-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_827726-1058932

-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_22-snap.185-T1
Valid prediction for snap_scaffold_22-snap.192-T1
Valid prediction for Augustus_model.g32672.t1
Couldn't classify 125517, 125638
Sorry, prediction pasa_asmbl_29905.p1 fails validation.
(TCT)	 AC	125517-125638	GT	AGG
(GCA)	 AG	126605-126708	GT	TGG
(ACA)	 AG	126894-127084	GT	AGG
(GCG)	 AG	127208-127328	GT	AGG
(TTC)	 AG	127755-127942	GT	AGG
(GAC)	 AG	128301-128378	GT	AGG
(ATG)	 AG	128488-128573	GT	AGG
(TGG)	 AG	129163-129282	GT	AGG
(ATA)	 AG	129508-129637	GT	AGG
(ATG)	 AG	129914-130009	GT	AGG
(GGA)	 AG	130190-130273	GT	TGG
(GCT)	 AG	130603-130660	GT	TGG
(GCA)	 AG	130766-130803	TG	GAT
-recovered pasa_asmbl_29905.p1, initial, 128488, 128573
-recovered pasa_asmbl_29905.p1, initial, 129914, 130009
-recovered pasa_asmbl_29905.p1, terminal, 130766, 130803
-recovered pasa_asmbl_29905.p1, internal, 126605, 126708
-recovered pasa_asmbl_29905.p1, internal, 126894, 127084
-recovered pasa_asmbl_29905.p1, internal, 127208, 127328
-recovered pasa_asmbl_29905.p1, internal, 127755, 127942
-recovered pasa_asmbl_29905.p1, internal, 128301, 128378
-recovered pasa_asmbl_29905.p1, internal, 128488, 128573
-recovered pasa_asmbl_29905.p1, internal, 129163, 129282
-recovered pasa_asmbl_29905.p1, internal, 129508, 129637
-recovered pasa_asmbl_29905.p1, internal, 129914, 130009
-recovered pasa_asmbl_29905.p1, internal, 130190, 130273
-recovered pasa_asmbl_29905.p1, internal, 130603, 130660
Valid prediction for snap_scaffold_22-snap.193-T1
Valid prediction for GlimmerHMM_glimmerT_48900-T1
Valid prediction for Augustus_model.g32652.t1
Valid prediction for pasa_asmbl_29919.p1
Valid prediction for snap_scaffold_22-snap.180-T1
Valid prediction for Augustus_model.g32671.t1
Couldn't classify 121835, 121846
Sorry, prediction pasa_asmbl_29904.p1 fails validation.
(TAT)	 AG	121835-121846	GT	AGG
(GAC)	 AG	122093-122752	GG	GAG
-recovered pasa_asmbl_29904.p1, terminal, 122093, 122752
-recovered pasa_asmbl_29904.p1, internal, 121835, 121846
Valid prediction for snap_scaffold_22-snap.197-T1
Valid prediction for Augustus_model.g32665.t1
Couldn't classify 117927, 117933
Couldn't classify 121250, 121326
Sorry, prediction pasa_asmbl_29903.p1 fails validation.
(GTC)	 AC	117927-117933	GT	CTG
(TCG)	 AG	118112-118239	GT	TGG
(GTG)	 AG	118405-118531	GT	CGG
(GCC)	 AG	118759-118859	GT	TAG
(GTG)	 AG	119898-120114	GT	AGG
(AAG)	 AG	120473-120580	GT	CAG
(GTC)	 AG	121250-121326	GA	AAG
-recovered pasa_asmbl_29903.p1, internal, 118112, 118239
-recovered pasa_asmbl_29903.p1, internal, 118405, 118531
-recovered pasa_asmbl_29903.p1, internal, 118759, 118859
-recovered pasa_asmbl_29903.p1, internal, 119898, 120114
-recovered pasa_asmbl_29903.p1, internal, 120473, 120580
Valid prediction for HiQ_model.g32670.t1
Valid prediction for snap_scaffold_22-snap.199-T1
Couldn't classify 114643, 114793
Couldn't classify 116919, 117068
Sorry, prediction pasa_asmbl_29902.p1 fails validation.
(GTG)	 TA	114643-114793	GT	GGG
(CTT)	 AG	115974-116123	GT	CAG
(TCC)	 AG	116428-116585	GT	CTG
(GAG)	 AG	116919-117068	CG	ACC
-recovered pasa_asmbl_29902.p1, internal, 115974, 116123
-recovered pasa_asmbl_29902.p1, internal, 116428, 116585
Valid prediction for Augustus_model.g32655.t1
Valid prediction for snap_scaffold_22-snap.198-T1
Couldn't classify 131444, 131630
Sorry, prediction pasa_asmbl_29907.p1 fails validation.
(TGT)	 CG	131444-131630	GT	TGG
(CCG)	 AG	133858-133949	GT	GGG
(GTG)	 AG	134301-134333	GT	CGG
(AAA)	 AG	134439-134459	GT	TGG
(GAA)	 AG	134870-134935	TA	AGT
-recovered pasa_asmbl_29907.p1, terminal, 134870, 134935
-recovered pasa_asmbl_29907.p1, internal, 133858, 133949
-recovered pasa_asmbl_29907.p1, internal, 134301, 134333
-recovered pasa_asmbl_29907.p1, internal, 134439, 134459
Valid prediction for Augustus_model.g32659.t1
Valid prediction for snap_scaffold_22-snap.174-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_48888-T1
Valid prediction for GlimmerHMM_glimmerT_48897-T1
Couldn't classify 189002, 189048
Couldn't classify 189085, 189179
Sorry, prediction CodingQuarry_transcript_34107-T1 fails validation.
(ATG)	 CA	187538-187554	GT	CTG
(AAA)	 AG	187751-187873	GT	AGG
(AGG)	 AG	187996-188086	GT	AGG
(GAT)	 AG	188559-188644	GT	AGG
(CTC)	 AG	189002-189048	CT	TGC
(CTC)	 CC	189085-189179	CT	AGC
-recovered CodingQuarry_transcript_34107-T1, initial, 187538, 187554
-recovered CodingQuarry_transcript_34107-T1, internal, 187751, 187873
-recovered CodingQuarry_transcript_34107-T1, internal, 187996, 188086
-recovered CodingQuarry_transcript_34107-T1, internal, 188559, 188644
Valid prediction for GlimmerHMM_glimmerT_48901-T1
Valid prediction for GlimmerHMM_glimmerT_48899-T1
Valid prediction for GlimmerHMM_glimmerT_48894-T1
Valid prediction for Augustus_model.g32658.t1
Couldn't classify 79771, 79803
Couldn't classify 87680, 87818
Sorry, prediction pasa_asmbl_29899.p1 fails validation.
(GGA)	 TG	79771-79803	GT	AGG
(GGC)	 AG	82439-82585	GT	AGG
(GTC)	 AG	83845-84055	GT	AAG
(CTG)	 AG	84797-84987	GT	AGG
(GTG)	 AG	87347-87447	GT	AGG
(GCA)	 AG	87680-87818	GT	AGG
add_exon() Sorry, pasa_asmbl_29899.p1 87347-87447-terminal-2 is invalid.
-recovered pasa_asmbl_29899.p1, terminal, 87347, 87447
-recovered pasa_asmbl_29899.p1, internal, 82439, 82585
-recovered pasa_asmbl_29899.p1, internal, 83845, 84055
-recovered pasa_asmbl_29899.p1, internal, 84797, 84987
-recovered pasa_asmbl_29899.p1, internal, 87347, 87447
-recovered pasa_asmbl_29899.p1, internal, 87680, 87818
Couldn't classify 154438, 154476
Sorry, prediction pasa_asmbl_30512.p2 fails validation.
(CTG)	 CG	154438-154476	GT	TGG
(GAA)	 AG	154828-154897	GT	AGG
(AGA)	 AG	155389-155576	GT	AGG
(ATC)	 AG	155734-155836	GT	GGG
(AAC)	 AG	155985-156070	GT	GGG
(CCC)	 AG	156449-156648	GT	CAG
(GCT)	 AG	156957-157068	CC	AGC
-recovered pasa_asmbl_30512.p2, terminal, 156957, 157068
-recovered pasa_asmbl_30512.p2, internal, 154828, 154897
-recovered pasa_asmbl_30512.p2, internal, 155389, 155576
-recovered pasa_asmbl_30512.p2, internal, 155734, 155836
-recovered pasa_asmbl_30512.p2, internal, 155985, 156070
-recovered pasa_asmbl_30512.p2, internal, 156449, 156648
Valid prediction for CodingQuarry_transcript_34100-T1
Couldn't classify 70895, 70999
Sorry, prediction pasa_asmbl_29895.p1 fails validation.
(ATG)	 AG	67574-67720	GT	AGG
(AGG)	 AG	67873-67956	GT	AGG
(GTT)	 AG	68303-68414	GT	AGG
(ACC)	 AG	69753-69934	GT	AGG
(AAC)	 AG	70895-70999	GC	TAG
-recovered pasa_asmbl_29895.p1, initial, 67574, 67720
-recovered pasa_asmbl_29895.p1, internal, 67574, 67720
-recovered pasa_asmbl_29895.p1, internal, 67873, 67956
-recovered pasa_asmbl_29895.p1, internal, 68303, 68414
-recovered pasa_asmbl_29895.p1, internal, 69753, 69934
-recovered pasa_asmbl_29895.p1, internal, 70895, 70999
Valid prediction for snap_scaffold_22-snap.176-T1
Valid prediction for HiQ_model.g32668.t1
Valid prediction for Augustus_model.g32654.t1
Valid prediction for snap_scaffold_22-snap.200-T1
Valid prediction for snap_scaffold_22-snap.191-T1
Valid prediction for GlimmerHMM_glimmerT_48878-T1
Valid prediction for CodingQuarry_transcript_34104-T1
Valid prediction for GlimmerHMM_glimmerT_48891-T1
Valid prediction for snap_scaffold_22-snap.188-T1
Valid prediction for snap_scaffold_22-snap.171-T1
Valid prediction for GlimmerHMM_glimmerT_48885-T1
Valid prediction for HiQ_model.g32661.t1
Valid prediction for pasa_asmbl_29913.p1
Valid prediction for GlimmerHMM_glimmerT_48886-T1
Valid prediction for snap_scaffold_22-snap.172-T1
Valid prediction for snap_scaffold_22-snap.201-T1
Valid prediction for snap_scaffold_22-snap.175-T1
Valid prediction for snap_scaffold_22-snap.170-T1
Valid prediction for GlimmerHMM_glimmerT_48881-T1
Valid prediction for snap_scaffold_22-snap.178-T1
Valid prediction for HiQ_model.g32664.t1
Valid prediction for CodingQuarry_transcript_34106-T1
Couldn't classify 71338, 71356
Couldn't classify 73018, 73054
Sorry, prediction pasa_asmbl_29897.p1 fails validation.
(GCC)	 CT	71338-71356	GT	CGG
(GTC)	 AG	71771-71856	GT	AGG
(CTG)	 AG	72592-72709	GT	AGG
(AGA)	 AG	72856-72922	GT	GAG
(GAC)	 AG	73018-73054	AG	GGA
-recovered pasa_asmbl_29897.p1, internal, 71771, 71856
-recovered pasa_asmbl_29897.p1, internal, 72592, 72709
-recovered pasa_asmbl_29897.p1, internal, 72856, 72922
Valid prediction for snap_scaffold_22-snap.194-T1
Valid prediction for Augustus_model.g32666.t1
Couldn't classify 182336, 183022
Sorry, prediction pasa_asmbl_29138.p1 fails validation.
(GCA)	 GT	182336-183022	AA	TCA
Valid prediction for snap_scaffold_22-snap.183-T1
Valid prediction for GlimmerHMM_glimmerT_48880-T1
Valid prediction for GlimmerHMM_glimmerT_48892-T1
Valid prediction for GlimmerHMM_glimmerT_48895-T1
Valid prediction for Augustus_model.g32662.t1
Valid prediction for pasa_asmbl_29901.p1
Valid prediction for snap_scaffold_22-snap.196-T1
Valid prediction for snap_scaffold_22-snap.182-T1
Valid prediction for GlimmerHMM_glimmerT_48903-T1
Valid prediction for snap_scaffold_22-snap.187-T1
Valid prediction for CodingQuarry_transcript_34102-T1
Valid prediction for CodingQuarry_transcript_34103-T1
Valid prediction for Augustus_model.g32657.t1
Valid prediction for HiQ_model.g32663.t1
Valid prediction for snap_scaffold_22-snap.177-T1
Valid prediction for GlimmerHMM_glimmerT_48889-T1
Valid prediction for pasa_asmbl_29917.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 GlimmerHMM_glimmerT_48898-T1
Valid prediction for snap_scaffold_22-snap.181-T1
Valid prediction for GlimmerHMM_glimmerT_48884-T1
Valid prediction for Augustus_model.g32669.t1
Valid prediction for Augustus_model.g32656.t1
Valid prediction for snap_scaffold_22-snap.190-T1
Valid prediction for snap_scaffold_22-snap.179-T1
Valid prediction for GlimmerHMM_glimmerT_48896-T1
Valid prediction for snap_scaffold_22-snap.189-T1
Valid prediction for snap_scaffold_22-snap.195-T1
Valid prediction for Augustus_model.g32667.t1
Valid prediction for GlimmerHMM_glimmerT_48882-T1
Valid prediction for GlimmerHMM_glimmerT_48887-T1
Valid prediction for snap_scaffold_22-snap.169-T1
Valid prediction for snap_scaffold_22-snap.184-T1
Valid prediction for Augustus_model.g32653.t1
Valid prediction for Augustus_model.g32660.t1
Valid prediction for GlimmerHMM_glimmerT_48902-T1
Valid prediction for GlimmerHMM_glimmerT_48879-T1
Valid prediction for snap_scaffold_22-snap.173-T1
Valid prediction for GlimmerHMM_glimmerT_48893-T1
Valid prediction for GlimmerHMM_glimmerT_48890-T1
Valid prediction for GlimmerHMM_glimmerT_48883-T1
Valid prediction for snap_scaffold_22-snap.186-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 122752, rend_intergenic: 115031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140615, rend_intergenic: 137266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169724, rend_intergenic: 168337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231207
-exon list size: 376


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.6    
2.9    
3.2    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.0    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.5    
9.8    
10.1    
10.3    
10.6    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.4    
12.7    
13.0    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.8    
15.1    
15.3    
15.6    
15.9    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.2    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
45.0    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.8    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.0    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.8    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 122752, rend_intergenic: 115031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140615, rend_intergenic: 137266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169724, rend_intergenic: 168337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support