-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_6123072-6362779

-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_4-snap.1338-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g6165.t1
Valid prediction for GlimmerHMM_glimmerT_9502-T1
Couldn't classify 121215, 121292
Sorry, prediction pasa_asmbl_41381.p1 fails validation.
(AGC)	 AC	121215-121292	GT	AGG
(CTG)	 AG	121442-121552	GT	AGG
(GTG)	 AG	122754-122894	GT	AGG
(GTG)	 AG	123094-123174	GT	AGG
(GTG)	 AG	123402-123503	GT	AGG
(CCC)	 AG	123787-123966	GT	AGG
(ATC)	 AG	124552-124676	GT	AGG
(ATA)	 AG	124803-124806	AG	AGA
-recovered pasa_asmbl_41381.p1, terminal, 124803, 124806
-recovered pasa_asmbl_41381.p1, internal, 121442, 121552
-recovered pasa_asmbl_41381.p1, internal, 122754, 122894
-recovered pasa_asmbl_41381.p1, internal, 123094, 123174
-recovered pasa_asmbl_41381.p1, internal, 123402, 123503
-recovered pasa_asmbl_41381.p1, internal, 123787, 123966
-recovered pasa_asmbl_41381.p1, internal, 124552, 124676
Valid prediction for pasa_asmbl_41403.p1
Valid prediction for GlimmerHMM_glimmerT_9486-T1
Valid prediction for snap_scaffold_4-snap.1359-T1
Valid prediction for snap_scaffold_4-snap.1352-T1
Valid prediction for GlimmerHMM_glimmerT_9497-T1
Valid prediction for snap_scaffold_4-snap.1365-T1
Valid prediction for snap_scaffold_4-snap.1353-T1
Valid prediction for Augustus_model.g6156.t1
Valid prediction for snap_scaffold_4-snap.1337-T1
Valid prediction for GlimmerHMM_glimmerT_9506-T1
Valid prediction for snap_scaffold_4-snap.1362-T1
Valid prediction for GlimmerHMM_glimmerT_9500-T1
Valid prediction for snap_scaffold_4-snap.1361-T1
Couldn't classify 107055, 107177
Sorry, prediction pasa_asmbl_41377.p1 fails validation.
(ATG)	 CC	102066-102251	GT	AGG
(GGC)	 AG	102916-103061	GT	AGG
(GTA)	 AG	103769-103853	GT	TGG
(TGT)	 AG	104127-104227	GT	AGG
(TGC)	 AG	104376-104568	GC	AGG
(GTT)	 AG	104826-104978	GT	GGG
(GTC)	 AG	106159-106272	GT	AGG
(GCA)	 AG	107055-107177	GA	GGG
-recovered pasa_asmbl_41377.p1, initial, 102066, 102251
-recovered pasa_asmbl_41377.p1, internal, 102916, 103061
-recovered pasa_asmbl_41377.p1, internal, 103769, 103853
-recovered pasa_asmbl_41377.p1, internal, 104127, 104227
-recovered pasa_asmbl_41377.p1, internal, 104376, 104568
-recovered pasa_asmbl_41377.p1, internal, 104826, 104978
-recovered pasa_asmbl_41377.p1, internal, 106159, 106272
Valid prediction for CodingQuarry_transcript_49026-T1
Valid prediction for pasa_asmbl_41402.p1
Valid prediction for GlimmerHMM_glimmerT_9510-T1
Couldn't classify 176236, 176429
Sorry, prediction pasa_asmbl_41389.p1 fails validation.
(TTC)	 CT	176236-176429	GT	AGG
(CTA)	 AG	176865-176980	GT	CTG
(ATT)	 AG	177529-177578	GT	AGG
(CGT)	 AG	177678-177770	GT	GGG
(CTG)	 AG	179896-179989	GT	AGG
(TTC)	 AG	180305-180489	GT	GGG
(CCT)	 AG	181173-181355	GT	AGG
(ATC)	 AG	181741-181884	GT	AGG
(GAT)	 AG	182075-182164	AA	GAA
-recovered pasa_asmbl_41389.p1, terminal, 182075, 182164
-recovered pasa_asmbl_41389.p1, internal, 176865, 176980
-recovered pasa_asmbl_41389.p1, internal, 177529, 177578
-recovered pasa_asmbl_41389.p1, internal, 177678, 177770
-recovered pasa_asmbl_41389.p1, internal, 179896, 179989
-recovered pasa_asmbl_41389.p1, internal, 180305, 180489
-recovered pasa_asmbl_41389.p1, internal, 181173, 181355
-recovered pasa_asmbl_41389.p1, internal, 181741, 181884
Valid prediction for GlimmerHMM_glimmerT_9512-T1
Valid prediction for GlimmerHMM_glimmerT_9490-T1
Valid prediction for snap_scaffold_4-snap.1328-T1
Valid prediction for GlimmerHMM_glimmerT_9501-T1
Valid prediction for Augustus_model.g6163.t1
Valid prediction for GlimmerHMM_glimmerT_9505-T1
Valid prediction for Augustus_model.g6150.t1
Valid prediction for Augustus_model.g6166.t1
Couldn't classify 110257, 110382
Couldn't classify 111655, 111744
Sorry, prediction pasa_asmbl_41379.p1 fails validation.
(TAT)	 CC	110257-110382	GT	AGG
(ATG)	 AG	110750-110879	GT	CGG
(AGA)	 AG	111447-111559	GT	AAG
(GTT)	 AG	111655-111744	AT	CCA
-recovered pasa_asmbl_41379.p1, initial, 110750, 110879
-recovered pasa_asmbl_41379.p1, internal, 110750, 110879
-recovered pasa_asmbl_41379.p1, internal, 111447, 111559
Valid prediction for Augustus_model.g6162.t1
Valid prediction for GlimmerHMM_glimmerT_9511-T1
Valid prediction for Augustus_model.g6144.t1
Valid prediction for snap_scaffold_4-snap.1346-T1
Valid prediction for GlimmerHMM_glimmerT_9492-T1
Valid prediction for GlimmerHMM_glimmerT_9513-T1
Valid prediction for Augustus_model.g6167.t1
Valid prediction for snap_scaffold_4-snap.1349-T1
Valid prediction for snap_scaffold_4-snap.1327-T1
Valid prediction for snap_scaffold_4-snap.1341-T1
Valid prediction for GlimmerHMM_glimmerT_9514-T1
Valid prediction for snap_scaffold_4-snap.1340-T1
Valid prediction for GlimmerHMM_glimmerT_9496-T1
Valid prediction for GlimmerHMM_glimmerT_9507-T1
Valid prediction for CodingQuarry_transcript_49025-T1
Valid prediction for GlimmerHMM_glimmerT_9495-T1
Valid prediction for GlimmerHMM_glimmerT_9509-T1
Valid prediction for Augustus_model.g6152.t1
Valid prediction for snap_scaffold_4-snap.1323-T1
Valid prediction for GlimmerHMM_glimmerT_9481-T1
Valid prediction for snap_scaffold_4-snap.1363-T1
Valid prediction for HiQ_model.g6160.t1
Valid prediction for snap_scaffold_4-snap.1364-T1
Valid prediction for snap_scaffold_4-snap.1358-T1
Valid prediction for GlimmerHMM_glimmerT_9485-T1
Valid prediction for Augustus_model.g6154.t1
Valid prediction for snap_scaffold_4-snap.1360-T1
Valid prediction for CodingQuarry_transcript_49024-T1
Valid prediction for GlimmerHMM_glimmerT_9494-T1
Valid prediction for pasa_asmbl_41396.p1
Valid prediction for snap_scaffold_4-snap.1351-T1
Valid prediction for snap_scaffold_4-snap.1342-T1
Couldn't classify 127890, 128054
Sorry, prediction pasa_asmbl_41384.p1 fails validation.
(AGA)	 TC	127890-128054	GT	AGG
(AAT)	 AG	128826-128928	GT	TGG
(CAA)	 AG	129018-129097	GT	AGG
(GTG)	 AG	129226-129329	GT	AAG
(GTC)	 AG	129512-129641	GT	AGG
(ATC)	 AG	129770-129866	GT	AGG
(GTA)	 AG	131019-131172	GT	AGG
(TCA)	 AG	131446-131533	GT	AGG
(GTG)	 AG	131636-131692	CA	GAC
add_exon() Sorry, pasa_asmbl_41384.p1 129226-129329-terminal-2 is invalid.
-recovered pasa_asmbl_41384.p1, terminal, 129226, 129329
-recovered pasa_asmbl_41384.p1, terminal, 131636, 131692
-recovered pasa_asmbl_41384.p1, internal, 128826, 128928
-recovered pasa_asmbl_41384.p1, internal, 129018, 129097
-recovered pasa_asmbl_41384.p1, internal, 129226, 129329
-recovered pasa_asmbl_41384.p1, internal, 129512, 129641
-recovered pasa_asmbl_41384.p1, internal, 129770, 129866
-recovered pasa_asmbl_41384.p1, internal, 131019, 131172
-recovered pasa_asmbl_41384.p1, internal, 131446, 131533
Valid prediction for Augustus_model.g6153.t1
Valid prediction for HiQ_model.g6155.t1
Valid prediction for CodingQuarry_transcript_49019-T1
Valid prediction for snap_scaffold_4-snap.1336-T1
Valid prediction for Augustus_model.g6157.t1
Valid prediction for Augustus_model.g6143.t1
Valid prediction for HiQ_model.g6159.t1
Valid prediction for CodingQuarry_transcript_49023-T1
Valid prediction for pasa_asmbl_41387.p1
Valid prediction for Augustus_model.g6164.t1
Valid prediction for GlimmerHMM_glimmerT_9484-T1
Valid prediction for snap_scaffold_4-snap.1343-T1
Valid prediction for snap_scaffold_4-snap.1326-T1
Valid prediction for Augustus_model.g6145.t1
Valid prediction for HiQ_model.g6151.t1
Valid prediction for snap_scaffold_4-snap.1347-T1
Valid prediction for GlimmerHMM_glimmerT_9483-T1
Valid prediction for snap_scaffold_4-snap.1350-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.1330-T1
Valid prediction for snap_scaffold_4-snap.1339-T1
Valid prediction for CodingQuarry_transcript_49021-T1
Valid prediction for Augustus_model.g6142.t1
Valid prediction for snap_scaffold_4-snap.1366-T1
Valid prediction for GlimmerHMM_glimmerT_9482-T1
Valid prediction for snap_scaffold_4-snap.1325-T1
Valid prediction for GlimmerHMM_glimmerT_9493-T1
Valid prediction for snap_scaffold_4-snap.1356-T1
Valid prediction for GlimmerHMM_glimmerT_9491-T1
Valid prediction for pasa_asmbl_42662.p1
Valid prediction for snap_scaffold_4-snap.1357-T1
Valid prediction for snap_scaffold_4-snap.1331-T1
Valid prediction for snap_scaffold_4-snap.1355-T1
Valid prediction for snap_scaffold_4-snap.1335-T1
Valid prediction for snap_scaffold_4-snap.1322-T1
Valid prediction for snap_scaffold_4-snap.1354-T1
Valid prediction for GlimmerHMM_glimmerT_9489-T1
Valid prediction for Augustus_model.g6148.t1
Valid prediction for GlimmerHMM_glimmerT_9488-T1
Valid prediction for pasa_asmbl_42667.p1
Valid prediction for CodingQuarry_transcript_49015-T1
Valid prediction for Augustus_model.g6161.t1
Valid prediction for GlimmerHMM_glimmerT_9498-T1
Valid prediction for snap_scaffold_4-snap.1332-T1
Valid prediction for GlimmerHMM_glimmerT_9503-T1
Valid prediction for snap_scaffold_4-snap.1333-T1
Valid prediction for GlimmerHMM_glimmerT_9499-T1
Valid prediction for HiQ_model.g6158.t1
Valid prediction for CodingQuarry_transcript_49017-T1
Valid prediction for CodingQuarry_transcript_49014-T1
Valid prediction for snap_scaffold_4-snap.1348-T1
Valid prediction for Augustus_model.g6149.t1
Couldn't classify 221998, 222098
Sorry, prediction pasa_asmbl_42656.p1 fails validation.
(GAC)	 TA	221998-222098	GT	GGG
(ACT)	 AG	223794-223943	GT	AGG
(CAA)	 AG	226172-226352	TT	AGT
-recovered pasa_asmbl_42656.p1, terminal, 226172, 226352
-recovered pasa_asmbl_42656.p1, internal, 223794, 223943
Valid prediction for CodingQuarry_transcript_49022-T1
Valid prediction for GlimmerHMM_glimmerT_9504-T1
Valid prediction for CodingQuarry_transcript_49018-T1
Valid prediction for pasa_asmbl_42658.p1
Valid prediction for snap_scaffold_4-snap.1345-T1
Valid prediction for snap_scaffold_4-snap.1344-T1
Valid prediction for CodingQuarry_transcript_49016-T1
Valid prediction for GlimmerHMM_glimmerT_9515-T1
Valid prediction for Augustus_model.g6146.t1
Valid prediction for HiQ_model.g6147.t1
Valid prediction for snap_scaffold_4-snap.1334-T1
Valid prediction for snap_scaffold_4-snap.1324-T1
Valid prediction for GlimmerHMM_glimmerT_9508-T1
Valid prediction for GlimmerHMM_glimmerT_9487-T1
Valid prediction for Augustus_model.g6168.t1
Valid prediction for snap_scaffold_4-snap.1329-T1
Sorry, intron length (4) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4421, rend_intergenic: 3718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69457, rend_intergenic: 67456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119218, rend_intergenic: 116800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 239708
-exon list size: 379


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.7    
5.0    
5.2    
5.5    
5.8    
6.0    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.9    
8.1    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
10.0    
10.2    
10.5    
10.8    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.1    
13.4    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.2    
15.5    
15.7    
16.0    
16.3    
16.5    
16.8    
17.1    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.5    
21.8    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.2    
35.4    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.5    
41.7    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.3    
58.5    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.6    
64.8    
65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.2    
78.5    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 4421, rend_intergenic: 3718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69457, rend_intergenic: 67456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119218, rend_intergenic: 116800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support