-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_3283165-3442936

-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: +)Couldn't classify 102152, 102208
Couldn't classify 102614, 102768
Sorry, prediction CodingQuarry_transcript_48912-T1 fails validation.
(ATG)	 TT	96587-96655	GT	CGG
(GAT)	 AG	97334-97396	GT	AGG
(GAA)	 AG	97724-97829	GT	GGG
(ATG)	 AG	97921-98011	GT	AGG
(TCA)	 AG	98276-98788	GT	AGG
(GAG)	 AG	98892-99014	GT	AGG
(GAA)	 AG	99307-99414	GT	AGG
(GAA)	 AG	99811-99909	GT	AGG
(AAA)	 AG	100146-100247	GT	AGG
(AAA)	 AG	100402-100467	GT	AGG
(GAA)	 AG	100610-100669	GT	AGG
(GAA)	 AG	100921-100992	GT	AGG
(GAA)	 AG	101091-101159	GT	AGG
(GAG)	 AG	101307-101369	GT	AGG
(AAA)	 AG	101500-101574	GT	CGG
(GAG)	 AG	101727-101887	GT	TGG
(ATA)	 AG	102152-102208	AT	CCA
(ATA)	 AC	102614-102768	GT	AGG
(GAG)	 AG	104757-104903	GT	AGG
(GTC)	 AG	105025-105096	GT	AGG
(TTC)	 AG	105455-105463	TG	GAT
-recovered CodingQuarry_transcript_48912-T1, initial, 96587, 96655
add_exon() Sorry, CodingQuarry_transcript_48912-T1 97921-98011-initial-1 is invalid.
-recovered CodingQuarry_transcript_48912-T1, initial, 97921, 98011
-recovered CodingQuarry_transcript_48912-T1, terminal, 105455, 105463
-recovered CodingQuarry_transcript_48912-T1, internal, 97334, 97396
-recovered CodingQuarry_transcript_48912-T1, internal, 97724, 97829
-recovered CodingQuarry_transcript_48912-T1, internal, 97921, 98011
-recovered CodingQuarry_transcript_48912-T1, internal, 98276, 98788
-recovered CodingQuarry_transcript_48912-T1, internal, 98892, 99014
-recovered CodingQuarry_transcript_48912-T1, internal, 99307, 99414
-recovered CodingQuarry_transcript_48912-T1, internal, 99811, 99909
-recovered CodingQuarry_transcript_48912-T1, internal, 100146, 100247
-recovered CodingQuarry_transcript_48912-T1, internal, 100402, 100467
-recovered CodingQuarry_transcript_48912-T1, internal, 100610, 100669
-recovered CodingQuarry_transcript_48912-T1, internal, 100921, 100992
-recovered CodingQuarry_transcript_48912-T1, internal, 101091, 101159
-recovered CodingQuarry_transcript_48912-T1, internal, 101307, 101369
-recovered CodingQuarry_transcript_48912-T1, internal, 101500, 101574
-recovered CodingQuarry_transcript_48912-T1, internal, 101727, 101887
-recovered CodingQuarry_transcript_48912-T1, internal, 104757, 104903
-recovered CodingQuarry_transcript_48912-T1, internal, 105025, 105096
Valid prediction for Augustus_model.g5813.t1
Valid prediction for GlimmerHMM_glimmerT_9068-T1
Valid prediction for Augustus_model.g5817.t1
Valid prediction for GlimmerHMM_glimmerT_9067-T1
Valid prediction for snap_scaffold_4-snap.754-T1
Valid prediction for snap_scaffold_4-snap.760-T1
Valid prediction for HiQ_model.g5811.t1
Valid prediction for GlimmerHMM_glimmerT_9064-T1
Valid prediction for CodingQuarry_transcript_48907-T1
Valid prediction for CodingQuarry_transcript_48908-T1
Valid prediction for Augustus_model.g5809.t1
Valid prediction for CodingQuarry_transcript_48913-T1
Valid prediction for snap_scaffold_4-snap.773-T1
Valid prediction for snap_scaffold_4-snap.756-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9051-T1
Valid prediction for GlimmerHMM_glimmerT_9056-T1
Valid prediction for snap_scaffold_4-snap.751-T1
Valid prediction for HiQ_model.g5812.t1
Valid prediction for snap_scaffold_4-snap.757-T1
Valid prediction for GlimmerHMM_glimmerT_9059-T1
Couldn't classify 55263, 55314
Couldn't classify 55929, 56031
Sorry, prediction pasa_asmbl_41181.p1 fails validation.
(ATG)	 TC	53561-53796	GT	GAG
(CTG)	 AG	54074-54234	GT	AGG
(ACA)	 AG	54500-54649	GT	CGG
(AGC)	 AG	54953-55090	GT	ACG
(GTT)	 AG	55263-55314	AT	AGA
(CAT)	 AC	55929-56031	GT	ATG
(ATC)	 AG	56184-56296	GT	AGG
(CCT)	 AG	57201-57321	TG	AGT
-recovered pasa_asmbl_41181.p1, initial, 53561, 53796
add_exon() Sorry, pasa_asmbl_41181.p1 54074-54234-terminal-2 is invalid.
-recovered pasa_asmbl_41181.p1, terminal, 54074, 54234
-recovered pasa_asmbl_41181.p1, terminal, 57201, 57321
-recovered pasa_asmbl_41181.p1, internal, 54074, 54234
-recovered pasa_asmbl_41181.p1, internal, 54500, 54649
-recovered pasa_asmbl_41181.p1, internal, 54953, 55090
-recovered pasa_asmbl_41181.p1, internal, 56184, 56296
Valid prediction for snap_scaffold_4-snap.767-T1
Valid prediction for Augustus_model.g5810.t1
Couldn't classify 36009, 36554
Sorry, prediction pasa_asmbl_41176.p1 fails validation.
(ATG)	 GG	35256-35365	GT	CGG
(GCA)	 AG	35744-35849	GT	AGG
(AAC)	 AG	36009-36554	AA	CCA
-recovered pasa_asmbl_41176.p1, initial, 35256, 35365
-recovered pasa_asmbl_41176.p1, internal, 35744, 35849
Valid prediction for GlimmerHMM_glimmerT_9055-T1
Valid prediction for HiQ_model.g5816.t1
Valid prediction for GlimmerHMM_glimmerT_9054-T1
Valid prediction for pasa_asmbl_41173.p2
Valid prediction for snap_scaffold_4-snap.755-T1
Valid prediction for snap_scaffold_4-snap.758-T1
Valid prediction for pasa_asmbl_41174.p1
Valid prediction for GlimmerHMM_glimmerT_9057-T1
Valid prediction for snap_scaffold_4-snap.771-T1
Valid prediction for snap_scaffold_4-snap.762-T1
Valid prediction for snap_scaffold_4-snap.747-T1
Valid prediction for Augustus_model.g5804.t1
Valid prediction for snap_scaffold_4-snap.761-T1
Valid prediction for Augustus_model.g5820.t1
Valid prediction for GlimmerHMM_glimmerT_9061-T1
Valid prediction for GlimmerHMM_glimmerT_9072-T1
Valid prediction for Augustus_model.g5815.t1
Valid prediction for snap_scaffold_4-snap.768-T1
Valid prediction for snap_scaffold_4-snap.763-T1
Valid prediction for Augustus_model.g5819.t1
Valid prediction for GlimmerHMM_glimmerT_9071-T1
Valid prediction for Augustus_model.g5808.t1
Valid prediction for GlimmerHMM_glimmerT_9062-T1
Couldn't classify 51906, 52349
Couldn't classify 52506, 52565
Sorry, prediction pasa_asmbl_41178.p1 fails validation.
(GCC)	 GG	51906-52349	GT	AGG
(CGT)	 AG	52506-52565	AC	AGA
Valid prediction for pasa_asmbl_41177.p1
Valid prediction for snap_scaffold_4-snap.744-T1
Valid prediction for snap_scaffold_4-snap.759-T1
Valid prediction for GlimmerHMM_glimmerT_9058-T1
Valid prediction for GlimmerHMM_glimmerT_9070-T1
Valid prediction for HiQ_model.g5806.t1
Valid prediction for snap_scaffold_4-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_9053-T1
Valid prediction for HiQ_model.g5807.t1
Valid prediction for snap_scaffold_4-snap.766-T1
Valid prediction for GlimmerHMM_glimmerT_9063-T1
Couldn't classify 55263, 55314
Couldn't classify 55929, 56031
Sorry, prediction CodingQuarry_transcript_48909-T1 fails validation.
(ATG)	 CC	54102-54234	GT	AGG
(ACA)	 AG	54500-54649	GT	CGG
(AGC)	 AG	54953-55090	GT	ACG
(GTT)	 AG	55263-55314	AT	AGA
(CAT)	 AC	55929-56031	GT	ATG
(ATC)	 AG	56184-56296	GT	AGG
(CCT)	 AG	57201-57303	GT	TGG
(GAA)	 AG	58249-58290	AG	AAA
-recovered CodingQuarry_transcript_48909-T1, initial, 54102, 54234
-recovered CodingQuarry_transcript_48909-T1, terminal, 58249, 58290
-recovered CodingQuarry_transcript_48909-T1, internal, 54500, 54649
-recovered CodingQuarry_transcript_48909-T1, internal, 54953, 55090
-recovered CodingQuarry_transcript_48909-T1, internal, 56184, 56296
-recovered CodingQuarry_transcript_48909-T1, internal, 57201, 57303
Valid prediction for snap_scaffold_4-snap.770-T1
Valid prediction for snap_scaffold_4-snap.765-T1
Valid prediction for snap_scaffold_4-snap.772-T1
Valid prediction for snap_scaffold_4-snap.749-T1
Valid prediction for GlimmerHMM_glimmerT_9065-T1
Valid prediction for GlimmerHMM_glimmerT_9073-T1
Couldn't classify 102152, 102208
Couldn't classify 102614, 102768
Sorry, prediction pasa_asmbl_41189.p1 fails validation.
(ATG)	 TT	96587-96655	GT	CGG
(GAT)	 AG	97334-97396	GT	AGG
(GAA)	 AG	97724-97829	GT	GGG
(ATG)	 AG	97921-98011	GT	AGG
(TCA)	 AG	98276-98788	GT	AGG
(GAG)	 AG	98892-99014	GT	AGG
(GAA)	 AG	99307-99414	GT	AGG
(GAA)	 AG	99811-99909	GT	AGG
(AAA)	 AG	100146-100247	GT	AGG
(AAA)	 AG	100402-100467	GT	AGG
(GAA)	 AG	100610-100669	GT	AGG
(GAA)	 AG	100921-100992	GT	AGG
(GAA)	 AG	101091-101159	GT	AGG
(GAG)	 AG	101307-101369	GT	AGG
(AAA)	 AG	101500-101574	GT	CGG
(GAG)	 AG	101727-101887	GT	TGG
(ATA)	 AG	102152-102208	AT	CCA
(ATA)	 AC	102614-102768	GT	AGG
(GAG)	 AG	104757-104903	GT	AGG
(GTC)	 AG	105025-105096	GT	AGG
(TTC)	 AG	105455-105463	TG	GAT
-recovered pasa_asmbl_41189.p1, initial, 96587, 96655
add_exon() Sorry, pasa_asmbl_41189.p1 97921-98011-initial-1 is invalid.
-recovered pasa_asmbl_41189.p1, initial, 97921, 98011
-recovered pasa_asmbl_41189.p1, terminal, 105455, 105463
-recovered pasa_asmbl_41189.p1, internal, 97334, 97396
-recovered pasa_asmbl_41189.p1, internal, 97724, 97829
-recovered pasa_asmbl_41189.p1, internal, 97921, 98011
-recovered pasa_asmbl_41189.p1, internal, 98276, 98788
-recovered pasa_asmbl_41189.p1, internal, 98892, 99014
-recovered pasa_asmbl_41189.p1, internal, 99307, 99414
-recovered pasa_asmbl_41189.p1, internal, 99811, 99909
-recovered pasa_asmbl_41189.p1, internal, 100146, 100247
-recovered pasa_asmbl_41189.p1, internal, 100402, 100467
-recovered pasa_asmbl_41189.p1, internal, 100610, 100669
-recovered pasa_asmbl_41189.p1, internal, 100921, 100992
-recovered pasa_asmbl_41189.p1, internal, 101091, 101159
-recovered pasa_asmbl_41189.p1, internal, 101307, 101369
-recovered pasa_asmbl_41189.p1, internal, 101500, 101574
-recovered pasa_asmbl_41189.p1, internal, 101727, 101887
-recovered pasa_asmbl_41189.p1, internal, 104757, 104903
-recovered pasa_asmbl_41189.p1, internal, 105025, 105096
Valid prediction for snap_scaffold_4-snap.780-T1
Valid prediction for snap_scaffold_4-snap.752-T1
Valid prediction for snap_scaffold_4-snap.753-T1
Valid prediction for snap_scaffold_4-snap.778-T1
Couldn't classify 55263, 55314
Couldn't classify 55929, 56031
Sorry, prediction CodingQuarry_transcript_48910-T1 fails validation.
(ATG)	 CC	54102-54234	GT	AGG
(ACA)	 AG	54500-54649	GT	CGG
(AGC)	 AG	54953-55090	GT	ACG
(GTT)	 AG	55263-55314	AT	AGA
(CAT)	 AC	55929-56031	GT	ATG
(ATC)	 AG	56184-56296	GT	AGG
(CCT)	 AG	57201-57303	GT	TGG
(TGT)	 AG	59499-59849	GC	GAG
-recovered CodingQuarry_transcript_48910-T1, initial, 54102, 54234
-recovered CodingQuarry_transcript_48910-T1, terminal, 59499, 59849
-recovered CodingQuarry_transcript_48910-T1, internal, 54500, 54649
-recovered CodingQuarry_transcript_48910-T1, internal, 54953, 55090
-recovered CodingQuarry_transcript_48910-T1, internal, 56184, 56296
-recovered CodingQuarry_transcript_48910-T1, internal, 57201, 57303
-recovered CodingQuarry_transcript_48910-T1, internal, 59499, 59849

-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.777-T1
Valid prediction for snap_scaffold_4-snap.775-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9075-T1
Valid prediction for snap_scaffold_4-snap.776-T1
Valid prediction for snap_scaffold_4-snap.764-T1
Valid prediction for Augustus_model.g5823.t1
Valid prediction for CodingQuarry_transcript_48914-T1
Valid prediction for Augustus_model.g5814.t1
Valid prediction for snap_scaffold_4-snap.774-T1
Valid prediction for GlimmerHMM_glimmerT_9052-T1
Couldn't classify 11762, 11895
Sorry, prediction pasa_asmbl_42442.p1 fails validation.
(CTG)	 CC	11762-11895	GT	CTG
(GGA)	 AG	12442-12746	GT	TAG
(GTG)	 AG	13044-13236	GT	AGG
(GCG)	 AG	13526-13581	GT	GCG
(CCA)	 AG	14034-14095	GT	AGG
(TTA)	 AG	14409-14546	GT	AGG
(GCT)	 AG	14683-14759	GT	AGG
(GTT)	 AG	14958-14973	TG	AGT
-recovered pasa_asmbl_42442.p1, terminal, 14958, 14973
-recovered pasa_asmbl_42442.p1, internal, 12442, 12746
-recovered pasa_asmbl_42442.p1, internal, 13044, 13236
-recovered pasa_asmbl_42442.p1, internal, 13526, 13581
-recovered pasa_asmbl_42442.p1, internal, 14034, 14095
-recovered pasa_asmbl_42442.p1, internal, 14409, 14546
-recovered pasa_asmbl_42442.p1, internal, 14683, 14759
Valid prediction for snap_scaffold_4-snap.769-T1
Valid prediction for GlimmerHMM_glimmerT_9069-T1
Valid prediction for snap_scaffold_4-snap.745-T1
Valid prediction for snap_scaffold_4-snap.746-T1
Valid prediction for GlimmerHMM_glimmerT_9074-T1
Valid prediction for HiQ_model.g5821.t1
Valid prediction for Augustus_model.g5805.t1
Valid prediction for snap_scaffold_4-snap.779-T1
Valid prediction for GlimmerHMM_glimmerT_9060-T1
Valid prediction for HiQ_model.g5822.t1
Valid prediction for GlimmerHMM_glimmerT_9066-T1
Valid prediction for Augustus_model.g5818.t1
Couldn't classify 543, 672
Couldn't classify 2626, 3101
Sorry, prediction pasa_asmbl_42443.p1 fails validation.
(GGG)	 AG	543-672	GT	AGG
(AAG)	 AG	2626-3101	GG	AGG
-recovered pasa_asmbl_42443.p1, internal, 543, 672
Valid prediction for snap_scaffold_4-snap.750-T1
Valid prediction for pasa_asmbl_42440.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39464, rend_intergenic: 30722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89209, rend_intergenic: 85575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95214, rend_intergenic: 91073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128183, rend_intergenic: 127769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150074, rend_intergenic: 145212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159755, rend_intergenic: 152297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159772
-exon list size: 324


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 39464, rend_intergenic: 30722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89209, rend_intergenic: 85575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95214, rend_intergenic: 91073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128183, rend_intergenic: 127769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150074, rend_intergenic: 145212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159755, rend_intergenic: 152297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support