-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_6872429-7040067

-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 Augustus_model.g6217.t1
Valid prediction for snap_scaffold_4-snap.1460-T1
Valid prediction for GlimmerHMM_glimmerT_9598-T1
Valid prediction for snap_scaffold_4-snap.1464-T1
Valid prediction for pasa_asmbl_41432.p1
Valid prediction for Augustus_model.g6210.t1
Valid prediction for Augustus_model.g6220.t1
Valid prediction for GlimmerHMM_glimmerT_9581-T1
Valid prediction for snap_scaffold_4-snap.1484-T1
Valid prediction for snap_scaffold_4-snap.1490-T1
Valid prediction for GlimmerHMM_glimmerT_9592-T1
Valid prediction for snap_scaffold_4-snap.1455-T1
Valid prediction for GlimmerHMM_glimmerT_9602-T1
Valid prediction for GlimmerHMM_glimmerT_9596-T1
Valid prediction for snap_scaffold_4-snap.1457-T1
Valid prediction for snap_scaffold_4-snap.1478-T1
Valid prediction for snap_scaffold_4-snap.1482-T1
Valid prediction for snap_scaffold_4-snap.1476-T1
Valid prediction for snap_scaffold_4-snap.1481-T1
Valid prediction for CodingQuarry_transcript_49032-T1
Valid prediction for GlimmerHMM_glimmerT_9599-T1
Valid prediction for GlimmerHMM_glimmerT_9577-T1
Valid prediction for GlimmerHMM_glimmerT_9589-T1
Valid prediction for GlimmerHMM_glimmerT_9594-T1
Valid prediction for snap_scaffold_4-snap.1488-T1
Valid prediction for GlimmerHMM_glimmerT_9597-T1
Couldn't classify 157387, 157440
Sorry, prediction pasa_asmbl_41448.p1 fails validation.
(CCC)	 AC	157387-157440	GC	AGG
(CCA)	 AG	159469-159561	GT	AGG
(ATG)	 AG	159671-159787	GT	AGG
(GAC)	 AG	159911-160027	GT	TGG
(AAG)	 AG	162370-162432	GT	CAG
(ACA)	 AG	163908-163947	GT	AGG
(AAC)	 AG	164670-164773	GT	AGG
(CTC)	 AG	166513-166668	GT	AGG
(GAT)	 AG	166863-166943	GT	AGG
(ATC)	 AG	167171-167398	CT	AGC
-recovered pasa_asmbl_41448.p1, initial, 159671, 159787
-recovered pasa_asmbl_41448.p1, terminal, 167171, 167398
-recovered pasa_asmbl_41448.p1, internal, 159469, 159561
-recovered pasa_asmbl_41448.p1, internal, 159671, 159787
-recovered pasa_asmbl_41448.p1, internal, 159911, 160027
-recovered pasa_asmbl_41448.p1, internal, 162370, 162432
-recovered pasa_asmbl_41448.p1, internal, 163908, 163947
-recovered pasa_asmbl_41448.p1, internal, 164670, 164773
-recovered pasa_asmbl_41448.p1, internal, 166513, 166668
-recovered pasa_asmbl_41448.p1, internal, 166863, 166943
Valid prediction for Augustus_model.g6216.t1
Valid prediction for snap_scaffold_4-snap.1453-T1
Valid prediction for GlimmerHMM_glimmerT_9580-T1
Valid prediction for snap_scaffold_4-snap.1454-T1
Valid prediction for GlimmerHMM_glimmerT_9591-T1
Valid prediction for CodingQuarry_transcript_49033-T1
Valid prediction for HiQ_model.g6214.t1
Valid prediction for snap_scaffold_4-snap.1483-T1
Valid prediction for GlimmerHMM_glimmerT_9587-T1
Valid prediction for snap_scaffold_4-snap.1475-T1
Valid prediction for GlimmerHMM_glimmerT_9586-T1
Valid prediction for snap_scaffold_4-snap.1473-T1
Valid prediction for Augustus_model.g6224.t1
Valid prediction for snap_scaffold_4-snap.1461-T1
Valid prediction for HiQ_model.g6215.t1
Valid prediction for Augustus_model.g6223.t1
Valid prediction for snap_scaffold_4-snap.1471-T1
Valid prediction for snap_scaffold_4-snap.1466-T1
Valid prediction for snap_scaffold_4-snap.1487-T1
Couldn't classify 135073, 135125
Couldn't classify 143971, 144026
Sorry, prediction pasa_asmbl_41439.p1 fails validation.
(GCA)	 TA	135073-135125	GT	AGG
(GAG)	 AG	135259-135321	GT	GAG
(AAA)	 AG	136458-136512	GT	AGG
(GCT)	 AG	138791-138931	GT	GCG
(TCA)	 AG	139439-139516	GT	TGG
(CCG)	 AG	139783-139890	GT	AGG
(CCT)	 AG	140010-140127	GT	AGG
(CAG)	 AG	140252-140285	GT	AAG
(GGT)	 AG	141275-141333	GT	AGG
(AGA)	 AG	143971-144026	AG	CCA
-recovered pasa_asmbl_41439.p1, internal, 135259, 135321
-recovered pasa_asmbl_41439.p1, internal, 136458, 136512
-recovered pasa_asmbl_41439.p1, internal, 138791, 138931
-recovered pasa_asmbl_41439.p1, internal, 139439, 139516
-recovered pasa_asmbl_41439.p1, internal, 139783, 139890
-recovered pasa_asmbl_41439.p1, internal, 140010, 140127
-recovered pasa_asmbl_41439.p1, internal, 140252, 140285
-recovered pasa_asmbl_41439.p1, internal, 141275, 141333
Valid prediction for snap_scaffold_4-snap.1480-T1
Valid prediction for snap_scaffold_4-snap.1477-T1
Valid prediction for snap_scaffold_4-snap.1459-T1
Valid prediction for GlimmerHMM_glimmerT_9588-T1
Valid prediction for GlimmerHMM_glimmerT_9593-T1
Couldn't classify 147053, 147151
Couldn't classify 150377, 150579
Sorry, prediction pasa_asmbl_41442.p1 fails validation.
(GCC)	 CA	147053-147151	GT	CGG
(GAG)	 AG	147891-147975	GT	CCG
(TGA)	 AG	148713-148813	GT	AGG
(CTC)	 AG	149554-149669	GT	AGG
(AGA)	 AG	149800-149900	GT	AGG
(CGT)	 AG	150098-150187	GT	CGG
(GGG)	 AG	150377-150579	AG	TCA
-recovered pasa_asmbl_41442.p1, internal, 147891, 147975
-recovered pasa_asmbl_41442.p1, internal, 148713, 148813
-recovered pasa_asmbl_41442.p1, internal, 149554, 149669
-recovered pasa_asmbl_41442.p1, internal, 149800, 149900
-recovered pasa_asmbl_41442.p1, internal, 150098, 150187
Valid prediction for Augustus_model.g6218.t1
Valid prediction for GlimmerHMM_glimmerT_9590-T1
Valid prediction for Augustus_model.g6222.t1
Valid prediction for snap_scaffold_4-snap.1469-T1
Valid prediction for Augustus_model.g6213.t1
Valid prediction for GlimmerHMM_glimmerT_9600-T1
Valid prediction for snap_scaffold_4-snap.1489-T1
Valid prediction for Augustus_model.g6221.t1
Valid prediction for snap_scaffold_4-snap.1486-T1
Valid prediction for GlimmerHMM_glimmerT_9579-T1
Valid prediction for GlimmerHMM_glimmerT_9601-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_4-snap.1467-T1
Valid prediction for snap_scaffold_4-snap.1468-T1
Valid prediction for snap_scaffold_4-snap.1485-T1
Valid prediction for snap_scaffold_4-snap.1491-T1
Valid prediction for Augustus_model.g6211.t1
Valid prediction for snap_scaffold_4-snap.1479-T1
Valid prediction for snap_scaffold_4-snap.1493-T1
Valid prediction for Augustus_model.g6219.t1
Valid prediction for snap_scaffold_4-snap.1456-T1
Valid prediction for snap_scaffold_4-snap.1472-T1
Valid prediction for snap_scaffold_4-snap.1462-T1
Valid prediction for GlimmerHMM_glimmerT_9584-T1
Valid prediction for GlimmerHMM_glimmerT_9578-T1
Valid prediction for snap_scaffold_4-snap.1494-T1
Valid prediction for snap_scaffold_4-snap.1465-T1
Valid prediction for Augustus_model.g6212.t1
Valid prediction for snap_scaffold_4-snap.1463-T1
Valid prediction for GlimmerHMM_glimmerT_9576-T1
Valid prediction for GlimmerHMM_glimmerT_9595-T1
Valid prediction for snap_scaffold_4-snap.1474-T1
Valid prediction for snap_scaffold_4-snap.1492-T1
Valid prediction for GlimmerHMM_glimmerT_9583-T1
Valid prediction for snap_scaffold_4-snap.1458-T1
Valid prediction for GlimmerHMM_glimmerT_9582-T1
Valid prediction for GlimmerHMM_glimmerT_9585-T1
Valid prediction for snap_scaffold_4-snap.1470-T1
Valid prediction for snap_scaffold_4-snap.1452-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5673, rend_intergenic: 2107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13932, rend_intergenic: 12210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17117, rend_intergenic: 14476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23977, rend_intergenic: 19036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37436, rend_intergenic: 24066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48923, rend_intergenic: 45988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50859, rend_intergenic: 50118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55809, rend_intergenic: 54262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58921, rend_intergenic: 56685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63824, rend_intergenic: 59243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94529, rend_intergenic: 92032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128329, rend_intergenic: 119944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167398, rend_intergenic: 138200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 167639
-exon list size: 365


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    
3.5    
3.8    
4.1    
4.4    
4.6    
4.9    
5.2    
5.4    
5.7    
6.0    
6.3    
6.5    
6.8    
7.1    
7.4    
7.6    
7.9    
8.2    
8.4    
8.7    
9.0    
9.3    
9.5    
9.8    
10.1    
10.4    
10.6    
10.9    
11.2    
11.4    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.3    
16.6    
16.9    
17.2    
17.4    
17.7    
18.0    
18.3    
18.5    
18.8    
19.1    
19.3    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.3    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.2    
23.4    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.1    
28.3    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
30.2    
30.5    
30.8    
31.1    
31.3    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
42.0    
42.2    
42.5    
42.8    
43.1    
43.3    
43.6    
43.9    
44.1    
44.4    
44.7    
45.0    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.9    
47.1    
47.4    
47.7    
48.0    
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    
52.0    
52.3    
52.6    
52.9    
53.1    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.0    
55.3    
55.6    
55.9    
56.1    
56.4    
56.7    
56.9    
57.2    
57.5    
57.8    
58.0    
58.3    
58.6    
58.9    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.7    
68.9    
69.2    
69.5    
69.8    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.7    
71.9    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.6    
76.8    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.7    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.7    
80.9    
81.2    
81.5    
81.7    
82.0    
82.3    
82.6    
82.8    
83.1    
83.4    
83.7    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.6    
88.8    
89.1    
89.4    
89.6    
89.9    
90.2    
90.5    
90.7    
91.0    
91.3    
91.6    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.5    
93.7    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.6    
95.9    
96.2    
96.5    
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 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 5673, rend_intergenic: 2107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13932, rend_intergenic: 12210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17117, rend_intergenic: 14476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23977, rend_intergenic: 19036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37436, rend_intergenic: 24066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48923, rend_intergenic: 45988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50859, rend_intergenic: 50118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55809, rend_intergenic: 54262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58921, rend_intergenic: 56685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63824, rend_intergenic: 59243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94529, rend_intergenic: 92032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128329, rend_intergenic: 119944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167398, rend_intergenic: 138200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support