-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_8518989-8775015

-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 snap_scaffold_10-snap.1697-T1
Valid prediction for snap_scaffold_10-snap.1695-T1
Valid prediction for snap_scaffold_10-snap.1687-T1
Valid prediction for GlimmerHMM_glimmerT_25133-T1
Valid prediction for snap_scaffold_10-snap.1700-T1
Valid prediction for Augustus_model.g16728.t1
Valid prediction for GlimmerHMM_glimmerT_25138-T1
Valid prediction for snap_scaffold_10-snap.1682-T1
Valid prediction for snap_scaffold_10-snap.1684-T1
Couldn't classify 122975, 123037
Sorry, prediction pasa_asmbl_3327.p1 fails validation.
(GAG)	 AG	122975-123037	GT	CGG
(GTG)	 AG	123611-123797	GT	AGG
(GGA)	 AG	124643-124811	GT	AGG
(GGA)	 AG	124985-125141	GC	AGG
(GAG)	 AG	125270-125353	GT	AAG
(AAT)	 AG	125489-125626	GT	AGG
(GTG)	 AG	126074-126310	GT	TGG
(GAG)	 AG	126674-126745	GT	TGG
(ACC)	 AG	126888-126911	CC	GAC
-recovered pasa_asmbl_3327.p1, terminal, 126888, 126911
-recovered pasa_asmbl_3327.p1, internal, 122975, 123037
-recovered pasa_asmbl_3327.p1, internal, 123611, 123797
-recovered pasa_asmbl_3327.p1, internal, 124643, 124811
-recovered pasa_asmbl_3327.p1, internal, 124985, 125141
-recovered pasa_asmbl_3327.p1, internal, 125270, 125353
-recovered pasa_asmbl_3327.p1, internal, 125489, 125626
-recovered pasa_asmbl_3327.p1, internal, 126074, 126310
-recovered pasa_asmbl_3327.p1, internal, 126674, 126745
Valid prediction for GlimmerHMM_glimmerT_25136-T1
Valid prediction for Augustus_model.g16725.t1
Valid prediction for snap_scaffold_10-snap.1712-T1
Valid prediction for GlimmerHMM_glimmerT_25130-T1
Valid prediction for GlimmerHMM_glimmerT_25135-T1
Valid prediction for snap_scaffold_10-snap.1693-T1
Valid prediction for snap_scaffold_10-snap.1694-T1
Valid prediction for GlimmerHMM_glimmerT_25117-T1
Valid prediction for snap_scaffold_10-snap.1704-T1
Valid prediction for Augustus_model.g16718.t1
Valid prediction for Augustus_model.g16726.t1
Valid prediction for Augustus_model.g16727.t1
Valid prediction for GlimmerHMM_glimmerT_25129-T1
Valid prediction for pasa_asmbl_3325.p1
Valid prediction for Augustus_model.g16723.t1
Couldn't classify 121761, 121848
Sorry, prediction pasa_asmbl_3326.p1 fails validation.
(ATG)	 AC	118523-118546	GT	AGG
(GGA)	 AG	118754-118840	GT	TGG
(GGC)	 AG	119112-119254	GT	AAG
(ATT)	 AG	121205-121341	GT	TGG
(GTT)	 AG	121522-121615	GT	AGG
(TAA)	 AG	121761-121848	GA	GTG
-recovered pasa_asmbl_3326.p1, initial, 118523, 118546
-recovered pasa_asmbl_3326.p1, internal, 118754, 118840
-recovered pasa_asmbl_3326.p1, internal, 119112, 119254
-recovered pasa_asmbl_3326.p1, internal, 121205, 121341
-recovered pasa_asmbl_3326.p1, internal, 121522, 121615
Valid prediction for snap_scaffold_10-snap.1708-T1
Valid prediction for snap_scaffold_10-snap.1678-T1
Valid prediction for snap_scaffold_10-snap.1685-T1
Valid prediction for HiQ_model.g16722.t1
Valid prediction for CodingQuarry_transcript_5500-T1
Valid prediction for GlimmerHMM_glimmerT_25121-T1
Valid prediction for snap_scaffold_10-snap.1702-T1
Valid prediction for pasa_asmbl_3329.p1
Valid prediction for snap_scaffold_10-snap.1692-T1
Valid prediction for GlimmerHMM_glimmerT_25126-T1
Valid prediction for snap_scaffold_10-snap.1699-T1
Valid prediction for GlimmerHMM_glimmerT_25137-T1
Valid prediction for snap_scaffold_10-snap.1683-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_25127-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.1713-T1
Valid prediction for CodingQuarry_transcript_5498-T1
Valid prediction for snap_scaffold_10-snap.1696-T1
Valid prediction for Augustus_model.g16720.t1
Couldn't classify 5343, 5376
Couldn't classify 5731, 5878
Sorry, prediction pasa_asmbl_4612.p1 fails validation.
(GAA)	 AC	5343-5376	GT	TGG
(AGG)	 AG	5513-5654	GT	AGG
(GTC)	 AG	5731-5878	CA	GAC
-recovered pasa_asmbl_4612.p1, internal, 5513, 5654
Valid prediction for snap_scaffold_10-snap.1690-T1
Couldn't classify 158999, 159541
Sorry, prediction pasa_asmbl_4606.p1 fails validation.
(CTG)	 TA	158999-159541	GA	CAG
Couldn't classify 18754, 19071
Sorry, prediction pasa_asmbl_4610.p1 fails validation.
(AAG)	 CT	18754-19071	CC	AGC
Valid prediction for GlimmerHMM_glimmerT_25128-T1
Valid prediction for Augustus_model.g16729.t1
Couldn't classify 120085, 120124
Sorry, prediction pasa_asmbl_5109.p1 fails validation.
(GAG)	 AG	120085-120124	GT	AGG
(CCC)	 AG	121445-121553	GT	AGG
(CTT)	 AG	122047-122155	GT	AGG
(TGT)	 AG	122268-122376	GT	AGG
(TGT)	 AG	122575-122688	GT	CAG
(AGT)	 AG	122912-123127	GT	AGG
(ATT)	 AG	123221-123283	GT	AGG
(GTC)	 AG	123826-123963	GT	TGG
(GTG)	 AG	124061-124230	TC	AAT
-recovered pasa_asmbl_5109.p1, terminal, 123221, 123283
-recovered pasa_asmbl_5109.p1, terminal, 124061, 124230
-recovered pasa_asmbl_5109.p1, internal, 120085, 120124
-recovered pasa_asmbl_5109.p1, internal, 121445, 121553
-recovered pasa_asmbl_5109.p1, internal, 122047, 122155
-recovered pasa_asmbl_5109.p1, internal, 122268, 122376
-recovered pasa_asmbl_5109.p1, internal, 122575, 122688
-recovered pasa_asmbl_5109.p1, internal, 122912, 123127
-recovered pasa_asmbl_5109.p1, internal, 123221, 123283
-recovered pasa_asmbl_5109.p1, internal, 123826, 123963
Valid prediction for GlimmerHMM_glimmerT_25124-T1
Valid prediction for snap_scaffold_10-snap.1680-T1
Valid prediction for GlimmerHMM_glimmerT_25118-T1
Valid prediction for CodingQuarry_transcript_5501-T1
Couldn't classify 232622, 232840
Couldn't classify 233089, 233202
Sorry, prediction CodingQuarry_transcript_5495-T1 fails validation.
(ATG)	 TA	227911-228532	GT	TGG
(ATC)	 AG	229444-229559	GT	AGG
(GGC)	 AG	230513-230635	GT	TGG
(ATA)	 AG	232245-232451	GT	AGG
(AAG)	 AG	232622-232840	GG	AAG
(AGT)	 AC	233089-233202	GT	AGG
(GCT)	 AG	233327-233338	GC	GAG
-recovered CodingQuarry_transcript_5495-T1, initial, 227911, 228532
-recovered CodingQuarry_transcript_5495-T1, terminal, 233327, 233338
-recovered CodingQuarry_transcript_5495-T1, internal, 229444, 229559
-recovered CodingQuarry_transcript_5495-T1, internal, 230513, 230635
-recovered CodingQuarry_transcript_5495-T1, internal, 232245, 232451
-recovered CodingQuarry_transcript_5495-T1, internal, 233327, 233338
Valid prediction for snap_scaffold_10-snap.1701-T1
Valid prediction for snap_scaffold_10-snap.1709-T1
Valid prediction for GlimmerHMM_glimmerT_25119-T1
Valid prediction for GlimmerHMM_glimmerT_25132-T1
Valid prediction for GlimmerHMM_glimmerT_25123-T1
Valid prediction for snap_scaffold_10-snap.1681-T1
Couldn't classify 4114, 4256
Sorry, prediction pasa_asmbl_4613.p1 fails validation.
(ATG)	 AA	630-960	GT	AGG
(GGT)	 AG	2468-2606	GT	GGG
(GTT)	 AG	3718-3890	GT	GGG
(CTG)	 AG	4114-4256	GG	TGG
-recovered pasa_asmbl_4613.p1, initial, 630, 960
-recovered pasa_asmbl_4613.p1, internal, 2468, 2606
-recovered pasa_asmbl_4613.p1, internal, 3718, 3890
Couldn't classify 10024, 10163
Couldn't classify 13383, 13462
Sorry, prediction pasa_asmbl_4611.p1 fails validation.
(GTA)	 GT	10024-10163	GT	AGG
(CGG)	 AG	12414-12619	GT	AGG
(ATC)	 AG	13383-13462	TA	GGT
-recovered pasa_asmbl_4611.p1, internal, 12414, 12619
Valid prediction for snap_scaffold_10-snap.1679-T1
Valid prediction for snap_scaffold_10-snap.1703-T1
Valid prediction for snap_scaffold_10-snap.1710-T1
Valid prediction for HiQ_model.g16719.t1
Valid prediction for snap_scaffold_10-snap.1689-T1
Valid prediction for GlimmerHMM_glimmerT_25131-T1
Couldn't classify 212852, 214242
Couldn't classify 222063, 222171
Sorry, prediction pasa_asmbl_4601.p1 fails validation.
(GGA)	 GG	212852-214242	GT	AGG
(ACC)	 AG	214393-214572	GT	TGG
(GGT)	 AG	216156-216315	GT	AGG
(GTG)	 AG	217734-217941	GT	ATG
(ACA)	 AG	218704-218920	GT	AGG
(GGT)	 AG	219049-219163	GT	GGG
(ATC)	 AG	220637-220876	GT	AGG
(GTC)	 AG	221664-221881	GT	AGG
(ATC)	 AG	222063-222171	AC	GCA
add_exon() Sorry, pasa_asmbl_4601.p1 218704-218920-terminal-3 is invalid.
-recovered pasa_asmbl_4601.p1, terminal, 218704, 218920
-recovered pasa_asmbl_4601.p1, internal, 214393, 214572
-recovered pasa_asmbl_4601.p1, internal, 216156, 216315
-recovered pasa_asmbl_4601.p1, internal, 217734, 217941
-recovered pasa_asmbl_4601.p1, internal, 218704, 218920
-recovered pasa_asmbl_4601.p1, internal, 219049, 219163
-recovered pasa_asmbl_4601.p1, internal, 220637, 220876
-recovered pasa_asmbl_4601.p1, internal, 221664, 221881
Valid prediction for CodingQuarry_transcript_5499-T1
Valid prediction for GlimmerHMM_glimmerT_25134-T1
Valid prediction for GlimmerHMM_glimmerT_25120-T1
Valid prediction for snap_scaffold_10-snap.1676-T1
Valid prediction for pasa_asmbl_4597.p1
Valid prediction for Augustus_model.g16721.t1
Valid prediction for GlimmerHMM_glimmerT_25122-T1
Valid prediction for snap_scaffold_10-snap.1675-T1
Valid prediction for snap_scaffold_10-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_25139-T1
Valid prediction for snap_scaffold_10-snap.1677-T1
Couldn't classify 232622, 232840
Couldn't classify 233089, 233202
Sorry, prediction CodingQuarry_transcript_5497-T1 fails validation.
(ATG)	 TA	227911-228532	GT	TGG
(ATC)	 AG	229444-229559	GT	AGG
(ATA)	 AG	232245-232451	GT	AGG
(AAG)	 AG	232622-232840	GG	AAG
(AGT)	 AC	233089-233202	GT	AGG
(GCT)	 AG	233327-233338	GC	GAG
-recovered CodingQuarry_transcript_5497-T1, initial, 227911, 228532
-recovered CodingQuarry_transcript_5497-T1, terminal, 233327, 233338
-recovered CodingQuarry_transcript_5497-T1, internal, 229444, 229559
-recovered CodingQuarry_transcript_5497-T1, internal, 232245, 232451
-recovered CodingQuarry_transcript_5497-T1, internal, 233327, 233338
Valid prediction for GlimmerHMM_glimmerT_25125-T1
Valid prediction for snap_scaffold_10-snap.1711-T1
Valid prediction for snap_scaffold_10-snap.1705-T1
Valid prediction for Augustus_model.g16730.t1
Valid prediction for snap_scaffold_10-snap.1688-T1
Valid prediction for snap_scaffold_10-snap.1707-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.1698-T1
Valid prediction for CodingQuarry_transcript_5496-T1
Valid prediction for snap_scaffold_10-snap.1706-T1
Valid prediction for GlimmerHMM_glimmerT_25140-T1
Valid prediction for Augustus_model.g16724.t1
Valid prediction for snap_scaffold_10-snap.1686-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17007, rend_intergenic: 13303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51844, rend_intergenic: 38897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71533, rend_intergenic: 70675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73899, rend_intergenic: 71751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145364, rend_intergenic: 132185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159668, rend_intergenic: 156936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172451, rend_intergenic: 167760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174708, rend_intergenic: 174480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205192, rend_intergenic: 175559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217445, rend_intergenic: 206150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233097, rend_intergenic: 217624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248359, rend_intergenic: 237121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253558, rend_intergenic: 249455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 256027
-exon list size: 344


building trellis

0.3    
0.6    
0.9    
1.2    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.8    
99.1    
99.4    
99.7    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 17007, rend_intergenic: 13303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51844, rend_intergenic: 38897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71533, rend_intergenic: 70675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73899, rend_intergenic: 71751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145364, rend_intergenic: 132185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159668, rend_intergenic: 156936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172451, rend_intergenic: 167760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174708, rend_intergenic: 174480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205192, rend_intergenic: 175559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217445, rend_intergenic: 206150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233097, rend_intergenic: 217624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248359, rend_intergenic: 237121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253558, rend_intergenic: 249455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support