-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_4991813-5164054

-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_54104-T1
Valid prediction for GlimmerHMM_glimmerT_54099-T1
Valid prediction for GlimmerHMM_glimmerT_54112-T1
Valid prediction for snap_scaffold_25-snap.1050-T1
Valid prediction for Augustus_model.g35920.t1
Valid prediction for Augustus_model.g35922.t1
Valid prediction for Augustus_model.g35914.t1
Valid prediction for GlimmerHMM_glimmerT_54097-T1
Valid prediction for snap_scaffold_25-snap.1062-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1045-T1
Valid prediction for GlimmerHMM_glimmerT_54114-T1
Valid prediction for snap_scaffold_25-snap.1051-T1
Valid prediction for snap_scaffold_25-snap.1064-T1
Valid prediction for Augustus_model.g35909.t1
Valid prediction for snap_scaffold_25-snap.1058-T1
Valid prediction for GlimmerHMM_glimmerT_54101-T1
Valid prediction for Augustus_model.g35918.t1
Valid prediction for GlimmerHMM_glimmerT_54111-T1
Valid prediction for pasa_asmbl_33552.p1
Couldn't classify 5178, 5264
Sorry, prediction pasa_asmbl_33548.p1 fails validation.
(CCC)	 GT	5178-5264	GT	AGG
(AGG)	 AG	5445-5550	GT	CAG
(TTC)	 AG	5797-5870	GT	CGG
(CTG)	 AG	6021-6181	GT	GGG
(TCT)	 AG	6710-6861	GT	CTG
(GTG)	 AG	6959-7209	TT	GAT
-recovered pasa_asmbl_33548.p1, terminal, 6959, 7209
-recovered pasa_asmbl_33548.p1, internal, 5445, 5550
-recovered pasa_asmbl_33548.p1, internal, 5797, 5870
-recovered pasa_asmbl_33548.p1, internal, 6021, 6181
-recovered pasa_asmbl_33548.p1, internal, 6710, 6861
Couldn't classify 51267, 51359
Sorry, prediction pasa_asmbl_33557.p1 fails validation.
(AGG)	 GT	51267-51359	GT	CGG
(ATG)	 AG	52760-52832	GT	AGG
(CTC)	 AG	55651-55721	GT	GGG
(CCC)	 AG	55827-55899	GT	AGG
(GTA)	 AG	55994-56034	GT	AGG
(CCT)	 AG	56227-56359	GT	AGG
(ACA)	 AG	56524-56570	GT	CTG
(GTG)	 AG	58872-58968	GT	AGG
(AAG)	 AG	59325-59458	GT	TGG
(AAC)	 AG	59566-59674	GT	GGG
(CCA)	 AG	60001-60056	GT	CAG
(ATC)	 AG	60242-60323	GT	AGG
(GTC)	 AG	61131-61210	GT	TGG
(CAA)	 AG	61364-61558	GT	TGG
(GGA)	 AG	61635-61749	GT	AAG
(GCC)	 AG	62037-62184	GT	AGG
(AAA)	 AG	62521-62574	GT	GAG
(TCA)	 AG	63186-63424	GT	AGG
(AAC)	 AG	63848-63990	TA	AAT
-recovered pasa_asmbl_33557.p1, initial, 52760, 52832
add_exon() Sorry, pasa_asmbl_33557.p1 56227-56359-terminal-3 is invalid.
-recovered pasa_asmbl_33557.p1, terminal, 56227, 56359
-recovered pasa_asmbl_33557.p1, terminal, 63848, 63990
-recovered pasa_asmbl_33557.p1, internal, 52760, 52832
-recovered pasa_asmbl_33557.p1, internal, 55651, 55721
-recovered pasa_asmbl_33557.p1, internal, 55827, 55899
-recovered pasa_asmbl_33557.p1, internal, 55994, 56034
-recovered pasa_asmbl_33557.p1, internal, 56227, 56359
-recovered pasa_asmbl_33557.p1, internal, 56524, 56570
-recovered pasa_asmbl_33557.p1, internal, 58872, 58968
-recovered pasa_asmbl_33557.p1, internal, 59325, 59458
-recovered pasa_asmbl_33557.p1, internal, 59566, 59674
-recovered pasa_asmbl_33557.p1, internal, 60001, 60056
-recovered pasa_asmbl_33557.p1, internal, 60242, 60323
-recovered pasa_asmbl_33557.p1, internal, 61131, 61210
-recovered pasa_asmbl_33557.p1, internal, 61364, 61558
-recovered pasa_asmbl_33557.p1, internal, 61635, 61749
-recovered pasa_asmbl_33557.p1, internal, 62037, 62184
-recovered pasa_asmbl_33557.p1, internal, 62521, 62574
-recovered pasa_asmbl_33557.p1, internal, 63186, 63424
Valid prediction for GlimmerHMM_glimmerT_54110-T1
Valid prediction for snap_scaffold_25-snap.1042-T1
Valid prediction for GlimmerHMM_glimmerT_54095-T1
Valid prediction for snap_scaffold_25-snap.1054-T1
Valid prediction for snap_scaffold_25-snap.1047-T1
Valid prediction for Augustus_model.g35919.t1
Valid prediction for snap_scaffold_25-snap.1065-T1
Valid prediction for snap_scaffold_25-snap.1055-T1
Valid prediction for HiQ_model.g35908.t1
Valid prediction for snap_scaffold_25-snap.1040-T1
Valid prediction for snap_scaffold_25-snap.1063-T1
Valid prediction for GlimmerHMM_glimmerT_54113-T1
Valid prediction for HiQ_model.g35910.t1
Valid prediction for snap_scaffold_25-snap.1061-T1
Valid prediction for Augustus_model.g35917.t1
Valid prediction for snap_scaffold_25-snap.1049-T1
Valid prediction for CodingQuarry_transcript_38722-T1
Valid prediction for Augustus_model.g35907.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_54106-T1
Valid prediction for Augustus_model.g35923.t1
Valid prediction for snap_scaffold_25-snap.1070-T1
Valid prediction for snap_scaffold_25-snap.1057-T1
Valid prediction for snap_scaffold_25-snap.1048-T1
Valid prediction for CodingQuarry_transcript_38727-T1
Valid prediction for snap_scaffold_25-snap.1068-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1046-T1
Valid prediction for GlimmerHMM_glimmerT_54109-T1
Couldn't classify 93137, 93199
Sorry, prediction pasa_asmbl_34237.p1 fails validation.
(AGC)	 GC	93137-93199	GT	AGG
(GTG)	 AG	93327-93503	GT	AGG
(GCC)	 AG	93645-94460	AG	GAA
-recovered pasa_asmbl_34237.p1, terminal, 93645, 94460
-recovered pasa_asmbl_34237.p1, internal, 93327, 93503
Valid prediction for GlimmerHMM_glimmerT_54107-T1
Valid prediction for GlimmerHMM_glimmerT_54105-T1
Valid prediction for snap_scaffold_25-snap.1043-T1
Valid prediction for Augustus_model.g35915.t1
Valid prediction for GlimmerHMM_glimmerT_54119-T1
Valid prediction for HiQ_model.g35924.t1
Valid prediction for snap_scaffold_25-snap.1067-T1
Valid prediction for snap_scaffold_25-snap.1053-T1
Valid prediction for CodingQuarry_transcript_38726-T1
Valid prediction for snap_scaffold_25-snap.1059-T1
Valid prediction for GlimmerHMM_glimmerT_54108-T1
Valid prediction for GlimmerHMM_glimmerT_54115-T1
Valid prediction for snap_scaffold_25-snap.1069-T1
Valid prediction for snap_scaffold_25-snap.1066-T1
Valid prediction for GlimmerHMM_glimmerT_54118-T1
Valid prediction for Augustus_model.g35912.t1
Valid prediction for GlimmerHMM_glimmerT_54117-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_54096-T1
Valid prediction for pasa_asmbl_34239.p1
Valid prediction for Augustus_model.g35925.t1
Valid prediction for CodingQuarry_transcript_38723-T1
Valid prediction for GlimmerHMM_glimmerT_54102-T1
Valid prediction for GlimmerHMM_glimmerT_54100-T1
Valid prediction for snap_scaffold_25-snap.1052-T1
Valid prediction for Augustus_model.g35926.t1
Valid prediction for pasa_asmbl_34244.p1
Couldn't classify 76117, 76236
Sorry, prediction pasa_asmbl_34238.p1 fails validation.
(CTT)	 AA	76117-76236	GT	TGG
(GTT)	 AG	76531-76670	GT	ACG
(TGC)	 AG	76797-76920	GT	AAG
(CGT)	 AG	77035-77150	GT	AAG
(GAG)	 AG	77534-77689	GT	AGG
(GGT)	 AG	77792-77900	GT	AGG
(ACC)	 AG	78096-78261	GT	AGG
(GAA)	 AG	78362-78432	GT	CTG
(GAC)	 AG	78657-78857	GT	AGG
(CAC)	 AG	78965-79127	GT	ATG
(CTA)	 AG	79398-79606	GT	AGG
(AGC)	 AG	79856-80029	GC	GAG
-recovered pasa_asmbl_34238.p1, terminal, 79856, 80029
-recovered pasa_asmbl_34238.p1, internal, 76531, 76670
-recovered pasa_asmbl_34238.p1, internal, 76797, 76920
-recovered pasa_asmbl_34238.p1, internal, 77035, 77150
-recovered pasa_asmbl_34238.p1, internal, 77534, 77689
-recovered pasa_asmbl_34238.p1, internal, 77792, 77900
-recovered pasa_asmbl_34238.p1, internal, 78096, 78261
-recovered pasa_asmbl_34238.p1, internal, 78362, 78432
-recovered pasa_asmbl_34238.p1, internal, 78657, 78857
-recovered pasa_asmbl_34238.p1, internal, 78965, 79127
-recovered pasa_asmbl_34238.p1, internal, 79398, 79606
-recovered pasa_asmbl_34238.p1, internal, 79856, 80029
Valid prediction for Augustus_model.g35913.t1
Valid prediction for Augustus_model.g35921.t1
Valid prediction for HiQ_model.g35916.t1
Valid prediction for GlimmerHMM_glimmerT_54103-T1
Valid prediction for snap_scaffold_25-snap.1044-T1
Couldn't classify 10059, 10197
Sorry, prediction pasa_asmbl_34241.p1 fails validation.
(GAG)	 GC	10059-10197	GT	GGG
(GTT)	 AG	10332-10687	CG	GAC
-recovered pasa_asmbl_34241.p1, terminal, 10332, 10687
Valid prediction for snap_scaffold_25-snap.1056-T1
Valid prediction for CodingQuarry_transcript_38725-T1
Valid prediction for snap_scaffold_25-snap.1041-T1
Valid prediction for CodingQuarry_transcript_38724-T1
Valid prediction for GlimmerHMM_glimmerT_54116-T1
Valid prediction for Augustus_model.g35911.t1
Valid prediction for snap_scaffold_25-snap.1060-T1
Valid prediction for GlimmerHMM_glimmerT_54098-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8722, rend_intergenic: 5304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14865, rend_intergenic: 11393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24039, rend_intergenic: 17174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27158, rend_intergenic: 24553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30856, rend_intergenic: 27211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37322, rend_intergenic: 32199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70414, rend_intergenic: 54855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82617, rend_intergenic: 77783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172242
-exon list size: 480


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.2    
6.4    
6.6    
6.8    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
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    
19.9    
20.1    
20.3    
20.5    
20.7    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
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    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.8    
44.0    
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    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
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    
56.0    
56.2    
56.4    
56.6    
56.8    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
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    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
79.9    
80.1    
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    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 8722, rend_intergenic: 5304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14865, rend_intergenic: 11393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24039, rend_intergenic: 17174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27158, rend_intergenic: 24553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30856, rend_intergenic: 27211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37322, rend_intergenic: 32199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70414, rend_intergenic: 54855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82617, rend_intergenic: 77783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support