-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_6707130-6914345

-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_49646-T1
Valid prediction for Augustus_model.g33125.t1
Valid prediction for GlimmerHMM_glimmerT_49656-T1
Valid prediction for snap_scaffold_22-snap.1335-T1
Valid prediction for pasa_asmbl_30133.p1
Valid prediction for GlimmerHMM_glimmerT_49643-T1
Valid prediction for GlimmerHMM_glimmerT_49660-T1
Valid prediction for snap_scaffold_22-snap.1343-T1
Valid prediction for Augustus_model.g33111.t1
Valid prediction for Augustus_model.g33110.t1
Valid prediction for GlimmerHMM_glimmerT_49645-T1
Valid prediction for snap_scaffold_22-snap.1321-T1
Valid prediction for snap_scaffold_22-snap.1330-T1
Valid prediction for Augustus_model.g33126.t1
Valid prediction for snap_scaffold_22-snap.1341-T1
Valid prediction for Augustus_model.g33121.t1
Valid prediction for GlimmerHMM_glimmerT_49661-T1
Valid prediction for snap_scaffold_22-snap.1309-T1
Valid prediction for GlimmerHMM_glimmerT_49654-T1
Valid prediction for snap_scaffold_22-snap.1331-T1
Valid prediction for snap_scaffold_22-snap.1317-T1
Valid prediction for HiQ_model.g33123.t1
Valid prediction for Augustus_model.g33115.t1
Valid prediction for snap_scaffold_22-snap.1345-T1
Valid prediction for snap_scaffold_22-snap.1325-T1
Valid prediction for snap_scaffold_22-snap.1333-T1
Valid prediction for Augustus_model.g33120.t1
Valid prediction for GlimmerHMM_glimmerT_49642-T1
Couldn't classify 130342, 131001
Sorry, prediction pasa_asmbl_30125.p1 fails validation.
(ATG)	 AC	130342-131001	AC	ACA
Valid prediction for GlimmerHMM_glimmerT_49649-T1
Valid prediction for snap_scaffold_22-snap.1337-T1
Valid prediction for snap_scaffold_22-snap.1339-T1
Valid prediction for GlimmerHMM_glimmerT_49644-T1
Valid prediction for snap_scaffold_22-snap.1313-T1
Valid prediction for snap_scaffold_22-snap.1320-T1
Valid prediction for GlimmerHMM_glimmerT_49647-T1
Valid prediction for GlimmerHMM_glimmerT_49655-T1
Valid prediction for GlimmerHMM_glimmerT_49663-T1
Valid prediction for GlimmerHMM_glimmerT_49652-T1
Valid prediction for GlimmerHMM_glimmerT_49662-T1
Valid prediction for GlimmerHMM_glimmerT_49658-T1
Valid prediction for Augustus_model.g33112.t1
Couldn't classify 135576, 135682
Sorry, prediction pasa_asmbl_30126.p1 fails validation.
(ATG)	 AC	131611-132926	GT	AAG
(GGG)	 AG	133093-133216	GT	ACG
(CTG)	 AG	133444-133549	GT	CAG
(ACC)	 AG	133698-134016	GT	AGG
(CGC)	 AG	134112-134180	GT	AGG
(GTG)	 AG	134403-134551	GT	TGG
(GTC)	 AG	134785-134899	GT	AAG
(ACA)	 AG	135112-135299	GT	CTG
(CCT)	 AG	135576-135682	NN	NNN
-recovered pasa_asmbl_30126.p1, initial, 131611, 132926
-recovered pasa_asmbl_30126.p1, internal, 133093, 133216
-recovered pasa_asmbl_30126.p1, internal, 133444, 133549
-recovered pasa_asmbl_30126.p1, internal, 133698, 134016
-recovered pasa_asmbl_30126.p1, internal, 134112, 134180
-recovered pasa_asmbl_30126.p1, internal, 134403, 134551
-recovered pasa_asmbl_30126.p1, internal, 134785, 134899
-recovered pasa_asmbl_30126.p1, internal, 135112, 135299
Valid prediction for Augustus_model.g33113.t1
Valid prediction for snap_scaffold_22-snap.1322-T1
Valid prediction for Augustus_model.g33118.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_22-snap.1318-T1
Couldn't classify 41040, 41154
Couldn't classify 41816, 41920
Sorry, prediction pasa_asmbl_29340.p1 fails validation.
(GTC)	 CA	41040-41154	GT	AGG
(AGG)	 AG	41444-41634	GT	CGG
(TCA)	 AG	41816-41920	AC	CCA
-recovered pasa_asmbl_29340.p1, internal, 41444, 41634
Valid prediction for Augustus_model.g33114.t1
Valid prediction for snap_scaffold_22-snap.1319-T1
Valid prediction for snap_scaffold_22-snap.1307-T1
Valid prediction for snap_scaffold_22-snap.1329-T1
Valid prediction for GlimmerHMM_glimmerT_49651-T1
Valid prediction for GlimmerHMM_glimmerT_49665-T1
Valid prediction for Augustus_model.g33124.t1
Valid prediction for Augustus_model.g33116.t1
Valid prediction for GlimmerHMM_glimmerT_49659-T1
Valid prediction for snap_scaffold_22-snap.1316-T1
Valid prediction for snap_scaffold_22-snap.1308-T1
Valid prediction for snap_scaffold_22-snap.1342-T1
Valid prediction for Augustus_model.g33128.t1
Valid prediction for snap_scaffold_22-snap.1315-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g33122.t1
Valid prediction for snap_scaffold_22-snap.1338-T1
Valid prediction for snap_scaffold_22-snap.1328-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_22-snap.1332-T1
Couldn't classify 12908, 12993
Sorry, prediction pasa_asmbl_29344.p1 fails validation.
(ATG)	 AC	10953-11063	GT	AGG
(AGG)	 AG	11536-11664	GT	AGG
(ACT)	 AG	11822-12104	GT	AGG
(GCA)	 AG	12290-12433	GT	GTG
(TTG)	 AG	12908-12993	GT	AGG
-recovered pasa_asmbl_29344.p1, initial, 10953, 11063
add_exon() Sorry, pasa_asmbl_29344.p1 11822-12104-terminal-3 is invalid.
-recovered pasa_asmbl_29344.p1, terminal, 11822, 12104
-recovered pasa_asmbl_29344.p1, internal, 11536, 11664
-recovered pasa_asmbl_29344.p1, internal, 11822, 12104
-recovered pasa_asmbl_29344.p1, internal, 12290, 12433
-recovered pasa_asmbl_29344.p1, internal, 12908, 12993
Valid prediction for GlimmerHMM_glimmerT_49653-T1
Valid prediction for snap_scaffold_22-snap.1311-T1
Valid prediction for GlimmerHMM_glimmerT_49648-T1
Valid prediction for Augustus_model.g33119.t1
Valid prediction for GlimmerHMM_glimmerT_49650-T1
Valid prediction for snap_scaffold_22-snap.1324-T1
Valid prediction for snap_scaffold_22-snap.1326-T1
Valid prediction for GlimmerHMM_glimmerT_49664-T1
Valid prediction for snap_scaffold_22-snap.1314-T1
Valid prediction for snap_scaffold_22-snap.1327-T1
Valid prediction for snap_scaffold_22-snap.1306-T1
Valid prediction for Augustus_model.g33117.t1
Valid prediction for Augustus_model.g33127.t1
Couldn't classify 13168, 13308
Sorry, prediction pasa_asmbl_29343.p1 fails validation.
(ATC)	 TC	13168-13308	GT	AGG
(TTG)	 AG	13435-13539	GT	CGG
(GCG)	 AG	14138-14300	GT	AGG
(GCT)	 AG	14446-14526	GT	AGG
(GCC)	 AG	14661-14797	AG	AAA
-recovered pasa_asmbl_29343.p1, terminal, 14661, 14797
-recovered pasa_asmbl_29343.p1, internal, 13435, 13539
-recovered pasa_asmbl_29343.p1, internal, 14138, 14300
-recovered pasa_asmbl_29343.p1, internal, 14446, 14526
Valid prediction for snap_scaffold_22-snap.1336-T1
Valid prediction for pasa_asmbl_29339.p1
Valid prediction for snap_scaffold_22-snap.1346-T1
Valid prediction for snap_scaffold_22-snap.1310-T1
Valid prediction for snap_scaffold_22-snap.1312-T1
Valid prediction for snap_scaffold_22-snap.1344-T1
Valid prediction for GlimmerHMM_glimmerT_49657-T1
Valid prediction for snap_scaffold_22-snap.1334-T1
Valid prediction for snap_scaffold_22-snap.1340-T1
Valid prediction for snap_scaffold_22-snap.1323-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42919, rend_intergenic: 39619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52304, rend_intergenic: 43256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64972, rend_intergenic: 52453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66014, rend_intergenic: 64972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68487, rend_intergenic: 66207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84270, rend_intergenic: 71413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117597, rend_intergenic: 84422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132930, rend_intergenic: 120004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135273, rend_intergenic: 133079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152495, rend_intergenic: 150484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179891, rend_intergenic: 176577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189325, rend_intergenic: 185325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207216
-exon list size: 443


building trellis

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0.4    
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1.1    
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1.6    
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2.7    
2.9    
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3.6    
3.8    
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4.5    
4.7    
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6.7    
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8.1    
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8.8    
9.0    
9.2    
9.4    
9.7    
9.9    
10.1    
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11.0    
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11.9    
12.1    
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12.6    
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13.3    
13.5    
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13.9    
14.2    
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14.6    
14.8    
15.1    
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15.5    
15.7    
16.0    
16.2    
16.4    
16.6    
16.9    
17.1    
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17.5    
17.8    
18.0    
18.2    
18.4    
18.7    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.2    
20.4    
20.7    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.2    
22.5    
22.7    
22.9    
23.1    
23.4    
23.6    
23.8    
24.0    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.4    
29.7    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.1    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.8    
35.1    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.0    
44.3    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.8    
46.1    
46.3    
46.5    
46.7    
47.0    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
48.5    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.5    
51.7    
51.9    
52.1    
52.4    
52.6    
52.8    
53.0    
53.3    
53.5    
53.7    
53.9    
54.2    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.7    
56.0    
56.2    
56.4    
56.6    
56.9    
57.1    
57.3    
57.5    
57.8    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.3    
61.6    
61.8    
62.0    
62.2    
62.5    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.0    
64.3    
64.5    
64.7    
64.9    
65.2    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.9    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.3    
70.6    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
73.9    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
76.0    
76.2    
76.4    
76.6    
76.9    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.2    
82.5    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.6    
87.9    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 42919, rend_intergenic: 39619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52304, rend_intergenic: 43256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64972, rend_intergenic: 52453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66014, rend_intergenic: 64972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68487, rend_intergenic: 66207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84270, rend_intergenic: 71413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117597, rend_intergenic: 84422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132930, rend_intergenic: 120004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135273, rend_intergenic: 133079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152495, rend_intergenic: 150484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179891, rend_intergenic: 176577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189325, rend_intergenic: 185325  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