22804, 22887
-recovered pasa_asmbl_35977.p1, internal, 21495, 21661
-recovered pasa_asmbl_35977.p1, internal, 21805, 21889
Valid prediction for Augustus_model.g37508.t1
Valid prediction for HiQ_model.g37521.t1
Valid prediction for GlimmerHMM_glimmerT_56629-T1
Valid prediction for snap_scaffold_27-snap.232-T1
Valid prediction for GlimmerHMM_glimmerT_56625-T1
Valid prediction for CodingQuarry_transcript_41773-T1
Valid prediction for CodingQuarry_transcript_41766-T1
Valid prediction for pasa_asmbl_35987.p1
Valid prediction for snap_scaffold_27-snap.254-T1
Couldn't classify 139578, 139686
Couldn't classify 141090, 141321
Sorry, prediction pasa_asmbl_35993.p1 fails validation.
(GAC)	 CT	139578-139686	GT	AGG
(AGA)	 AG	139904-140031	GT	AGG
(GTG)	 AG	140818-140897	GT	AGG
(GGG)	 AG	141090-141321	GG	GAG
-recovered pasa_asmbl_35993.p1, internal, 139904, 140031
-recovered pasa_asmbl_35993.p1, internal, 140818, 140897
Valid prediction for snap_scaffold_27-snap.258-T1
Valid prediction for Augustus_model.g37509.t1
Valid prediction for CodingQuarry_transcript_41768-T1
Valid prediction for snap_scaffold_27-snap.224-T1
Valid prediction for snap_scaffold_27-snap.230-T1
Valid prediction for snap_scaffold_27-snap.247-T1
Valid prediction for HiQ_model.g37524.t1
Valid prediction for snap_scaffold_27-snap.222-T1
Valid prediction for GlimmerHMM_glimmerT_56626-T1
Valid prediction for pasa_asmbl_35995.p1
Valid prediction for snap_scaffold_27-snap.246-T1
Valid prediction for GlimmerHMM_glimmerT_56612-T1
Couldn't classify 16664, 16671
Sorry, prediction CodingQuarry_transcript_41767-T1 fails validation.
(ATG)	 CC	15164-15293	GT	CGG
(GGG)	 AG	15446-15555	GT	GCG
(TTC)	 AG	15772-15907	GT	GCG
(AGC)	 AG	16163-16246	GT	GGG
(GTA)	 AG	16339-16434	GT	CAG
(TCA)	 TG	16664-16671	CC	AAC
-recovered CodingQuarry_transcript_41767-T1, initial, 15164, 15293
-recovered CodingQuarry_transcript_41767-T1, internal, 15446, 15555
-recovered CodingQuarry_transcript_41767-T1, internal, 15772, 15907
-recovered CodingQuarry_transcript_41767-T1, internal, 16163, 16246
-recovered CodingQuarry_transcript_41767-T1, internal, 16339, 16434
Valid prediction for CodingQuarry_transcript_41774-T1
Valid prediction for GlimmerHMM_glimmerT_56621-T1
Valid prediction for snap_scaffold_27-snap.229-T1
Valid prediction for GlimmerHMM_glimmerT_56630-T1
Couldn't classify 53821, 54798
Sorry, prediction pasa_asmbl_35980.p1 fails validation.
(GTA)	 TC	53821-54798	TA	GGT
Valid prediction for GlimmerHMM_glimmerT_56605-T1
Valid prediction for CodingQuarry_transcript_41762-T1
Couldn't classify 58222, 58557
Sorry, prediction pasa_asmbl_35981.p1 fails validation.
(AAG)	 GT	58222-58557	CA	GAC
Valid prediction for snap_scaffold_27-snap.233-T1
Valid prediction for CodingQuarry_transcript_41763-T1
Couldn't classify 144411, 144441
Couldn't classify 145900, 145962
Sorry, prediction pasa_asmbl_35994.p1 fails validation.
(CTC)	 GC	144411-144441	GT	AGG
(CGG)	 AG	144560-144698	GT	AAG
(GCC)	 AG	145038-145191	GT	AGG
(GTG)	 AG	145541-145735	GT	AGG
(GTG)	 AG	145900-145962	GC	CAG
-recovered pasa_asmbl_35994.p1, internal, 144560, 144698
-recovered pasa_asmbl_35994.p1, internal, 145038, 145191
-recovered pasa_asmbl_35994.p1, internal, 145541, 145735
-recovered pasa_asmbl_35994.p1, internal, 145900, 145962
Valid prediction for pasa_asmbl_35990.p1
Valid prediction for CodingQuarry_transcript_41775-T1
Valid prediction for GlimmerHMM_glimmerT_56613-T1
Valid prediction for snap_scaffold_27-snap.255-T1
Couldn't classify 16664, 16671
Sorry, prediction CodingQuarry_transcript_41764-T1 fails validation.
(ATG)	 CC	12651-12735	GT	AGG
(ATT)	 AG	12849-13004	GT	AGG
(TCT)	 AG	13137-13280	GT	AGG
(GGG)	 AG	15446-15555	GT	GCG
(TTC)	 AG	15772-15907	GT	GCG
(AGC)	 AG	16163-16225	GT	AGG
(GTA)	 AG	16339-16434	GT	CAG
(TCA)	 TG	16664-16671	CC	AAC
-recovered CodingQuarry_transcript_41764-T1, initial, 12651, 12735
-recovered CodingQuarry_transcript_41764-T1, internal, 12849, 13004
-recovered CodingQuarry_transcript_41764-T1, internal, 13137, 13280
-recovered CodingQuarry_transcript_41764-T1, internal, 15446, 15555
-recovered CodingQuarry_transcript_41764-T1, internal, 15772, 15907
-recovered CodingQuarry_transcript_41764-T1, internal, 16163, 16225
-recovered CodingQuarry_transcript_41764-T1, internal, 16339, 16434
Valid prediction for GlimmerHMM_glimmerT_56623-T1
Valid prediction for snap_scaffold_27-snap.240-T1
Valid prediction for HiQ_model.g37507.t1
Valid prediction for GlimmerHMM_glimmerT_56603-T1
Valid prediction for CodingQuarry_transcript_41765-T1
Valid prediction for snap_scaffold_27-snap.257-T1
Valid prediction for snap_scaffold_27-snap.250-T1
Valid prediction for GlimmerHMM_glimmerT_56618-T1
Valid prediction for Augustus_model.g37512.t1
Valid prediction for Augustus_model.g37523.t1
Valid prediction for Augustus_model.g37518.t1
Valid prediction for snap_scaffold_27-snap.226-T1
Valid prediction for HiQ_model.g37522.t1
Valid prediction for snap_scaffold_27-snap.248-T1
Valid prediction for GlimmerHMM_glimmerT_56602-T1
Valid prediction for GlimmerHMM_glimmerT_56608-T1
Valid prediction for GlimmerHMM_glimmerT_56624-T1
Valid prediction for pasa_asmbl_35968.p1
Valid prediction for GlimmerHMM_glimmerT_56620-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_56601-T1
Valid prediction for snap_scaffold_27-snap.227-T1
Valid prediction for Augustus_model.g37510.t1
Valid prediction for GlimmerHMM_glimmerT_56616-T1
Valid prediction for snap_scaffold_27-snap.221-T1
Valid prediction for pasa_asmbl_36742.p1
Valid prediction for snap_scaffold_27-snap.252-T1
Valid prediction for Augustus_model.g37515.t1
Valid prediction for GlimmerHMM_glimmerT_56606-T1
Valid prediction for snap_scaffold_27-snap.225-T1
Valid prediction for snap_scaffold_27-snap.239-T1
Valid prediction for pasa_asmbl_36744.p1
Valid prediction for Augustus_model.g37525.t1
Valid prediction for GlimmerHMM_glimmerT_56614-T1
Valid prediction for Augustus_model.g37519.t1
Valid prediction for snap_scaffold_27-snap.256-T1
Valid prediction for snap_scaffold_27-snap.251-T1
Valid prediction for GlimmerHMM_glimmerT_56619-T1
Valid prediction for GlimmerHMM_glimmerT_56615-T1
Valid prediction for GlimmerHMM_glimmerT_56604-T1
Valid prediction for GlimmerHMM_glimmerT_56617-T1
Valid prediction for GlimmerHMM_glimmerT_56628-T1
Valid prediction for snap_scaffold_27-snap.241-T1
Valid prediction for GlimmerHMM_glimmerT_56609-T1
Valid prediction for snap_scaffold_27-snap.242-T1
Couldn't classify 17884, 18063
Couldn't classify 18913, 18948
Sorry, prediction pasa_asmbl_36747.p2 fails validation.
(AAG)	 GC	17884-18063	GT	CGG
(GAG)	 AG	18467-18649	GT	AGG
(GTG)	 AG	18913-18948	AG	CCA
-recovered pasa_asmbl_36747.p2, internal, 18467, 18649
Valid prediction for snap_scaffold_27-snap.236-T1
Valid prediction for GlimmerHMM_glimmerT_56627-T1
Valid prediction for CodingQuarry_transcript_41771-T1
Valid prediction for snap_scaffold_27-snap.231-T1
Valid prediction for GlimmerHMM_glimmerT_56610-T1
Valid prediction for pasa_asmbl_36735.p1
Valid prediction for snap_scaffold_27-snap.249-T1
Valid prediction for HiQ_model.g37513.t1
Valid prediction for snap_scaffold_27-snap.234-T1
Couldn't classify 146571, 146676
Sorry, prediction pasa_asmbl_36737.p1 fails validation.
(CTC)	 CT	146571-146676	GT	TGG
(GAA)	 AG	147165-147340	GT	AAG
(GCC)	 AG	147484-147573	GT	AGG
(ACC)	 AG	147888-147938	AC	AGA
-recovered pasa_asmbl_36737.p1, terminal, 147888, 147938
-recovered pasa_asmbl_36737.p1, internal, 147165, 147340
-recovered pasa_asmbl_36737.p1, internal, 147484, 147573
Valid prediction for Augustus_model.g37514.t1
Valid prediction for Augustus_model.g37520.t1
Valid prediction for snap_scaffold_27-snap.238-T1
Valid prediction for Augustus_model.g37516.t1
Valid prediction for HiQ_model.g37511.t1
Couldn't classify 14398, 14550
Couldn't classify 16611, 16748
Sorry, prediction pasa_asmbl_36748.p2 fails validation.
(CTG)	 TG	14398-14550	GT	AGG
(GTG)	 AG	14817-14945	GT	AGG
(GTG)	 AG	16611-16748	GT	CCG
-recovered pasa_asmbl_36748.p2, internal, 14817, 14945
-recovered pasa_asmbl_36748.p2, internal, 16611, 16748
Valid prediction for Augustus_model.g37506.t1
Valid prediction for snap_scaffold_27-snap.244-T1
Valid prediction for Augustus_model.g37517.t1
Valid prediction for snap_scaffold_27-snap.220-T1
Valid prediction for snap_scaffold_27-snap.253-T1
Valid prediction for CodingQuarry_transcript_41770-T1
Valid prediction for Augustus_model.g37526.t1
Valid prediction for snap_scaffold_27-snap.243-T1
Valid prediction for GlimmerHMM_glimmerT_56611-T1
Valid prediction for snap_scaffold_27-snap.228-T1
Valid prediction for CodingQuarry_transcript_41769-T1
Valid prediction for GlimmerHMM_glimmerT_56607-T1
Valid prediction for snap_scaffold_27-snap.237-T1
Valid prediction for snap_scaffold_27-snap.235-T1
Couldn't classify 155189, 156352
Couldn't classify 156647, 156766
Sorry, prediction pasa_asmbl_36736.p1 fails validation.
(GGA)	 CG	155189-156352	GT	AGG
(GAG)	 AG	156647-156766	GA	AGG

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34071, rend_intergenic: 29863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44491, rend_intergenic: 38317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48261, rend_intergenic: 47857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67765, rend_intergenic: 65498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152223, rend_intergenic: 149363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179670, rend_intergenic: 173870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195794
-exon list size: 363


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.5    
2.7    
3.0    
3.3    
3.6    
3.8    
4.1    
4.4    
4.7    
4.9    
5.2    
5.5    
5.8    
6.0    
6.3    
6.6    
6.8    
7.1    
7.4    
7.7    
7.9    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.9    
10.1    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.2    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.3    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.1    
21.4    
21.6    
21.9    
22.2    
22.5    
22.7    
23.0    
23.3    
23.6    
23.8    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.8    
26.0    
26.3    
26.6    
26.8    
27.1    
27.4    
27.7    
27.9    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.9    
30.1    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.1    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.8    
47.1    
47.4    
47.7    
47.9    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.1    
52.3    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
64.9    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.9    
70.1    
70.4    
70.7    
71.0    
71.2    
71.5    
71.8    
72.1    
72.3    
72.6    
72.9    
73.2    
73.4    
73.7    
74.0    
74.2    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.2    
76.4    
76.7    
77.0    
77.3    
77.5    
77.8    
78.1    
78.4    
78.6    
78.9    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.7    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.2    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.1    
95.3    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 34071, rend_intergenic: 29863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44491, rend_intergenic: 38317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48261, rend_intergenic: 47857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67765, rend_intergenic: 65498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152223, rend_intergenic: 149363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179670, rend_intergenic: 173870  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