-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_1069030-1269223

-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_5-snap.219-T1
Valid prediction for snap_scaffold_5-snap.231-T1
Valid prediction for Augustus_model.g7485.t1
Valid prediction for GlimmerHMM_glimmerT_11432-T1
Valid prediction for snap_scaffold_5-snap.252-T1
Valid prediction for snap_scaffold_5-snap.249-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.237-T1
Valid prediction for Augustus_model.g7488.t1
Couldn't classify 178149, 178216
Sorry, prediction pasa_asmbl_45117.p1 fails validation.
(AAG)	 AG	178149-178216	GT	AGG
(AAT)	 AG	178328-178703	TT	GAT
-recovered pasa_asmbl_45117.p1, terminal, 178328, 178703
-recovered pasa_asmbl_45117.p1, internal, 178149, 178216
Valid prediction for GlimmerHMM_glimmerT_11434-T1
Valid prediction for Augustus_model.g7476.t1
Valid prediction for snap_scaffold_5-snap.247-T1
Valid prediction for snap_scaffold_5-snap.234-T1
Valid prediction for GlimmerHMM_glimmerT_11428-T1
Valid prediction for GlimmerHMM_glimmerT_11435-T1
Valid prediction for snap_scaffold_5-snap.227-T1
Valid prediction for snap_scaffold_5-snap.224-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.215-T1
Valid prediction for snap_scaffold_5-snap.229-T1
Valid prediction for snap_scaffold_5-snap.240-T1
Valid prediction for GlimmerHMM_glimmerT_11450-T1
Valid prediction for snap_scaffold_5-snap.217-T1
Valid prediction for snap_scaffold_5-snap.220-T1
Valid prediction for GlimmerHMM_glimmerT_11453-T1
Valid prediction for snap_scaffold_5-snap.242-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_11443-T1
Valid prediction for GlimmerHMM_glimmerT_11439-T1
Valid prediction for GlimmerHMM_glimmerT_11429-T1
Valid prediction for snap_scaffold_5-snap.230-T1
Valid prediction for snap_scaffold_5-snap.238-T1
Valid prediction for snap_scaffold_5-snap.244-T1
Valid prediction for snap_scaffold_5-snap.236-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_5-snap.232-T1
Valid prediction for GlimmerHMM_glimmerT_11426-T1
Valid prediction for GlimmerHMM_glimmerT_11440-T1
Valid prediction for GlimmerHMM_glimmerT_11425-T1
Valid prediction for Augustus_model.g7480.t1
Valid prediction for pasa_asmbl_45001.p2
Valid prediction for GlimmerHMM_glimmerT_11436-T1
Valid prediction for GlimmerHMM_glimmerT_11427-T1
Valid prediction for snap_scaffold_5-snap.241-T1
Valid prediction for GlimmerHMM_glimmerT_11433-T1
Valid prediction for GlimmerHMM_glimmerT_11445-T1
Valid prediction for snap_scaffold_5-snap.225-T1
Valid prediction for Augustus_model.g7475.t1
Valid prediction for CodingQuarry_transcript_51984-T1
Couldn't classify 43953, 44025
Couldn't classify 44358, 44361
Sorry, prediction CodingQuarry_transcript_51981-T1 fails validation.
(ATG)	 AC	42807-42934	GT	AGG
(TGG)	 AG	43193-43292	GT	TCG
(CTC)	 AG	43741-43774	GT	GGG
(GAA)	 AG	43953-44025	CT	CTC
(TTA)	 TC	44358-44361	CC	AGC
-recovered CodingQuarry_transcript_51981-T1, initial, 42807, 42934
-recovered CodingQuarry_transcript_51981-T1, internal, 43193, 43292
-recovered CodingQuarry_transcript_51981-T1, internal, 43741, 43774
Valid prediction for CodingQuarry_transcript_51982-T1
Valid prediction for snap_scaffold_5-snap.235-T1
Valid prediction for snap_scaffold_5-snap.221-T1
Valid prediction for HiQ_model.g7486.t1
Valid prediction for snap_scaffold_5-snap.251-T1
Valid prediction for GlimmerHMM_glimmerT_11437-T1
Valid prediction for snap_scaffold_5-snap.222-T1
Valid prediction for Augustus_model.g7473.t1
Valid prediction for CodingQuarry_transcript_51978-T1
Valid prediction for Augustus_model.g7479.t1
Valid prediction for snap_scaffold_5-snap.250-T1
Valid prediction for pasa_asmbl_43846.p1
Valid prediction for GlimmerHMM_glimmerT_11446-T1
Valid prediction for GlimmerHMM_glimmerT_11449-T1
Valid prediction for GlimmerHMM_glimmerT_11448-T1
Valid prediction for GlimmerHMM_glimmerT_11451-T1
Couldn't classify 135164, 135700
Sorry, prediction pasa_asmbl_43825.p1 fails validation.
(CCA)	 CC	135164-135700	CA	AGC
Valid prediction for snap_scaffold_5-snap.213-T1
Couldn't classify 165851, 165964
Couldn't classify 167861, 167956
Sorry, prediction pasa_asmbl_43823.p1 fails validation.
(GGG)	 AG	165851-165964	GT	AGG
(CTT)	 AG	166515-166618	GT	AGG
(TAG)	 AG	166740-166817	GT	AGG
(GTT)	 AG	167201-167366	GT	GGG
(GCG)	 AG	167861-167956	GT	ATG
-recovered pasa_asmbl_43823.p1, internal, 165851, 165964
-recovered pasa_asmbl_43823.p1, internal, 166515, 166618
-recovered pasa_asmbl_43823.p1, internal, 166740, 166817
-recovered pasa_asmbl_43823.p1, internal, 167201, 167366
-recovered pasa_asmbl_43823.p1, internal, 167861, 167956
Valid prediction for pasa_asmbl_43829.p1
Valid prediction for Augustus_model.g7471.t1
Valid prediction for GlimmerHMM_glimmerT_11424-T1
Valid prediction for GlimmerHMM_glimmerT_11441-T1
Valid prediction for snap_scaffold_5-snap.218-T1
Valid prediction for Augustus_model.g7472.t1
Valid prediction for Augustus_model.g7474.t1
Valid prediction for HiQ_model.g7470.t1
Couldn't classify 132579, 132926
Sorry, prediction pasa_asmbl_43827.p1 fails validation.
(GAG)	 GA	132579-132926	GA	AAG
Couldn't classify 170011, 170147
Sorry, prediction pasa_asmbl_43821.p1 fails validation.
(GAG)	 GG	170011-170147	GT	AGG
(CGC)	 AG	170895-171071	GT	AGG
(CGT)	 AG	171544-171706	TG	GAT
-recovered pasa_asmbl_43821.p1, terminal, 171544, 171706
-recovered pasa_asmbl_43821.p1, internal, 170895, 171071
Valid prediction for snap_scaffold_5-snap.248-T1
Valid prediction for snap_scaffold_5-snap.228-T1
Valid prediction for GlimmerHMM_glimmerT_11431-T1
Valid prediction for GlimmerHMM_glimmerT_11430-T1
Valid prediction for HiQ_model.g7483.t1
Valid prediction for snap_scaffold_5-snap.246-T1
Valid prediction for Augustus_model.g7484.t1
Valid prediction for Augustus_model.g7481.t1
Valid prediction for snap_scaffold_5-snap.223-T1
Valid prediction for HiQ_model.g7487.t1
Couldn't classify 82602, 82750
Sorry, prediction pasa_asmbl_43835.p1 fails validation.
(ATG)	 GC	79069-79125	GT	AGG
(GCC)	 AG	79667-79797	GT	CGG
(GGG)	 AG	80266-80395	GT	AGG
(AAG)	 AG	80565-80700	GT	AGG
(ACA)	 AG	81543-81681	GT	GCG
(CTT)	 AG	82160-82217	GT	CGG
(GAC)	 AG	82301-82418	GT	TAG
(GGC)	 AG	82602-82750	GA	GGG
-recovered pasa_asmbl_43835.p1, initial, 79069, 79125
-recovered pasa_asmbl_43835.p1, internal, 79667, 79797
-recovered pasa_asmbl_43835.p1, internal, 80266, 80395
-recovered pasa_asmbl_43835.p1, internal, 80565, 80700
-recovered pasa_asmbl_43835.p1, internal, 81543, 81681
-recovered pasa_asmbl_43835.p1, internal, 82160, 82217
-recovered pasa_asmbl_43835.p1, internal, 82301, 82418
Valid prediction for GlimmerHMM_glimmerT_11452-T1
Valid prediction for GlimmerHMM_glimmerT_11447-T1
Couldn't classify 39861, 39927
Sorry, prediction pasa_asmbl_43840.p1 fails validation.
(GGG)	 AG	39861-39927	GT	CAG
(ACC)	 AG	40469-40657	GT	GGG
(GTC)	 AG	41076-41153	GT	AGG
(GTC)	 AG	41250-41411	GT	AGG
(AAG)	 AG	41679-41707	GC	GAG
-recovered pasa_asmbl_43840.p1, terminal, 41679, 41707
-recovered pasa_asmbl_43840.p1, internal, 39861, 39927
-recovered pasa_asmbl_43840.p1, internal, 40469, 40657
-recovered pasa_asmbl_43840.p1, internal, 41076, 41153
-recovered pasa_asmbl_43840.p1, internal, 41250, 41411
-recovered pasa_asmbl_43840.p1, internal, 41679, 41707
Valid prediction for Augustus_model.g7478.t1
Valid prediction for GlimmerHMM_glimmerT_11438-T1
Valid prediction for pasa_asmbl_43816.p1
Valid prediction for Augustus_model.g7477.t1
Couldn't classify 54303, 54359
Couldn't classify 56430, 57263
Sorry, prediction pasa_asmbl_43837.p1 fails validation.
(AAG)	 TC	54303-54359	GT	AGG
(GAC)	 AG	56430-57263	GT	AGG
-recovered pasa_asmbl_43837.p1, internal, 56430, 57263
Valid prediction for snap_scaffold_5-snap.226-T1
Valid prediction for GlimmerHMM_glimmerT_11442-T1
Valid prediction for snap_scaffold_5-snap.243-T1
Valid prediction for snap_scaffold_5-snap.233-T1
Valid prediction for snap_scaffold_5-snap.216-T1
Valid prediction for GlimmerHMM_glimmerT_11444-T1
Valid prediction for snap_scaffold_5-snap.239-T1
Valid prediction for Augustus_model.g7482.t1
Valid prediction for snap_scaffold_5-snap.245-T1
Valid prediction for snap_scaffold_5-snap.214-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18282, rend_intergenic: 11938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25988, rend_intergenic: 20974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34332, rend_intergenic: 31222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59919, rend_intergenic: 38272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62663, rend_intergenic: 60841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73153, rend_intergenic: 62848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75262, rend_intergenic: 73457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85229, rend_intergenic: 80650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97989, rend_intergenic: 89534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109352, rend_intergenic: 100953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131263, rend_intergenic: 113356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150704, rend_intergenic: 141583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163824, rend_intergenic: 153611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168079, rend_intergenic: 164948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172952, rend_intergenic: 172067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186491, rend_intergenic: 182894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200194
-exon list size: 377


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.2    
3.4    
3.7    
4.0    
4.2    
4.5    
4.7    
5.0    
5.3    
5.5    
5.8    
6.1    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.0    
10.3    
10.6    
10.8    
11.1    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.8    
16.1    
16.4    
16.6    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.5    
18.7    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.4    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
31.9    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.3    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.2    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.7    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.1    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
69.9    
70.2    
70.4    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.6    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.5    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.4    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
90.0    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.5    
94.7    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 18282, rend_intergenic: 11938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25988, rend_intergenic: 20974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34332, rend_intergenic: 31222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59919, rend_intergenic: 38272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62663, rend_intergenic: 60841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73153, rend_intergenic: 62848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75262, rend_intergenic: 73457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85229, rend_intergenic: 80650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97989, rend_intergenic: 89534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109352, rend_intergenic: 100953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131263, rend_intergenic: 113356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150704, rend_intergenic: 141583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163824, rend_intergenic: 153611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168079, rend_intergenic: 164948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172952, rend_intergenic: 172067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186491, rend_intergenic: 182894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 190152 - 200194
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support