-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_5958541-6141548

-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_3890-T1
Valid prediction for GlimmerHMM_glimmerT_3906-T1
Valid prediction for GlimmerHMM_glimmerT_3908-T1
Valid prediction for Augustus_model.g2608.t1
Valid prediction for GlimmerHMM_glimmerT_3904-T1
Valid prediction for Augustus_model.g2596.t1
Valid prediction for Augustus_model.g2603.t1
Valid prediction for GlimmerHMM_glimmerT_3891-T1
Valid prediction for snap_scaffold_2-snap.1355-T1
Valid prediction for Augustus_model.g2612.t1
Valid prediction for snap_scaffold_2-snap.1358-T1
Valid prediction for snap_scaffold_2-snap.1346-T1
Valid prediction for snap_scaffold_2-snap.1334-T1
Valid prediction for HiQ_model.g2610.t1
Valid prediction for Augustus_model.g2607.t1
Valid prediction for GlimmerHMM_glimmerT_3893-T1
Valid prediction for snap_scaffold_2-snap.1336-T1
Valid prediction for snap_scaffold_2-snap.1360-T1
Valid prediction for snap_scaffold_2-snap.1330-T1
Valid prediction for snap_scaffold_2-snap.1362-T1
Valid prediction for snap_scaffold_2-snap.1357-T1
Valid prediction for GlimmerHMM_glimmerT_3884-T1
Valid prediction for GlimmerHMM_glimmerT_3888-T1
Valid prediction for snap_scaffold_2-snap.1343-T1
Valid prediction for snap_scaffold_2-snap.1341-T1
Valid prediction for snap_scaffold_2-snap.1340-T1
Valid prediction for snap_scaffold_2-snap.1338-T1
Valid prediction for snap_scaffold_2-snap.1327-T1
Valid prediction for snap_scaffold_2-snap.1333-T1
Valid prediction for GlimmerHMM_glimmerT_3910-T1
Valid prediction for snap_scaffold_2-snap.1356-T1
Valid prediction for Augustus_model.g2597.t1
Valid prediction for GlimmerHMM_glimmerT_3885-T1
Valid prediction for Augustus_model.g2595.t1
Valid prediction for snap_scaffold_2-snap.1348-T1
Valid prediction for CodingQuarry_transcript_28567-T1
Valid prediction for pasa_asmbl_24448.p1
Valid prediction for snap_scaffold_2-snap.1324-T1
Valid prediction for Augustus_model.g2600.t1
Valid prediction for GlimmerHMM_glimmerT_3886-T1
Valid prediction for GlimmerHMM_glimmerT_3898-T1
Valid prediction for Augustus_model.g2599.t1
Valid prediction for GlimmerHMM_glimmerT_3889-T1
Valid prediction for snap_scaffold_2-snap.1331-T1
Valid prediction for GlimmerHMM_glimmerT_3896-T1
Valid prediction for snap_scaffold_2-snap.1325-T1
Valid prediction for snap_scaffold_2-snap.1339-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_3902-T1
Valid prediction for snap_scaffold_2-snap.1342-T1
Valid prediction for GlimmerHMM_glimmerT_3883-T1
Valid prediction for snap_scaffold_2-snap.1347-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3909-T1
Valid prediction for GlimmerHMM_glimmerT_3894-T1
Couldn't classify 77870, 78271
Sorry, prediction pasa_asmbl_25362.p1 fails validation.
(ACG)	 TT	77870-78271	CA	TAC
Valid prediction for Augustus_model.g2606.t1
Valid prediction for GlimmerHMM_glimmerT_3900-T1
Valid prediction for Augustus_model.g2594.t1
Valid prediction for Augustus_model.g2601.t1
Valid prediction for snap_scaffold_2-snap.1332-T1
Valid prediction for HiQ_model.g2604.t1
Valid prediction for GlimmerHMM_glimmerT_3905-T1
Valid prediction for snap_scaffold_2-snap.1326-T1
Valid prediction for snap_scaffold_2-snap.1350-T1
Valid prediction for GlimmerHMM_glimmerT_3907-T1
Valid prediction for snap_scaffold_2-snap.1335-T1
Valid prediction for snap_scaffold_2-snap.1323-T1
Valid prediction for snap_scaffold_2-snap.1349-T1
Valid prediction for HiQ_model.g2611.t1
Valid prediction for snap_scaffold_2-snap.1337-T1
Valid prediction for snap_scaffold_2-snap.1361-T1
Valid prediction for GlimmerHMM_glimmerT_3892-T1
Valid prediction for GlimmerHMM_glimmerT_3895-T1
Valid prediction for GlimmerHMM_glimmerT_3899-T1
Valid prediction for Augustus_model.g2602.t1
Valid prediction for GlimmerHMM_glimmerT_3897-T1
Valid prediction for Augustus_model.g2598.t1
Valid prediction for GlimmerHMM_glimmerT_3901-T1
Valid prediction for snap_scaffold_2-snap.1345-T1
Valid prediction for snap_scaffold_2-snap.1353-T1
Couldn't classify 168682, 168858
Sorry, prediction pasa_asmbl_23165.p1 fails validation.
(ACT)	 TG	168682-168858	GT	AGG
(AAT)	 AG	170108-170173	GT	AGG
(ATA)	 AG	170505-170624	GT	AGG
(GTG)	 AG	172623-172755	GT	AGG
(ATG)	 AG	173463-174571	GA	AGG
-recovered pasa_asmbl_23165.p1, terminal, 173463, 174571
-recovered pasa_asmbl_23165.p1, internal, 170108, 170173
-recovered pasa_asmbl_23165.p1, internal, 170505, 170624
-recovered pasa_asmbl_23165.p1, internal, 172623, 172755
Valid prediction for GlimmerHMM_glimmerT_3903-T1
Valid prediction for CodingQuarry_transcript_28568-T1
Valid prediction for Augustus_model.g2605.t1
Valid prediction for snap_scaffold_2-snap.1322-T1
Valid prediction for snap_scaffold_2-snap.1359-T1
Valid prediction for snap_scaffold_2-snap.1351-T1
Couldn't classify 20664, 20665
Sorry, prediction pasa_asmbl_23180.p1 fails validation.
(ATG)	 AC	20664-20665	GT	ATG
(GAG)	 AG	20762-20907	GT	TGG
(ACA)	 AG	21118-21270	GT	TGG
(GAT)	 AG	21660-21820	GT	CAG
(ATG)	 AG	21922-21986	GT	ACG
(GTT)	 AG	22411-22525	GT	TGG
(GAC)	 AG	22631-22740	GT	AGG
(TGG)	 AG	22883-23069	GT	TGG
(GTG)	 AG	23644-23706	GT	TAG
(ATG)	 AG	23867-24025	GT	AGG
(GTT)	 AG	24409-24480	CA	AGC
-recovered pasa_asmbl_23180.p1, initial, 21922, 21986
-recovered pasa_asmbl_23180.p1, initial, 23867, 24025
-recovered pasa_asmbl_23180.p1, terminal, 24409, 24480
-recovered pasa_asmbl_23180.p1, internal, 20762, 20907
-recovered pasa_asmbl_23180.p1, internal, 21118, 21270
-recovered pasa_asmbl_23180.p1, internal, 21660, 21820
-recovered pasa_asmbl_23180.p1, internal, 21922, 21986
-recovered pasa_asmbl_23180.p1, internal, 22411, 22525
-recovered pasa_asmbl_23180.p1, internal, 22631, 22740
-recovered pasa_asmbl_23180.p1, internal, 22883, 23069
-recovered pasa_asmbl_23180.p1, internal, 23644, 23706
-recovered pasa_asmbl_23180.p1, internal, 23867, 24025
Valid prediction for snap_scaffold_2-snap.1352-T1
Valid prediction for snap_scaffold_2-snap.1329-T1
Valid prediction for snap_scaffold_2-snap.1354-T1
Valid prediction for snap_scaffold_2-snap.1363-T1
Valid prediction for GlimmerHMM_glimmerT_3882-T1
Valid prediction for snap_scaffold_2-snap.1344-T1
Valid prediction for GlimmerHMM_glimmerT_3887-T1
Valid prediction for Augustus_model.g2609.t1
Couldn't classify 50859, 50957
Sorry, prediction pasa_asmbl_23173.p1 fails validation.
(CCA)	 GG	50859-50957	GT	TGG
(GTA)	 AG	52182-52279	GT	TGG
(GAC)	 AG	53557-53716	GT	AGG
(GAT)	 AG	56259-56388	GT	AGG
(GTA)	 AG	57867-58534	CC	GAC
-recovered pasa_asmbl_23173.p1, terminal, 57867, 58534
-recovered pasa_asmbl_23173.p1, internal, 52182, 52279
-recovered pasa_asmbl_23173.p1, internal, 53557, 53716
-recovered pasa_asmbl_23173.p1, internal, 56259, 56388
Valid prediction for snap_scaffold_2-snap.1328-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22723, rend_intergenic: 10516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30944, rend_intergenic: 29279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44965, rend_intergenic: 42020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85214, rend_intergenic: 84332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96413, rend_intergenic: 94228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108252, rend_intergenic: 105982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166581, rend_intergenic: 166093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181232, rend_intergenic: 179143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 120731, rend_intergenic: 120728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183008
-exon list size: 306


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.3    
2.6    
2.9    
3.2    
3.6    
3.9    
4.2    
4.5    
4.9    
5.2    
5.5    
5.8    
6.2    
6.5    
6.8    
7.1    
7.5    
7.8    
8.1    
8.4    
8.8    
9.1    
9.4    
9.7    
10.1    
10.4    
10.7    
11.0    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
14.0    
14.3    
14.6    
14.9    
15.3    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.9    
18.2    
18.5    
18.8    
19.2    
19.5    
19.8    
20.1    
20.5    
20.8    
21.1    
21.4    
21.8    
22.1    
22.4    
22.7    
23.1    
23.4    
23.7    
24.0    
24.4    
24.7    
25.0    
25.3    
25.6    
26.0    
26.3    
26.6    
26.9    
27.3    
27.6    
27.9    
28.2    
28.6    
28.9    
29.2    
29.5    
29.9    
30.2    
30.5    
30.8    
31.2    
31.5    
31.8    
32.1    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.1    
35.4    
35.7    
36.0    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
39.0    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.2    
41.6    
41.9    
42.2    
42.5    
42.9    
43.2    
43.5    
43.8    
44.2    
44.5    
44.8    
45.1    
45.5    
45.8    
46.1    
46.4    
46.8    
47.1    
47.4    
47.7    
48.1    
48.4    
48.7    
49.0    
49.4    
49.7    
50.0    
50.3    
50.6    
51.0    
51.3    
51.6    
51.9    
52.3    
52.6    
52.9    
53.2    
53.6    
53.9    
54.2    
54.5    
54.9    
55.2    
55.5    
55.8    
56.2    
56.5    
56.8    
57.1    
57.5    
57.8    
58.1    
58.4    
58.8    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.0    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
64.0    
64.3    
64.6    
64.9    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.9    
68.2    
68.5    
68.8    
69.2    
69.5    
69.8    
70.1    
70.5    
70.8    
71.1    
71.4    
71.8    
72.1    
72.4    
72.7    
73.1    
73.4    
73.7    
74.0    
74.4    
74.7    
75.0    
75.3    
75.6    
76.0    
76.3    
76.6    
76.9    
77.3    
77.6    
77.9    
78.2    
78.6    
78.9    
79.2    
79.5    
79.9    
80.2    
80.5    
80.8    
81.2    
81.5    
81.8    
82.1    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.7    
85.1    
85.4    
85.7    
86.0    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
89.0    
89.3    
89.6    
89.9    
90.3    
90.6    
90.9    
91.2    
91.6    
91.9    
92.2    
92.5    
92.9    
93.2    
93.5    
93.8    
94.2    
94.5    
94.8    
95.1    
95.5    
95.8    
96.1    
96.4    
96.8    
97.1    
97.4    
97.7    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 22723, rend_intergenic: 10516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30944, rend_intergenic: 29279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44965, rend_intergenic: 42020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85214, rend_intergenic: 84332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96413, rend_intergenic: 94228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108252, rend_intergenic: 105982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166581, rend_intergenic: 166093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181232, rend_intergenic: 179143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 120731, rend_intergenic: 120728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support