-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_714883-889758

-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_19188-T1
Valid prediction for snap_scaffold_8-snap.131-T1
Couldn't classify 9626, 9693
Couldn't classify 11453, 11500
Sorry, prediction pasa_asmbl_52659.p1 fails validation.
(CAG)	 TA	9626-9693	GT	GGG
(CCC)	 AG	10112-10271	GT	ACG
(GGC)	 AG	10779-10904	GT	GGG
(GTG)	 AG	11453-11500	GT	GTG
-recovered pasa_asmbl_52659.p1, internal, 10112, 10271
-recovered pasa_asmbl_52659.p1, internal, 10779, 10904
-recovered pasa_asmbl_52659.p1, internal, 11453, 11500
Valid prediction for Augustus_model.g12809.t1
Valid prediction for GlimmerHMM_glimmerT_19178-T1
Valid prediction for GlimmerHMM_glimmerT_19185-T1
Couldn't classify 32655, 32867
Sorry, prediction pasa_asmbl_52662.p1 fails validation.
(ATG)	 CC	23807-23851	GT	CTG
(GCC)	 AG	25132-25293	GT	AGG
(GCG)	 AG	25727-25852	GT	AGG
(CAG)	 AG	26063-26179	GT	AGG
(ACA)	 AG	26656-26817	GT	AGG
(ATG)	 AG	28145-28324	GT	ACG
(ATC)	 AG	29019-29141	GT	AGG
(CTC)	 AG	29443-29556	GT	AGG
(GAG)	 AG	30320-30608	GT	GGG
(TAC)	 AG	30838-30953	GT	AGG
(GGT)	 AG	31088-31205	GT	CGG
(ATG)	 AG	31461-31552	GT	AGG
(GCC)	 AG	32655-32867	AA	TCA
-recovered pasa_asmbl_52662.p1, initial, 23807, 23851
-recovered pasa_asmbl_52662.p1, initial, 28145, 28324
add_exon() Sorry, pasa_asmbl_52662.p1 31461-31552-initial-1 is invalid.
-recovered pasa_asmbl_52662.p1, initial, 31461, 31552
-recovered pasa_asmbl_52662.p1, internal, 25132, 25293
-recovered pasa_asmbl_52662.p1, internal, 25727, 25852
-recovered pasa_asmbl_52662.p1, internal, 26063, 26179
-recovered pasa_asmbl_52662.p1, internal, 26656, 26817
-recovered pasa_asmbl_52662.p1, internal, 28145, 28324
-recovered pasa_asmbl_52662.p1, internal, 29019, 29141
-recovered pasa_asmbl_52662.p1, internal, 29443, 29556
-recovered pasa_asmbl_52662.p1, internal, 30320, 30608
-recovered pasa_asmbl_52662.p1, internal, 30838, 30953
-recovered pasa_asmbl_52662.p1, internal, 31088, 31205
-recovered pasa_asmbl_52662.p1, internal, 31461, 31552
Valid prediction for snap_scaffold_8-snap.166-T1
Valid prediction for snap_scaffold_8-snap.139-T1
Valid prediction for CodingQuarry_transcript_59589-T1
Valid prediction for GlimmerHMM_glimmerT_19176-T1
Valid prediction for CodingQuarry_transcript_59590-T1
Couldn't classify 3045, 3098
Couldn't classify 7636, 7708
Sorry, prediction pasa_asmbl_52658.p1 fails validation.
(AAG)	 AG	3045-3098	GT	TTG
(GGC)	 AG	3650-3876	GT	CAG
(GTT)	 AG	4485-4607	GT	AAG
(GTA)	 AG	7075-7152	GT	AGG
(GCA)	 AG	7636-7708	TA	GAT
-recovered pasa_asmbl_52658.p1, internal, 3045, 3098
-recovered pasa_asmbl_52658.p1, internal, 3650, 3876
-recovered pasa_asmbl_52658.p1, internal, 4485, 4607
-recovered pasa_asmbl_52658.p1, internal, 7075, 7152
Valid prediction for GlimmerHMM_glimmerT_19181-T1
Valid prediction for Augustus_model.g12815.t1
Valid prediction for GlimmerHMM_glimmerT_19177-T1
Valid prediction for snap_scaffold_8-snap.169-T1
Valid prediction for Augustus_model.g12808.t1
Valid prediction for snap_scaffold_8-snap.160-T1
Valid prediction for pasa_asmbl_52667.p1
Valid prediction for GlimmerHMM_glimmerT_19182-T1
Valid prediction for GlimmerHMM_glimmerT_19183-T1
Couldn't classify 133068, 133487
Sorry, prediction pasa_asmbl_52669.p1 fails validation.
(ATG)	 GG	132691-132969	GT	AGG
(AAA)	 AG	133068-133487	GG	CAG
-recovered pasa_asmbl_52669.p1, initial, 132691, 132969
Valid prediction for snap_scaffold_8-snap.145-T1
Valid prediction for snap_scaffold_8-snap.156-T1
Valid prediction for GlimmerHMM_glimmerT_19175-T1
Valid prediction for GlimmerHMM_glimmerT_19189-T1
Valid prediction for Augustus_model.g12814.t1
Valid prediction for snap_scaffold_8-snap.136-T1
Valid prediction for Augustus_model.g12816.t1
Valid prediction for snap_scaffold_8-snap.148-T1
Valid prediction for Augustus_model.g12810.t1
Valid prediction for snap_scaffold_8-snap.134-T1
Valid prediction for snap_scaffold_8-snap.135-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_19190-T1
Valid prediction for snap_scaffold_8-snap.158-T1
Couldn't classify 136124, 136321
Sorry, prediction pasa_asmbl_52670.p1 fails validation.
(GGG)	 TA	136124-136321	GT	AGG
(GCC)	 AG	136641-136840	GT	CTG
(ACC)	 AG	137125-137183	GT	GGG
(AGA)	 AG	137397-137564	GT	AGG
(CGG)	 AG	137806-138039	GT	GGG
(GGA)	 AG	138409-138551	CC	AAC
-recovered pasa_asmbl_52670.p1, terminal, 138409, 138551
-recovered pasa_asmbl_52670.p1, internal, 136641, 136840
-recovered pasa_asmbl_52670.p1, internal, 137125, 137183
-recovered pasa_asmbl_52670.p1, internal, 137397, 137564
-recovered pasa_asmbl_52670.p1, internal, 137806, 138039
Valid prediction for snap_scaffold_8-snap.161-T1
Valid prediction for Augustus_model.g12812.t1
Valid prediction for snap_scaffold_8-snap.164-T1
Valid prediction for Augustus_model.g12817.t1
Valid prediction for GlimmerHMM_glimmerT_19187-T1
Valid prediction for Augustus_model.g12811.t1
Valid prediction for snap_scaffold_8-snap.157-T1
Valid prediction for GlimmerHMM_glimmerT_19174-T1
Valid prediction for snap_scaffold_8-snap.150-T1
Valid prediction for snap_scaffold_8-snap.155-T1
Valid prediction for snap_scaffold_8-snap.141-T1
Valid prediction for GlimmerHMM_glimmerT_19184-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_19186-T1
Valid prediction for snap_scaffold_8-snap.140-T1
Valid prediction for snap_scaffold_8-snap.144-T1
Valid prediction for snap_scaffold_8-snap.165-T1
Valid prediction for snap_scaffold_8-snap.152-T1
Valid prediction for snap_scaffold_8-snap.162-T1
Valid prediction for snap_scaffold_8-snap.168-T1
Valid prediction for snap_scaffold_8-snap.154-T1
Valid prediction for snap_scaffold_8-snap.137-T1
Valid prediction for snap_scaffold_8-snap.163-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_8-snap.142-T1
Valid prediction for snap_scaffold_8-snap.147-T1
Valid prediction for snap_scaffold_8-snap.159-T1
Valid prediction for snap_scaffold_8-snap.149-T1
Valid prediction for snap_scaffold_8-snap.151-T1
Valid prediction for snap_scaffold_8-snap.143-T1
Valid prediction for snap_scaffold_8-snap.167-T1
Valid prediction for Augustus_model.g12813.t1
Valid prediction for snap_scaffold_8-snap.133-T1
Valid prediction for snap_scaffold_8-snap.138-T1
Valid prediction for snap_scaffold_8-snap.153-T1
Valid prediction for snap_scaffold_8-snap.130-T1
Valid prediction for snap_scaffold_8-snap.132-T1
Valid prediction for GlimmerHMM_glimmerT_19180-T1
Valid prediction for snap_scaffold_8-snap.170-T1
Valid prediction for GlimmerHMM_glimmerT_19179-T1
Valid prediction for snap_scaffold_8-snap.146-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13155, rend_intergenic: 4187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15956, rend_intergenic: 13187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32909, rend_intergenic: 24424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39324, rend_intergenic: 35005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52544, rend_intergenic: 45837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62377, rend_intergenic: 55237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64558, rend_intergenic: 62432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65049, rend_intergenic: 64803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67551, rend_intergenic: 65197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70821, rend_intergenic: 67649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97021, rend_intergenic: 71108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123700, rend_intergenic: 97037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129871, rend_intergenic: 126926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138551, rend_intergenic: 133418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148582, rend_intergenic: 141910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153058, rend_intergenic: 148694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166409, rend_intergenic: 157326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169287, rend_intergenic: 167202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174876
-exon list size: 354


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.6    
7.9    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.1    
17.4    
17.7    
18.0    
18.3    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.0    
23.3    
23.6    
23.9    
24.2    
24.4    
24.7    
25.0    
25.3    
25.6    
25.8    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.8    
39.0    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.1    
42.4    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.8    
46.1    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
53.9    
54.2    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.6    
57.9    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
61.0    
61.2    
61.5    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.5    
68.8    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.2    
74.4    
74.7    
75.0    
75.3    
75.6    
75.8    
76.1    
76.4    
76.7    
77.0    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.7    
82.0    
82.3    
82.6    
82.9    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 13155, rend_intergenic: 4187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15956, rend_intergenic: 13187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32909, rend_intergenic: 24424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39324, rend_intergenic: 35005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52544, rend_intergenic: 45837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62377, rend_intergenic: 55237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64558, rend_intergenic: 62432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65049, rend_intergenic: 64803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67551, rend_intergenic: 65197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70821, rend_intergenic: 67649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97021, rend_intergenic: 71108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123700, rend_intergenic: 97037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129871, rend_intergenic: 126926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138551, rend_intergenic: 133418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148582, rend_intergenic: 141910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153058, rend_intergenic: 148694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166409, rend_intergenic: 157326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169287, rend_intergenic: 167202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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