Mercurial > repos > iuc > funannotate_predict

comparison test-data/predict_scratch/Genus_species.stats.json @ 0:ec3b462fc579 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
author iuc
date Thu, 26 Aug 2021 06:51:59 +0000
parents
children c8b01160610c
comparison
equal deleted inserted replaced
-1:000000000000 0:ec3b462fc579
1 {
2 "format": "annotation",
3 "command": "/home/abretaud/miniconda3/envs/__funannotate@1.8.7/bin/funannotate predict --input /tmp/tmpm833xrq1/files/e/1/c/dataset_e1c34c74-e579-4cab-b0ed-5ce938ce4e4b.dat --out output --database /home/abretaud/.planemo/planemo_tmp_yntx6ieu/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 --min_training_models 3 --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",
4 "organism": "Genus_species",
5 "software": {
6 "name": "funannotate",
7 "version": "1.8.7",
8 "date": "2021-07-21",
9 "resources": {
10 "merops": {
11 "type": "diamond",
12 "version": "12.0",
13 "date": "2017-10-04",
14 "num-records": "5009"
15 },
16 "uniprot": {
17 "type": "diamond",
18 "version": "2021_03",
19 "date": "2021-06-02",
20 "num-records": "565254"
21 },
22 "dbCAN": {
23 "type": "hmmer3",
24 "version": "9.0",
25 "date": "2020-08-04",
26 "num-records": "641"
27 },
28 "pfam": {
29 "type": "hmmer3",
30 "version": "34.0",
31 "date": "2021-03",
32 "num-records": "19179"
33 },
34 "repeats": {
35 "type": "diamond",
36 "version": "1.0",
37 "date": "2021-07-19",
38 "num-records": "11950"
39 },
40 "go": {
41 "type": "text",
42 "version": "2021-07-02",
43 "date": "2021-07-02",
44 "num-records": "47228"
45 },
46 "mibig": {
47 "type": "diamond",
48 "version": "1.4",
49 "date": "2021-07-19",
50 "num-records": "31023"
51 },
52 "interpro": {
53 "type": "xml",
54 "version": "86.0",
55 "date": "2021-06-03",
56 "num-records": "38913"
57 },
58 "busco_outgroups": {
59 "type": "outgroups",
60 "version": "1.0",
61 "date": "2021-07-19",
62 "num-records": "8"
63 },
64 "gene2product": {
65 "type": "text",
66 "version": "1.70",
67 "date": "2021-06-15",
68 "num-records": "34039"
69 }
70 }
71 },
72 "assembly": {
73 "num_contigs": 4,
74 "length": 227430,
75 "mean_length": 56857.5,
76 "N50": 215740,
77 "L50": 1,
78 "N90": 215740,
79 "L90": 1,
80 "GC_content": 42.86
81 },
82 "annotation": {
83 "genes": 16,
84 "common_name": 0,
85 "mRNA": 16,
86 "tRNA": 0,
87 "ncRNA": 0,
88 "rRNA": 0,
89 "avg_gene_length": 1660.69,
90 "transcript-level": {
91 "CDS_transcripts": 16,
92 "CDS_five_utr": 0,
93 "CDS_three_utr": 0,
94 "CDS_no_utr": 16,
95 "CDS_five_three_utr": 0,
96 "CDS_complete": 15,
97 "CDS_no-start": 0,
98 "CDS_no-stop": 1,
99 "CDS_no-start_no-stop": 0,
100 "total_exons": 42,
101 "total_cds_exons": 42,
102 "multiple_exon_transcript": 13,
103 "single_exon_transcript": 3,
104 "avg_exon_length": 402.36,
105 "avg_protein_length": 359.81,
106 "functional": {
107 "go_terms": 0,
108 "interproscan": 0,
109 "eggnog": 0,
110 "pfam": 0,
111 "cazyme": 0,
112 "merops": 0,
113 "busco": 0,
114 "secretion": 0
115 },
116 "pct_exon_overlap_protein_evidence": 11.9
117 }
118 }
119 }