-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_14976585-15133723

-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_1984-T1
Couldn't classify 124070, 124175
Couldn't classify 127629, 127702
Sorry, prediction pasa_asmbl_2421.p1 fails validation.
(TCG)	 CC	124070-124175	GT	AGG
(AAT)	 AG	125387-125506	GT	ACG
(GAG)	 AG	127337-127522	GT	AGG
(GCG)	 AG	127629-127702	AC	AGA
-recovered pasa_asmbl_2421.p1, internal, 125387, 125506
-recovered pasa_asmbl_2421.p1, internal, 127337, 127522
Valid prediction for GlimmerHMM_glimmerT_1962-T1
Valid prediction for GlimmerHMM_glimmerT_1979-T1
Valid prediction for GlimmerHMM_glimmerT_1956-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_1963-T1
Valid prediction for GlimmerHMM_glimmerT_1957-T1
Valid prediction for snap_scaffold_1-snap.2598-T1
Valid prediction for GlimmerHMM_glimmerT_1982-T1
Valid prediction for snap_scaffold_1-snap.2619-T1
Valid prediction for snap_scaffold_1-snap.2591-T1
Valid prediction for GlimmerHMM_glimmerT_1974-T1
Valid prediction for snap_scaffold_1-snap.2603-T1
Couldn't classify 142977, 143199
Sorry, prediction pasa_asmbl_2425.p1 fails validation.
(GAG)	 AG	142977-143199	GT	CGG
(GGC)	 AG	145490-145657	GT	TGG
(AGT)	 AG	148475-148568	GT	AGG
(AAT)	 AG	148683-148770	GT	AGG
(GAC)	 AG	149395-149538	GT	GGG
(GTT)	 AG	151119-151257	GT	TGG
(GGA)	 AG	152840-152928	GT	CGG
(ACA)	 AG	154006-154053	AC	AAA
-recovered pasa_asmbl_2425.p1, terminal, 148475, 148568
-recovered pasa_asmbl_2425.p1, terminal, 154006, 154053
-recovered pasa_asmbl_2425.p1, internal, 142977, 143199
-recovered pasa_asmbl_2425.p1, internal, 145490, 145657
-recovered pasa_asmbl_2425.p1, internal, 148475, 148568
-recovered pasa_asmbl_2425.p1, internal, 148683, 148770
-recovered pasa_asmbl_2425.p1, internal, 149395, 149538
-recovered pasa_asmbl_2425.p1, internal, 151119, 151257
-recovered pasa_asmbl_2425.p1, internal, 152840, 152928
Valid prediction for snap_scaffold_1-snap.2623-T1
Valid prediction for snap_scaffold_1-snap.2608-T1
Valid prediction for Augustus_model.g1478.t1
Valid prediction for snap_scaffold_1-snap.2610-T1
Valid prediction for snap_scaffold_1-snap.2597-T1
Valid prediction for snap_scaffold_1-snap.2601-T1
Valid prediction for GlimmerHMM_glimmerT_1965-T1
Valid prediction for GlimmerHMM_glimmerT_1968-T1
Valid prediction for Augustus_model.g1487.t1
Valid prediction for snap_scaffold_1-snap.2620-T1
Valid prediction for GlimmerHMM_glimmerT_1972-T1
Valid prediction for snap_scaffold_1-snap.2593-T1
Valid prediction for snap_scaffold_1-snap.2589-T1
Valid prediction for snap_scaffold_1-snap.2599-T1
Valid prediction for GlimmerHMM_glimmerT_1970-T1
Valid prediction for GlimmerHMM_glimmerT_1983-T1
Valid prediction for GlimmerHMM_glimmerT_1977-T1
Valid prediction for snap_scaffold_1-snap.2605-T1
Valid prediction for snap_scaffold_1-snap.2595-T1
Valid prediction for GlimmerHMM_glimmerT_1958-T1
Valid prediction for GlimmerHMM_glimmerT_1967-T1
Valid prediction for snap_scaffold_1-snap.2590-T1
Valid prediction for snap_scaffold_1-snap.2622-T1
Valid prediction for snap_scaffold_1-snap.2614-T1
Valid prediction for snap_scaffold_1-snap.2587-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_1981-T1
Valid prediction for CodingQuarry_transcript_2933-T1
Valid prediction for snap_scaffold_1-snap.2618-T1
Valid prediction for Augustus_model.g1481.t1
Valid prediction for snap_scaffold_1-snap.2616-T1
Valid prediction for Augustus_model.g1486.t1
Valid prediction for snap_scaffold_1-snap.2611-T1
Valid prediction for GlimmerHMM_glimmerT_1960-T1
Valid prediction for snap_scaffold_1-snap.2585-T1
Valid prediction for Augustus_model.g1488.t1
Valid prediction for Augustus_model.g1485.t1
Couldn't classify 154512, 155180
Sorry, prediction pasa_asmbl_2426.p1 fails validation.
(CAG)	 CC	154512-155180	TT	GAT

-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_1973-T1
Valid prediction for snap_scaffold_1-snap.2613-T1
Valid prediction for GlimmerHMM_glimmerT_1966-T1
Valid prediction for snap_scaffold_1-snap.2592-T1
Valid prediction for Augustus_model.g1476.t1
Valid prediction for snap_scaffold_1-snap.2606-T1
Valid prediction for snap_scaffold_1-snap.2602-T1
Valid prediction for snap_scaffold_1-snap.2609-T1
Valid prediction for snap_scaffold_1-snap.2596-T1
Valid prediction for snap_scaffold_1-snap.2584-T1
Valid prediction for GlimmerHMM_glimmerT_1976-T1
Valid prediction for snap_scaffold_1-snap.2615-T1
Valid prediction for GlimmerHMM_glimmerT_1964-T1
Valid prediction for snap_scaffold_1-snap.2600-T1
Valid prediction for snap_scaffold_1-snap.2607-T1
Valid prediction for Augustus_model.g1482.t1
Valid prediction for GlimmerHMM_glimmerT_1955-T1
Valid prediction for GlimmerHMM_glimmerT_1975-T1
Valid prediction for snap_scaffold_1-snap.2621-T1
Valid prediction for snap_scaffold_1-snap.2586-T1
Valid prediction for snap_scaffold_1-snap.2594-T1
Valid prediction for Augustus_model.g1480.t1
Valid prediction for snap_scaffold_1-snap.2588-T1
Valid prediction for Augustus_model.g1479.t1
Valid prediction for snap_scaffold_1-snap.2604-T1
Valid prediction for Augustus_model.g1484.t1
Valid prediction for Augustus_model.g1477.t1
Valid prediction for GlimmerHMM_glimmerT_1961-T1
Couldn't classify 121024, 121139
Sorry, prediction pasa_asmbl_952.p1 fails validation.
(ATG)	 AC	119817-119849	GT	TGG
(GCA)	 AG	120135-120291	GT	TGG
(CCG)	 AG	121024-121139	GT	TCG
-recovered pasa_asmbl_952.p1, initial, 119817, 119849
-recovered pasa_asmbl_952.p1, internal, 120135, 120291
-recovered pasa_asmbl_952.p1, internal, 121024, 121139
Valid prediction for GlimmerHMM_glimmerT_1971-T1
Valid prediction for snap_scaffold_1-snap.2617-T1
Valid prediction for GlimmerHMM_glimmerT_1978-T1
Valid prediction for GlimmerHMM_glimmerT_1969-T1
Valid prediction for GlimmerHMM_glimmerT_1959-T1
Valid prediction for Augustus_model.g1483.t1
Valid prediction for GlimmerHMM_glimmerT_1980-T1
Valid prediction for snap_scaffold_1-snap.2612-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11353, rend_intergenic: 6791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14840, rend_intergenic: 11906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18435, rend_intergenic: 14984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25927, rend_intergenic: 18598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30365, rend_intergenic: 26378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43382, rend_intergenic: 41144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47498, rend_intergenic: 44602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65345, rend_intergenic: 63764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72677, rend_intergenic: 67163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74029, rend_intergenic: 73485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77204, rend_intergenic: 74930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98502, rend_intergenic: 84010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109253, rend_intergenic: 106344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128314, rend_intergenic: 118509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129204, rend_intergenic: 128548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133107, rend_intergenic: 129552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137425, rend_intergenic: 133276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138506, rend_intergenic: 137910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143282, rend_intergenic: 138927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151307, rend_intergenic: 145999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157139
-exon list size: 324


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 11353, rend_intergenic: 6791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14840, rend_intergenic: 11906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18435, rend_intergenic: 14984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25927, rend_intergenic: 18598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30365, rend_intergenic: 26378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43382, rend_intergenic: 41144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47498, rend_intergenic: 44602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65345, rend_intergenic: 63764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72677, rend_intergenic: 67163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74029, rend_intergenic: 73485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77204, rend_intergenic: 74930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98502, rend_intergenic: 84010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109253, rend_intergenic: 106344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128314, rend_intergenic: 118509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129204, rend_intergenic: 128548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133107, rend_intergenic: 129552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137425, rend_intergenic: 133276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138506, rend_intergenic: 137910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143282, rend_intergenic: 138927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151307, rend_intergenic: 145999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support