nextgenusfs
commented
1 year ago Unable to help without more details. There are many many issues related to "why are most of my genes named hypothetical?" so please look through the issues to understand why that is.
But I think this is likely due to what you passed to --rename here, ie here's the help menu -- rename should be a new locus_tag base name, certainly not a file.....
$ funannotate annotate
Usage: funannotate annotate <arguments>
version: 1.8.14
Description: Script functionally annotates the results from funannotate predict. It pulls
annotation from PFAM, InterPro, EggNog, UniProtKB, MEROPS, CAZyme, and GO ontology.
Required:
-i, --input Folder from funannotate predict
or
--genbank Genome in GenBank format
-o, --out Output folder for results
or
--gff Genome GFF3 annotation file
--fasta Genome in multi-fasta format
-s, --species Species name, use quotes for binomial, e.g. "Aspergillus fumigatus"
-o, --out Output folder for results
Optional:
--sbt NCBI submission template file. (Recommended)
-a, --annotations Custom annotations (3 column tsv file)
-m, --mito-pass-thru Mitochondrial genome/contigs. append with :mcode
--eggnog Eggnog-mapper annotations file (if NOT installed)
--antismash antiSMASH secondary metabolism results (GBK file from output)
--iprscan InterProScan5 XML file
--phobius Phobius pre-computed results (if phobius NOT installed)
--signalp SignalP pre-computed results (-org euk -format short)
--isolate Isolate name
--strain Strain name
--rename Rename GFF gene models with locus_tag from NCBI.
--fix Gene/Product names fixed (TSV: GeneID Name Product)
--remove Gene/Product names to remove (TSV: Gene Product)
--busco_db BUSCO models. Default: dikarya
-t, --tbl2asn Additional parameters for tbl2asn. Default: "-l paired-ends"
-d, --database Path to funannotate database. Default: $FUNANNOTATE_DB
--force Force over-write of output folder
--cpus Number of CPUs to use. Default: 2
--tmpdir Volume/location to write temporary files. Default: /tmp
--p2g protein2genome pre-computed results
--header_length Maximum length of FASTA headers. Default: 16
--no-progress Do not print progress to stdout for long sub jobs
sunilicrsat
Dear team I ran following command, funannotate annotate -i ../10mAF_1/predict_results/ -o ../10mAF_fun/ --rename 10mAF_rename_ncbi.txt --annotations 10mAF_annotations.txt --eggnog 10mAF_eggnog.txt I am getting all hypothetical proteins in the annotation.txt file.