-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_16380290-16531197

-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_6-snap.3472-T1
Valid prediction for GlimmerHMM_glimmerT_16262-T1
Valid prediction for GlimmerHMM_glimmerT_16270-T1
Valid prediction for Augustus_model.g10904.t1
Valid prediction for Augustus_model.g10910.t1
Valid prediction for snap_scaffold_6-snap.3476-T1
Valid prediction for GlimmerHMM_glimmerT_16271-T1
Valid prediction for snap_scaffold_6-snap.3494-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.3478-T1
Valid prediction for GlimmerHMM_glimmerT_16278-T1
Valid prediction for snap_scaffold_6-snap.3500-T1
Valid prediction for snap_scaffold_6-snap.3490-T1
Valid prediction for Augustus_model.g10903.t1
Couldn't classify 103167, 103865
Sorry, prediction pasa_asmbl_49136.p1 fails validation.
(AGA)	 CA	103167-103865	CA	AAC
Valid prediction for snap_scaffold_6-snap.3473-T1
Valid prediction for GlimmerHMM_glimmerT_16272-T1
Valid prediction for Augustus_model.g10917.t1
Valid prediction for snap_scaffold_6-snap.3467-T1
Valid prediction for GlimmerHMM_glimmerT_16266-T1
Valid prediction for GlimmerHMM_glimmerT_16264-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g10906.t1
Valid prediction for snap_scaffold_6-snap.3485-T1
Couldn't classify 86616, 86722
Sorry, prediction pasa_asmbl_47698.p1 fails validation.
(ATC)	 GT	86616-86722	GT	AGG
(ACT)	 AG	86905-87035	GT	AGG
(GGT)	 AG	87199-87299	GT	CTG
(ATA)	 AG	88816-88866	GA	GAG
-recovered pasa_asmbl_47698.p1, terminal, 88816, 88866
-recovered pasa_asmbl_47698.p1, internal, 86905, 87035
-recovered pasa_asmbl_47698.p1, internal, 87199, 87299
Valid prediction for snap_scaffold_6-snap.3468-T1
Valid prediction for Augustus_model.g10915.t1
Valid prediction for GlimmerHMM_glimmerT_16276-T1
Valid prediction for snap_scaffold_6-snap.3486-T1
Valid prediction for GlimmerHMM_glimmerT_16268-T1
Valid prediction for snap_scaffold_6-snap.3484-T1
Valid prediction for snap_scaffold_6-snap.3470-T1
Valid prediction for GlimmerHMM_glimmerT_16269-T1
Valid prediction for snap_scaffold_6-snap.3487-T1
Valid prediction for snap_scaffold_6-snap.3488-T1
Valid prediction for snap_scaffold_6-snap.3492-T1
Valid prediction for snap_scaffold_6-snap.3499-T1
Valid prediction for Augustus_model.g10912.t1
Valid prediction for snap_scaffold_6-snap.3496-T1
Valid prediction for Augustus_model.g10913.t1
Valid prediction for Augustus_model.g10908.t1
Valid prediction for Augustus_model.g10911.t1
Couldn't classify 73573, 73779
Sorry, prediction CodingQuarry_transcript_55378-T1 fails validation.
(ATG)	 AC	71132-71195	GT	GCG
(AGA)	 AG	71736-71840	GT	AGG
(GTG)	 AG	72034-72256	GT	TGG
(GTG)	 AG	72740-72847	GT	AGG
(AAT)	 GA	73573-73779	GT	GAG
(GGT)	 AG	74080-74155	GT	CGG
(GGC)	 AG	74847-75037	GT	ACG
(TCA)	 AG	75259-75349	GT	AGG
(CAT)	 AG	76017-76022	GT	AAG
-recovered CodingQuarry_transcript_55378-T1, initial, 71132, 71195
-recovered CodingQuarry_transcript_55378-T1, terminal, 76017, 76022
-recovered CodingQuarry_transcript_55378-T1, internal, 71736, 71840
-recovered CodingQuarry_transcript_55378-T1, internal, 72034, 72256
-recovered CodingQuarry_transcript_55378-T1, internal, 72740, 72847
-recovered CodingQuarry_transcript_55378-T1, internal, 74080, 74155
-recovered CodingQuarry_transcript_55378-T1, internal, 74847, 75037
-recovered CodingQuarry_transcript_55378-T1, internal, 75259, 75349
-recovered CodingQuarry_transcript_55378-T1, internal, 76017, 76022
Valid prediction for GlimmerHMM_glimmerT_16280-T1
Valid prediction for snap_scaffold_6-snap.3481-T1
Valid prediction for GlimmerHMM_glimmerT_16261-T1
Valid prediction for pasa_asmbl_47703.p1

-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_6-snap.3493-T1
Valid prediction for snap_scaffold_6-snap.3482-T1
Valid prediction for CodingQuarry_transcript_55376-T1
Valid prediction for snap_scaffold_6-snap.3489-T1
Valid prediction for snap_scaffold_6-snap.3483-T1
Valid prediction for snap_scaffold_6-snap.3495-T1
Valid prediction for Augustus_model.g10918.t1
Couldn't classify 10389, 10454
Sorry, prediction pasa_asmbl_49140.p1 fails validation.
(ATG)	 TC	4543-4851	GT	AGG
(AGC)	 AG	5177-5421	GT	AGG
(AGC)	 AG	6011-6192	GT	CGG
(GCT)	 AG	7039-7215	GT	AGG
(GGA)	 AG	7652-7808	GT	ATG
(GTG)	 AG	8056-8266	GT	AGG
(GCC)	 AG	8801-9164	GT	AGG
(GTG)	 AG	9348-9814	GT	AGG
(GAG)	 AG	10389-10454	AC	CCA
-recovered pasa_asmbl_49140.p1, initial, 4543, 4851
-recovered pasa_asmbl_49140.p1, internal, 5177, 5421
-recovered pasa_asmbl_49140.p1, internal, 6011, 6192
-recovered pasa_asmbl_49140.p1, internal, 7039, 7215
-recovered pasa_asmbl_49140.p1, internal, 7652, 7808
-recovered pasa_asmbl_49140.p1, internal, 8056, 8266
-recovered pasa_asmbl_49140.p1, internal, 8801, 9164
-recovered pasa_asmbl_49140.p1, internal, 9348, 9814
Valid prediction for snap_scaffold_6-snap.3491-T1
Valid prediction for GlimmerHMM_glimmerT_16263-T1
Valid prediction for snap_scaffold_6-snap.3480-T1
Valid prediction for pasa_asmbl_49128.p1
Valid prediction for snap_scaffold_6-snap.3474-T1
Couldn't classify 149452, 149832
Sorry, prediction pasa_asmbl_49127.p1 fails validation.
(ATG)	 GC	149452-149832	CA	CAC
Valid prediction for GlimmerHMM_glimmerT_16274-T1
Valid prediction for snap_scaffold_6-snap.3471-T1
Valid prediction for pasa_asmbl_49135.p1
Valid prediction for GlimmerHMM_glimmerT_16275-T1
Valid prediction for GlimmerHMM_glimmerT_16265-T1
Valid prediction for HiQ_model.g10905.t1
Valid prediction for HiQ_model.g10907.t1
Valid prediction for CodingQuarry_transcript_55377-T1
Valid prediction for GlimmerHMM_glimmerT_16259-T1
Valid prediction for GlimmerHMM_glimmerT_16267-T1
Valid prediction for Augustus_model.g10909.t1
Couldn't classify 89438, 89514
Sorry, prediction pasa_asmbl_49129.p1 fails validation.
(GAC)	 TA	89438-89514	GT	GGG
(AGC)	 AG	91094-91165	GT	GTG
(GTT)	 AG	91440-91557	GT	CGG
(GAT)	 AG	92452-92514	GT	AGG
(TGG)	 AG	92854-93013	GT	AGG
(GGT)	 AG	93301-93431	GA	GAG
add_exon() Sorry, pasa_asmbl_49129.p1 92854-93013-terminal-3 is invalid.
-recovered pasa_asmbl_49129.p1, terminal, 92854, 93013
-recovered pasa_asmbl_49129.p1, terminal, 93301, 93431
-recovered pasa_asmbl_49129.p1, internal, 91094, 91165
-recovered pasa_asmbl_49129.p1, internal, 91440, 91557
-recovered pasa_asmbl_49129.p1, internal, 92452, 92514
-recovered pasa_asmbl_49129.p1, internal, 92854, 93013
Valid prediction for GlimmerHMM_glimmerT_16273-T1
Valid prediction for snap_scaffold_6-snap.3479-T1
Valid prediction for CodingQuarry_transcript_55375-T1
Valid prediction for CodingQuarry_transcript_55379-T1
Valid prediction for GlimmerHMM_glimmerT_16260-T1
Valid prediction for HiQ_model.g10902.t1
Valid prediction for CodingQuarry_transcript_55374-T1
Couldn't classify 43949, 44149
Sorry, prediction pasa_asmbl_49137.p1 fails validation.
(GAC)	 AG	43949-44149	GT	AGG
(GTG)	 AG	44251-44622	AT	GAA
-recovered pasa_asmbl_49137.p1, terminal, 44251, 44622
-recovered pasa_asmbl_49137.p1, internal, 43949, 44149
Valid prediction for GlimmerHMM_glimmerT_16279-T1
Valid prediction for Augustus_model.g10916.t1
Valid prediction for snap_scaffold_6-snap.3477-T1
Valid prediction for snap_scaffold_6-snap.3475-T1
Valid prediction for GlimmerHMM_glimmerT_16277-T1
Valid prediction for snap_scaffold_6-snap.3497-T1
Valid prediction for snap_scaffold_6-snap.3469-T1
Valid prediction for snap_scaffold_6-snap.3498-T1
Valid prediction for Augustus_model.g10919.t1
Valid prediction for snap_scaffold_6-snap.3466-T1
Valid prediction for Augustus_model.g10914.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 121131, rend_intergenic: 121128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6811, rend_intergenic: 3447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13066, rend_intergenic: 8277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38817, rend_intergenic: 32269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46356, rend_intergenic: 42840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49109, rend_intergenic: 47344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105933, rend_intergenic: 102109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111769, rend_intergenic: 110427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114991, rend_intergenic: 112522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133892, rend_intergenic: 131670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146366, rend_intergenic: 137180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150908
-exon list size: 339


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.0    
24.3    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 25 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 121131, rend_intergenic: 121128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6811, rend_intergenic: 3447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13066, rend_intergenic: 8277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38817, rend_intergenic: 32269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46356, rend_intergenic: 42840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49109, rend_intergenic: 47344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105933, rend_intergenic: 102109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111769, rend_intergenic: 110427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114991, rend_intergenic: 112522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133892, rend_intergenic: 131670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146366, rend_intergenic: 137180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support