annotate test-data/predict_augustus/Genus_species.stats.json @ 10:d0336d67702b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 737d7e9a31c9d340a38ddfef3ac20847989718e0
author iuc
date Sun, 11 Feb 2024 00:08:00 +0000
parents a5baa4ff168d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
1 {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
2 "format": "annotation",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
3 "command": "/home/abretaud/miniconda3/envs/__funannotate@1.8.7/bin/funannotate predict --input /tmp/tmpkgev4773/files/c/e/8/dataset_ce85d0fa-1534-47df-8c1e-5f0a5c1b82f0.dat --out output --database /home/abretaud/.planemo/planemo_tmp__fmxm4ll/test-data/funannotate_db --species Genus species --isolate --strain --organism other --ploidy 1 --SeqCenter CFMR --SeqAccession 12345 --name FUN_ --numbering 1 --p2g_pident 80 --p2g_prefilter diamond --augustus_species fly --min_training_models 200 --busco_seed_species fly --busco_db insecta --evm-partition-interval 1500 --min_intronlen 10 --max_intronlen 3000 --min_protlen 50 --repeat_filter overlap blast --cpus 1",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
4 "organism": "Genus_species",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
5 "software": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
6 "name": "funannotate",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
7 "version": "1.8.7",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
8 "date": "2021-07-21",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
9 "resources": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
10 "merops": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
11 "type": "diamond",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
12 "version": "12.0",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
13 "date": "2017-10-04",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
14 "num-records": "5009"
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
15 },
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
16 "uniprot": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
17 "type": "diamond",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
18 "version": "2021_03",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
19 "date": "2021-06-02",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
20 "num-records": "565254"
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
21 },
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
22 "dbCAN": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
23 "type": "hmmer3",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
24 "version": "9.0",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
25 "date": "2020-08-04",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
26 "num-records": "641"
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
27 },
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
28 "pfam": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
29 "type": "hmmer3",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
30 "version": "34.0",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
31 "date": "2021-03",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
32 "num-records": "19179"
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
33 },
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
34 "repeats": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
35 "type": "diamond",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
36 "version": "1.0",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
37 "date": "2021-07-19",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
38 "num-records": "11950"
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
39 },
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
40 "go": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
41 "type": "text",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
42 "version": "2021-07-02",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
43 "date": "2021-07-02",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
44 "num-records": "47228"
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
45 },
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
46 "mibig": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
47 "type": "diamond",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
48 "version": "1.4",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
49 "date": "2021-07-19",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
50 "num-records": "31023"
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
51 },
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
52 "interpro": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
53 "type": "xml",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
54 "version": "86.0",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
55 "date": "2021-06-03",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
56 "num-records": "38913"
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
57 },
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
58 "busco_outgroups": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
59 "type": "outgroups",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
60 "version": "1.0",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
61 "date": "2021-07-19",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
62 "num-records": "8"
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
63 },
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
64 "gene2product": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
65 "type": "text",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
66 "version": "1.70",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
67 "date": "2021-06-15",
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
68 "num-records": "34039"
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
69 }
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
70 }
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
71 },
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
72 "assembly": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
73 "num_contigs": 4,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
74 "length": 227430,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
75 "mean_length": 56857.5,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
76 "N50": 215740,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
77 "L50": 1,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
78 "N90": 215740,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
79 "L90": 1,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
80 "GC_content": 42.86
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
81 },
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
82 "annotation": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
83 "genes": 18,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
84 "common_name": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
85 "mRNA": 18,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
86 "tRNA": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
87 "ncRNA": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
88 "rRNA": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
89 "avg_gene_length": 2695.06,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
90 "transcript-level": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
91 "CDS_transcripts": 18,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
92 "CDS_five_utr": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
93 "CDS_three_utr": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
94 "CDS_no_utr": 18,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
95 "CDS_five_three_utr": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
96 "CDS_complete": 18,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
97 "CDS_no-start": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
98 "CDS_no-stop": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
99 "CDS_no-start_no-stop": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
100 "total_exons": 57,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
101 "total_cds_exons": 57,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
102 "multiple_exon_transcript": 16,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
103 "single_exon_transcript": 2,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
104 "avg_exon_length": 558.58,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
105 "avg_protein_length": 582.83,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
106 "functional": {
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
107 "go_terms": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
108 "interproscan": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
109 "eggnog": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
110 "pfam": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
111 "cazyme": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
112 "merops": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
113 "busco": 0,
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
114 "secretion": 0
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
115 },
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
116 "pct_exon_overlap_protein_evidence": 17.54
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
117 }
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
118 }
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
119 }