Mercurial > repos > iuc > funannotate_predict
view test-data/predict_bam/Genus_species.stats.json @ 4:d3ff5fd62517 draft
"planemo upload commit 9cbeba115a6e13dd4c007065b7d77dcb400f72fb"
author | iuc |
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date | Thu, 25 Nov 2021 09:45:23 +0000 |
parents | 40b87aef5241 |
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{ "format": "annotation", "command": "/home/abretaud/miniconda3/envs/__funannotate@1.8.7/bin/funannotate predict --input /tmp/tmp2z22js7e/files/c/c/3/dataset_cc3f66b5-ec9b-4669-93d6-4ddeac0e33c1.dat --out output --database /home/abretaud/.planemo/planemo_tmp_z_14xthq/test-data/funannotate_db --species Genus species --isolate --strain --organism other --ploidy 1 --SeqCenter CFMR --SeqAccession 12345 --name FUN_ --numbering 1 --rna_bam /tmp/tmp2z22js7e/files/9/6/5/dataset_965b5091-b838-4f4a-8ec8-9fb84c12cdc5.dat --transcript_evidence /tmp/tmp2z22js7e/files/d/a/e/dataset_daea4ce7-3191-40eb-ad83-b35e9e058d46.dat --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", "organism": "Genus_species", "software": { "name": "funannotate", "version": "1.8.7", "date": "2021-07-22", "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": 227430, "mean_length": 56857.5, "N50": 215740, "L50": 1, "N90": 215740, "L90": 1, "GC_content": 42.86 }, "annotation": { "genes": 18, "common_name": 0, "mRNA": 18, "tRNA": 0, "ncRNA": 0, "rRNA": 0, "avg_gene_length": 2775.33, "transcript-level": { "CDS_transcripts": 18, "CDS_five_utr": 0, "CDS_three_utr": 0, "CDS_no_utr": 18, "CDS_five_three_utr": 0, "CDS_complete": 16, "CDS_no-start": 1, "CDS_no-stop": 1, "CDS_no-start_no-stop": 0, "total_exons": 54, "total_cds_exons": 54, "multiple_exon_transcript": 15, "single_exon_transcript": 3, "avg_exon_length": 563.63, "avg_protein_length": 571.83, "functional": { "go_terms": 0, "interproscan": 0, "eggnog": 0, "pfam": 0, "cazyme": 0, "merops": 0, "busco": 0, "secretion": 0 }, "pct_exon_overlap_transcript_evidence": 31.48, "pct_exon_overlap_protein_evidence": 9.26 } } }