-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_7348100-7715407

-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 pasa_asmbl_45497.p1
Valid prediction for snap_scaffold_5-snap.1469-T1
Valid prediction for snap_scaffold_5-snap.1455-T1
Valid prediction for Augustus_model.g8020.t1
Valid prediction for HiQ_model.g8011.t1
Valid prediction for CodingQuarry_transcript_52118-T1
Valid prediction for snap_scaffold_5-snap.1468-T1
Valid prediction for snap_scaffold_5-snap.1491-T1
Valid prediction for pasa_asmbl_45499.p1
Valid prediction for snap_scaffold_5-snap.1473-T1
Valid prediction for Augustus_model.g8022.t1
Valid prediction for CodingQuarry_transcript_52125-T1
Valid prediction for GlimmerHMM_glimmerT_12196-T1
Valid prediction for GlimmerHMM_glimmerT_12201-T1
Valid prediction for Augustus_model.g8021.t1
Valid prediction for snap_scaffold_5-snap.1476-T1
Valid prediction for CodingQuarry_transcript_52122-T1
Valid prediction for GlimmerHMM_glimmerT_12189-T1
Valid prediction for snap_scaffold_5-snap.1479-T1
Valid prediction for GlimmerHMM_glimmerT_12203-T1
Valid prediction for GlimmerHMM_glimmerT_12207-T1
Valid prediction for HiQ_model.g8031.t1
Valid prediction for snap_scaffold_5-snap.1477-T1
Valid prediction for HiQ_model.g8014.t1
Valid prediction for Augustus_model.g8023.t1
Valid prediction for GlimmerHMM_glimmerT_12191-T1
Valid prediction for GlimmerHMM_glimmerT_12204-T1
Valid prediction for snap_scaffold_5-snap.1459-T1
Valid prediction for snap_scaffold_5-snap.1453-T1
Valid prediction for snap_scaffold_5-snap.1464-T1
Valid prediction for snap_scaffold_5-snap.1474-T1
Valid prediction for CodingQuarry_transcript_52119-T1
Couldn't classify 359051, 359128
Sorry, prediction pasa_asmbl_45500.p1 fails validation.
(CTC)	 GT	359051-359128	GT	AGG
(GTG)	 AG	359310-359436	GT	ATG
(TTG)	 AG	359613-359798	GT	GGG
(GGC)	 AG	359869-359948	GT	AGG
(GTG)	 AG	360108-360275	GT	AGG
(GGT)	 AG	360645-360745	GT	CGG
(GAT)	 AG	360851-361052	TT	GAT
-recovered pasa_asmbl_45500.p1, terminal, 360851, 361052
-recovered pasa_asmbl_45500.p1, internal, 359310, 359436
-recovered pasa_asmbl_45500.p1, internal, 359613, 359798
-recovered pasa_asmbl_45500.p1, internal, 359869, 359948
-recovered pasa_asmbl_45500.p1, internal, 360108, 360275
-recovered pasa_asmbl_45500.p1, internal, 360645, 360745
Valid prediction for CodingQuarry_transcript_52126-T1
Valid prediction for GlimmerHMM_glimmerT_12213-T1
Valid prediction for snap_scaffold_5-snap.1461-T1
Valid prediction for snap_scaffold_5-snap.1478-T1
Couldn't classify 285994, 286290
Sorry, prediction pasa_asmbl_44186.p1 fails validation.
(ATG)	 CC	285994-286290	TT	CAT
Valid prediction for snap_scaffold_5-snap.1484-T1
Valid prediction for GlimmerHMM_glimmerT_12205-T1
Valid prediction for GlimmerHMM_glimmerT_12195-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 pasa_asmbl_44187.p1
Valid prediction for snap_scaffold_5-snap.1456-T1
Valid prediction for GlimmerHMM_glimmerT_12194-T1
Valid prediction for GlimmerHMM_glimmerT_12211-T1
Valid prediction for snap_scaffold_5-snap.1463-T1
Valid prediction for snap_scaffold_5-snap.1462-T1
Valid prediction for Augustus_model.g8030.t1
Valid prediction for Augustus_model.g8009.t1
Couldn't classify 347920, 347958
Sorry, prediction pasa_asmbl_44169.p1 fails validation.
(CCC)	 CC	347920-347958	GT	GGG
(TTG)	 AG	348780-348958	GT	AGG
(GTT)	 AG	349174-349367	GT	AGG
(AGT)	 AG	349631-349696	GT	AGG
(ACC)	 AG	349800-350041	CC	GAC
-recovered pasa_asmbl_44169.p1, terminal, 349800, 350041
-recovered pasa_asmbl_44169.p1, internal, 348780, 348958
-recovered pasa_asmbl_44169.p1, internal, 349174, 349367
-recovered pasa_asmbl_44169.p1, internal, 349631, 349696
Valid prediction for HiQ_model.g8008.t1
Valid prediction for GlimmerHMM_glimmerT_12188-T1
Valid prediction for snap_scaffold_5-snap.1481-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.1467-T1
Valid prediction for CodingQuarry_transcript_52127-T1
Valid prediction for Augustus_model.g8013.t1
Valid prediction for Augustus_model.g8028.t1
Valid prediction for snap_scaffold_5-snap.1454-T1
Valid prediction for GlimmerHMM_glimmerT_12192-T1
Valid prediction for Augustus_model.g8015.t1
Valid prediction for Augustus_model.g8027.t1
Valid prediction for snap_scaffold_5-snap.1457-T1
Valid prediction for CodingQuarry_transcript_52124-T1
Valid prediction for snap_scaffold_5-snap.1489-T1
Valid prediction for snap_scaffold_5-snap.1470-T1
Valid prediction for Augustus_model.g8024.t1
Valid prediction for GlimmerHMM_glimmerT_12186-T1
Valid prediction for HiQ_model.g8010.t1
Valid prediction for GlimmerHMM_glimmerT_12190-T1
Valid prediction for snap_scaffold_5-snap.1472-T1
Valid prediction for GlimmerHMM_glimmerT_12197-T1
Valid prediction for Augustus_model.g8025.t1
Valid prediction for pasa_asmbl_44176.p1
Valid prediction for HiQ_model.g8032.t1
Valid prediction for pasa_asmbl_44173.p1
Valid prediction for pasa_asmbl_44184.p1
Valid prediction for snap_scaffold_5-snap.1488-T1
Valid prediction for GlimmerHMM_glimmerT_12210-T1
Valid prediction for GlimmerHMM_glimmerT_12193-T1
Valid prediction for GlimmerHMM_glimmerT_12184-T1
Valid prediction for GlimmerHMM_glimmerT_12198-T1
Valid prediction for snap_scaffold_5-snap.1480-T1
Couldn't classify 286957, 287070
Sorry, prediction pasa_asmbl_44946.p1 fails validation.
(GCC)	 CA	286957-287070	GT	AGG
(ATG)	 AG	287205-287313	GT	AGG
(ATC)	 AG	287403-287488	GT	AGG
(GAG)	 AG	287628-287730	GT	GGG
(GTA)	 AG	287884-288026	GT	AGG
(GTG)	 AG	288668-288767	GT	TGG
(GTG)	 AG	289140-289297	GT	AGG
(ATT)	 AG	289469-289551	GT	AGG
(TAT)	 AG	289916-290063	GG	GAG
-recovered pasa_asmbl_44946.p1, initial, 287205, 287313
-recovered pasa_asmbl_44946.p1, terminal, 289916, 290063
-recovered pasa_asmbl_44946.p1, internal, 287205, 287313
-recovered pasa_asmbl_44946.p1, internal, 287403, 287488
-recovered pasa_asmbl_44946.p1, internal, 287628, 287730
-recovered pasa_asmbl_44946.p1, internal, 287884, 288026
-recovered pasa_asmbl_44946.p1, internal, 288668, 288767
-recovered pasa_asmbl_44946.p1, internal, 289140, 289297
-recovered pasa_asmbl_44946.p1, internal, 289469, 289551
Valid prediction for Augustus_model.g8007.t1
Valid prediction for snap_scaffold_5-snap.1485-T1
Valid prediction for Augustus_model.g8019.t1
Valid prediction for CodingQuarry_transcript_52123-T1
Valid prediction for snap_scaffold_5-snap.1458-T1
Valid prediction for GlimmerHMM_glimmerT_12206-T1
Couldn't classify 337230, 337335
Sorry, prediction pasa_asmbl_44171.p1 fails validation.
(GTG)	 GA	337230-337335	GT	CGG
(GAG)	 AG	338900-339094	GT	AGG
(GTG)	 AG	339252-339394	GT	AGG
(TAC)	 AG	339757-339864	GT	AGG
(GTG)	 AG	340062-340166	GT	CTG
(GCT)	 AG	340810-340972	GT	AAG
(ACA)	 AG	341657-341790	GT	AGG
(GTG)	 AG	341904-342052	GT	GGG
(GAA)	 AG	342405-342561	GT	AGG
(GAT)	 AG	343310-343468	GT	GAG
add_exon() Sorry, pasa_asmbl_44171.p1 338900-339094-terminal-1 is invalid.
-recovered pasa_asmbl_44171.p1, terminal, 338900, 339094
-recovered pasa_asmbl_44171.p1, terminal, 343310, 343468
-recovered pasa_asmbl_44171.p1, internal, 338900, 339094
-recovered pasa_asmbl_44171.p1, internal, 339252, 339394
-recovered pasa_asmbl_44171.p1, internal, 339757, 339864
-recovered pasa_asmbl_44171.p1, internal, 340062, 340166
-recovered pasa_asmbl_44171.p1, internal, 340810, 340972
-recovered pasa_asmbl_44171.p1, internal, 341657, 341790
-recovered pasa_asmbl_44171.p1, internal, 341904, 342052
-recovered pasa_asmbl_44171.p1, internal, 342405, 342561
-recovered pasa_asmbl_44171.p1, internal, 343310, 343468
Valid prediction for GlimmerHMM_glimmerT_12209-T1
Valid prediction for snap_scaffold_5-snap.1486-T1
Valid prediction for snap_scaffold_5-snap.1465-T1
Valid prediction for snap_scaffold_5-snap.1471-T1
Valid prediction for snap_scaffold_5-snap.1487-T1
Valid prediction for GlimmerHMM_glimmerT_12212-T1
Valid prediction for CodingQuarry_transcript_52117-T1
Valid prediction for snap_scaffold_5-snap.1490-T1
Valid prediction for HiQ_model.g8012.t1
Valid prediction for GlimmerHMM_glimmerT_12199-T1
Couldn't classify 298813, 298862
Couldn't classify 300068, 300107
Sorry, prediction pasa_asmbl_44179.p1 fails validation.
(GAG)	 CC	298813-298862	GT	AGG
(GTT)	 AG	299210-299337	GT	AGG
(GGC)	 AG	299529-299649	GT	TGG
(TTT)	 AG	299890-299943	GT	AGG
(TCC)	 AG	300068-300107	AT	TGA
-recovered pasa_asmbl_44179.p1, internal, 299210, 299337
-recovered pasa_asmbl_44179.p1, internal, 299529, 299649
-recovered pasa_asmbl_44179.p1, internal, 299890, 299943
Valid prediction for HiQ_model.g8017.t1
Valid prediction for snap_scaffold_5-snap.1466-T1
Valid prediction for GlimmerHMM_glimmerT_12208-T1
Valid prediction for CodingQuarry_transcript_52120-T1
Couldn't classify 329995, 330268
Sorry, prediction pasa_asmbl_44172.p1 fails validation.
(GCA)	 CT	329995-330268	GT	TGG
(GTG)	 AG	331226-331401	GT	GAG
-recovered pasa_asmbl_44172.p1, terminal, 331226, 331401
-recovered pasa_asmbl_44172.p1, internal, 331226, 331401
Valid prediction for GlimmerHMM_glimmerT_12202-T1
Valid prediction for snap_scaffold_5-snap.1475-T1
Valid prediction for GlimmerHMM_glimmerT_12187-T1
Valid prediction for snap_scaffold_5-snap.1482-T1
Valid prediction for GlimmerHMM_glimmerT_12185-T1
Valid prediction for Augustus_model.g8026.t1
Valid prediction for snap_scaffold_5-snap.1460-T1
Valid prediction for Augustus_model.g8029.t1
Valid prediction for HiQ_model.g8016.t1
Couldn't classify 351492, 351595
Couldn't classify 351666, 351744
Sorry, prediction CodingQuarry_transcript_52116-T1 fails validation.
(ATG)	 TC	351492-351595	CT	ACC
(CTC)	 AC	351666-351744	TC	GAT
Valid prediction for GlimmerHMM_glimmerT_12200-T1
Valid prediction for Augustus_model.g8018.t1
Valid prediction for snap_scaffold_5-snap.1483-T1
Valid prediction for CodingQuarry_transcript_52121-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20566, rend_intergenic: 18633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25453, rend_intergenic: 21200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 314353, rend_intergenic: 313662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 367308
-exon list size: 432


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.5    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.1    
5.3    
5.5    
5.8    
6.0    
6.2    
6.5    
6.7    
6.9    
7.1    
7.4    
7.6    
7.8    
8.1    
8.3    
8.5    
8.8    
9.0    
9.2    
9.4    
9.7    
9.9    
10.1    
10.4    
10.6    
10.8    
11.1    
11.3    
11.5    
11.8    
12.0    
12.2    
12.4    
12.7    
12.9    
13.1    
13.4    
13.6    
13.8    
14.1    
14.3    
14.5    
14.7    
15.0    
15.2    
15.4    
15.7    
15.9    
16.1    
16.4    
16.6    
16.8    
17.1    
17.3    
17.5    
17.7    
18.0    
18.2    
18.4    
18.7    
18.9    
19.1    
19.4    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.0    
23.3    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.6    
28.8    
29.0    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.2    
48.4    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.6    
51.8    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.5    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.1    
61.3    
61.5    
61.8    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.7    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.4    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
71.0    
71.2    
71.4    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.3    
82.5    
82.7    
82.9    
83.2    
83.4    
83.6    
83.9    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 20566, rend_intergenic: 18633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25453, rend_intergenic: 21200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 314353, rend_intergenic: 313662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15638
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 2507 - 15638
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support