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view test-data/predict_scratch/Genus_species.stats.json @ 11:9c15ca7e764e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 9e3708d04faea0f1be4ea8918e859d6f2c7eb31d
author iuc
date Wed, 26 Jun 2024 09:41:52 +0000
parents 9feee7fc49a1
children
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{
    "format": "annotation",
    "command": "/home/abretaud/miniconda3/envs/__funannotate@1.8.15/bin/funannotate predict --input input/input.fasta --out output --database /home/abretaud/git/iuc_tools/tools/funannotate/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 --busco_seed_species fly --busco_db insecta --min_training_models 3 --evm-partition-interval 1500 --min_intronlen 10 --max_intronlen 3000 --min_protlen 50 --repeat_filter overlap blast --cpus 1",
    "organism": "Genus_species",
    "software": {
        "name": "funannotate",
        "version": "1.8.15",
        "date": "2023-04-13",
        "resources": {
            "merops": {
                "type": "diamond",
                "version": "12.0",
                "date": "2017-10-04",
                "num-records": "5009"
            },
            "uniprot": {
                "type": "diamond",
                "version": "2021_03",
                "date": "2021-06-02",
                "num-records": "565254"
            },
            "dbCAN": {
                "type": "hmmer3",
                "version": "9.0",
                "date": "2020-08-04",
                "num-records": "641"
            },
            "pfam": {
                "type": "hmmer3",
                "version": "34.0",
                "date": "2021-03",
                "num-records": "19179"
            },
            "repeats": {
                "type": "diamond",
                "version": "1.0",
                "date": "2021-07-19",
                "num-records": "11950"
            },
            "go": {
                "type": "text",
                "version": "2021-07-02",
                "date": "2021-07-02",
                "num-records": "47228"
            },
            "mibig": {
                "type": "diamond",
                "version": "1.4",
                "date": "2021-07-19",
                "num-records": "31023"
            },
            "interpro": {
                "type": "xml",
                "version": "86.0",
                "date": "2021-06-03",
                "num-records": "38913"
            },
            "busco_outgroups": {
                "type": "outgroups",
                "version": "1.0",
                "date": "2021-07-19",
                "num-records": "8"
            },
            "gene2product": {
                "type": "text",
                "version": "1.70",
                "date": "2021-06-15",
                "num-records": "34039"
            }
        }
    },
    "assembly": {
        "num_contigs": 4,
        "length": 732270,
        "mean_length": 183067.5,
        "N50": 720580,
        "L50": 1,
        "N90": 720580,
        "L90": 1,
        "GC_content": 43.15
    },
    "annotation": {
        "genes": 70,
        "common_name": 0,
        "mRNA": 69,
        "tRNA": 1,
        "ncRNA": 0,
        "rRNA": 0,
        "avg_gene_length": 1544.77,
        "transcript-level": {
            "CDS_transcripts": 69,
            "CDS_five_utr": 0,
            "CDS_three_utr": 0,
            "CDS_no_utr": 69,
            "CDS_five_three_utr": 0,
            "CDS_complete": 68,
            "CDS_no-start": 0,
            "CDS_no-stop": 1,
            "CDS_no-start_no-stop": 0,
            "total_exons": 209,
            "total_cds_exons": 209,
            "multiple_exon_transcript": 58,
            "single_exon_transcript": 11,
            "avg_exon_length": 362.67,
            "avg_protein_length": 393.62,
            "functional": {
                "go_terms": 0,
                "interproscan": 0,
                "eggnog": 0,
                "pfam": 0,
                "cazyme": 0,
                "merops": 0,
                "busco": 0,
                "secretion": 0
            },
            "pct_exon_overlap_protein_evidence": 3.81
        }
    }
}