-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_3850270-4091848

-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 Augustus_model.g5900.t1
Valid prediction for snap_scaffold_4-snap.921-T1
Valid prediction for CodingQuarry_transcript_48927-T1
Valid prediction for snap_scaffold_4-snap.892-T1
Valid prediction for CodingQuarry_transcript_48918-T1
Valid prediction for Augustus_model.g5891.t1
Valid prediction for Augustus_model.g5897.t1
Valid prediction for GlimmerHMM_glimmerT_9184-T1
Couldn't classify 164310, 164488
Sorry, prediction pasa_asmbl_41208.p1 fails validation.
(GAG)	 CA	164310-164488	GT	AGG
(GTG)	 AG	164823-164963	GT	AGG
(GTC)	 AG	165224-165566	GT	TGG
(GCC)	 AG	165788-165988	AC	GAA
-recovered pasa_asmbl_41208.p1, terminal, 165788, 165988
-recovered pasa_asmbl_41208.p1, internal, 164823, 164963
-recovered pasa_asmbl_41208.p1, internal, 165224, 165566
Valid prediction for snap_scaffold_4-snap.934-T1
Valid prediction for snap_scaffold_4-snap.932-T1
Couldn't classify 7554, 7584
Couldn't classify 8103, 8289
Sorry, prediction pasa_asmbl_42201.p1 fails validation.
(GTG)	 GA	7554-7584	GT	GGG
(GTG)	 AG	7736-7919	GT	AAG
(CAT)	 AG	8103-8289	AC	CAA
-recovered pasa_asmbl_42201.p1, internal, 7736, 7919
Valid prediction for snap_scaffold_4-snap.926-T1
Valid prediction for snap_scaffold_4-snap.909-T1
Valid prediction for snap_scaffold_4-snap.916-T1
Valid prediction for Augustus_model.g5903.t1
Valid prediction for Augustus_model.g5905.t1
Valid prediction for HiQ_model.g5877.t1
Valid prediction for GlimmerHMM_glimmerT_9182-T1
Valid prediction for snap_scaffold_4-snap.911-T1
Valid prediction for GlimmerHMM_glimmerT_9169-T1
Couldn't classify 223066, 223406
Sorry, prediction pasa_asmbl_42195.p1 fails validation.
(ATG)	 AT	222788-222842	GT	AGG
(CGT)	 AG	223066-223406	AA	ATA
-recovered pasa_asmbl_42195.p1, initial, 222788, 222842
Valid prediction for snap_scaffold_4-snap.893-T1
Couldn't classify 199726, 199823
Sorry, prediction pasa_asmbl_41210.p1 fails validation.
(ACA)	 AG	199726-199823	GT	AGG
(AGG)	 AG	200085-200196	GT	AGG
(CCC)	 AG	200294-200389	GT	AGG
(TCT)	 AG	200581-200666	GT	AGG
(GTT)	 AG	200754-200860	GT	AGG
(TTT)	 AG	200935-201042	GT	AGG
(GCA)	 AG	201406-201531	GT	AGG
(GAT)	 AG	202258-202402	GT	TGG
(GTT)	 AG	202631-202709	CA	AGC
add_exon() Sorry, pasa_asmbl_41210.p1 200754-200860-terminal-2 is invalid.
-recovered pasa_asmbl_41210.p1, terminal, 200754, 200860
-recovered pasa_asmbl_41210.p1, terminal, 202631, 202709
-recovered pasa_asmbl_41210.p1, internal, 199726, 199823
-recovered pasa_asmbl_41210.p1, internal, 200085, 200196
-recovered pasa_asmbl_41210.p1, internal, 200294, 200389
-recovered pasa_asmbl_41210.p1, internal, 200581, 200666
-recovered pasa_asmbl_41210.p1, internal, 200754, 200860
-recovered pasa_asmbl_41210.p1, internal, 200935, 201042
-recovered pasa_asmbl_41210.p1, internal, 201406, 201531
-recovered pasa_asmbl_41210.p1, internal, 202258, 202402
Valid prediction for GlimmerHMM_glimmerT_9186-T1
Valid prediction for pasa_asmbl_41206.p1
Valid prediction for snap_scaffold_4-snap.930-T1
Valid prediction for snap_scaffold_4-snap.920-T1
Valid prediction for snap_scaffold_4-snap.919-T1
Valid prediction for HiQ_model.g5899.t1
Valid prediction for pasa_asmbl_41204.p1
Valid prediction for Augustus_model.g5893.t1
Valid prediction for GlimmerHMM_glimmerT_9158-T1
Valid prediction for CodingQuarry_transcript_48929-T1
Valid prediction for snap_scaffold_4-snap.937-T1
Valid prediction for GlimmerHMM_glimmerT_9188-T1
Valid prediction for GlimmerHMM_glimmerT_9176-T1
Valid prediction for Augustus_model.g5901.t1
Valid prediction for GlimmerHMM_glimmerT_9168-T1
Valid prediction for snap_scaffold_4-snap.925-T1
Valid prediction for Augustus_model.g5906.t1
Valid prediction for HiQ_model.g5904.t1
Valid prediction for GlimmerHMM_glimmerT_9172-T1
Valid prediction for snap_scaffold_4-snap.928-T1
Valid prediction for snap_scaffold_4-snap.918-T1
Valid prediction for snap_scaffold_4-snap.905-T1
Valid prediction for Augustus_model.g5896.t1
Valid prediction for GlimmerHMM_glimmerT_9173-T1
Valid prediction for GlimmerHMM_glimmerT_9183-T1
Valid prediction for GlimmerHMM_glimmerT_9163-T1
Valid prediction for snap_scaffold_4-snap.913-T1
Valid prediction for snap_scaffold_4-snap.891-T1
Couldn't classify 223674, 223962
Couldn't classify 224310, 224557
Sorry, prediction pasa_asmbl_42292.p1 fails validation.
(TTG)	 CG	223674-223962	GT	ATG
(ACT)	 AG	224310-224557	AT	TGA
Couldn't classify 216412, 216607
Couldn't classify 218446, 218488
Sorry, prediction pasa_asmbl_41214.p1 fails validation.
(CAT)	 AC	216412-216607	GT	AAG
(CGT)	 AG	216850-216897	GT	AGG
(ACT)	 AG	217487-217738	GT	CTG
(ATC)	 AG	217855-218115	GT	AGG
(CCA)	 AG	218252-218342	GT	TGG
(TCG)	 AG	218446-218488	AC	ACA
add_exon() Sorry, pasa_asmbl_41214.p1 216850-216897-terminal-1 is invalid.
-recovered pasa_asmbl_41214.p1, terminal, 216850, 216897
-recovered pasa_asmbl_41214.p1, internal, 216850, 216897
-recovered pasa_asmbl_41214.p1, internal, 217487, 217738
-recovered pasa_asmbl_41214.p1, internal, 217855, 218115
-recovered pasa_asmbl_41214.p1, internal, 218252, 218342
Valid prediction for GlimmerHMM_glimmerT_9187-T1
Valid prediction for snap_scaffold_4-snap.915-T1
Valid prediction for pasa_asmbl_41212.p1
Valid prediction for GlimmerHMM_glimmerT_9189-T1
Valid prediction for GlimmerHMM_glimmerT_9178-T1
Valid prediction for snap_scaffold_4-snap.917-T1
Valid prediction for Augustus_model.g5888.t1
Valid prediction for GlimmerHMM_glimmerT_9177-T1
Valid prediction for snap_scaffold_4-snap.906-T1
Valid prediction for Augustus_model.g5882.t1
Valid prediction for snap_scaffold_4-snap.898-T1
Valid prediction for snap_scaffold_4-snap.935-T1
Valid prediction for snap_scaffold_4-snap.927-T1
Valid prediction for snap_scaffold_4-snap.936-T1
Valid prediction for snap_scaffold_4-snap.931-T1
Valid prediction for Augustus_model.g5892.t1
Valid prediction for Augustus_model.g5878.t1
Valid prediction for CodingQuarry_transcript_48928-T1
Valid prediction for snap_scaffold_4-snap.907-T1
Valid prediction for snap_scaffold_4-snap.910-T1
Valid prediction for Augustus_model.g5876.t1
Valid prediction for GlimmerHMM_glimmerT_9179-T1
Valid prediction for snap_scaffold_4-snap.890-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9170-T1
Valid prediction for Augustus_model.g5887.t1
Valid prediction for Augustus_model.g5875.t1
Valid prediction for snap_scaffold_4-snap.929-T1
Valid prediction for GlimmerHMM_glimmerT_9162-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 Augustus_model.g5884.t1
Valid prediction for CodingQuarry_transcript_48923-T1
Valid prediction for snap_scaffold_4-snap.914-T1
Valid prediction for CodingQuarry_transcript_48921-T1
Valid prediction for snap_scaffold_4-snap.912-T1
Couldn't classify 2817, 2865
Couldn't classify 4955, 5078
Sorry, prediction pasa_asmbl_42476.p1 fails validation.
(AAA)	 TG	2817-2865	GT	TGG
(GTG)	 AG	2969-3349	GT	TGG
(GGG)	 AG	3451-3483	GT	AGG
(ATA)	 AG	3590-3619	GT	TGG
(CAA)	 AG	3818-3935	GT	AGG
(AGA)	 AG	4759-4836	GT	AAG
(TAT)	 AG	4955-5078	AC	ACA
-recovered pasa_asmbl_42476.p1, internal, 2969, 3349
-recovered pasa_asmbl_42476.p1, internal, 3451, 3483
-recovered pasa_asmbl_42476.p1, internal, 3590, 3619
-recovered pasa_asmbl_42476.p1, internal, 3818, 3935
-recovered pasa_asmbl_42476.p1, internal, 4759, 4836
Valid prediction for GlimmerHMM_glimmerT_9181-T1
Valid prediction for GlimmerHMM_glimmerT_9175-T1
Valid prediction for snap_scaffold_4-snap.903-T1
Valid prediction for Augustus_model.g5890.t1
Valid prediction for snap_scaffold_4-snap.899-T1
Valid prediction for Augustus_model.g5885.t1
Valid prediction for GlimmerHMM_glimmerT_9161-T1
Valid prediction for GlimmerHMM_glimmerT_9165-T1
Valid prediction for Augustus_model.g5889.t1
Valid prediction for snap_scaffold_4-snap.901-T1
Valid prediction for snap_scaffold_4-snap.900-T1
Valid prediction for snap_scaffold_4-snap.896-T1
Valid prediction for Augustus_model.g5907.t1
Valid prediction for Augustus_model.g5880.t1
Valid prediction for snap_scaffold_4-snap.902-T1
Valid prediction for GlimmerHMM_glimmerT_9180-T1
Valid prediction for CodingQuarry_transcript_48922-T1
Couldn't classify 179214, 181928
Sorry, prediction pasa_asmbl_42465.p1 fails validation.
(ATG)	 TG	179214-181928	GG	CAG
Valid prediction for Augustus_model.g5895.t1
Valid prediction for snap_scaffold_4-snap.922-T1
Valid prediction for Augustus_model.g5894.t1
Valid prediction for snap_scaffold_4-snap.924-T1
Valid prediction for GlimmerHMM_glimmerT_9185-T1
Valid prediction for snap_scaffold_4-snap.897-T1
Valid prediction for Augustus_model.g5879.t1
Valid prediction for snap_scaffold_4-snap.894-T1
Valid prediction for GlimmerHMM_glimmerT_9166-T1
Couldn't classify 155208, 157073
Sorry, prediction pasa_asmbl_42469.p1 fails validation.
(TCT)	 GG	155208-157073	TT	AGT
Valid prediction for pasa_asmbl_42462.p1
Valid prediction for Augustus_model.g5902.t1
Valid prediction for Augustus_model.g5898.t1
Valid prediction for GlimmerHMM_glimmerT_9160-T1
Valid prediction for snap_scaffold_4-snap.908-T1
Valid prediction for Augustus_model.g5881.t1
Valid prediction for snap_scaffold_4-snap.923-T1
Valid prediction for GlimmerHMM_glimmerT_9171-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9174-T1
Couldn't classify 213707, 214039
Sorry, prediction pasa_asmbl_42458.p1 fails validation.
(TGG)	 TA	213707-214039	CG	ATC
Valid prediction for snap_scaffold_4-snap.895-T1
Valid prediction for Augustus_model.g5886.t1
Couldn't classify 220744, 221859
Sorry, prediction pasa_asmbl_42457.p1 fails validation.
(AAG)	 CA	220744-221859	AA	AGA
Valid prediction for GlimmerHMM_glimmerT_9159-T1
Valid prediction for GlimmerHMM_glimmerT_9167-T1
Valid prediction for GlimmerHMM_glimmerT_9164-T1
Valid prediction for Augustus_model.g5883.t1
Valid prediction for snap_scaffold_4-snap.933-T1
Valid prediction for snap_scaffold_4-snap.904-T1
Sorry, intron length (6) 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: 134533, rend_intergenic: 130364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135916, rend_intergenic: 135102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151436, rend_intergenic: 148064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160502, rend_intergenic: 155472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 241579
-exon list size: 392


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.0    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.5    
15.7    
16.0    
16.2    
16.5    
16.8    
17.0    
17.3    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
47.0    
47.2    
47.5    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.5    
52.8    
53.0    
53.3    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
62.9    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.5    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 134533, rend_intergenic: 130364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135916, rend_intergenic: 135102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151436, rend_intergenic: 148064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160502, rend_intergenic: 155472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 42 predictions persist after filtering for low support