We need YOUR help to improve gene names/product descriptions

[alexvasilikop]

Are you using the latest release? 1.8.11

What command did you issue? funannotate annotate -i update_results -oannotated --eggnog $emapper_annotations --iprscan iprscan.fasta.xml --cpus 10 --busco_db metazoa

Logfiles

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[Jul 14 02:10 PM]: OS: Ubuntu 18.10, 48 cores, ~ 264 GB RAM. Python: 3.8.12
[Jul 14 02:10 PM]: Running 1.8.11
[Jul 14 02:10 PM]: No NCBI SBT file given, will use default, however if you plan to submit to NCBI, create one and pass it here '--sbt'
[Jul 14 02:10 PM]: Found existing output directory /mnt/sda1/Alex/09.GENOME_ANNOTATIONS. Warning, will re-use any intermediate files found.
[Jul 14 02:10 PM]: Parsing input files
[Jul 14 02:10 PM]: Existing tbl found: update_results/species.tbl
[Jul 14 02:11 PM]: Adding Functional Annotation to species, NCBI accession: None
[Jul 14 02:11 PM]: Annotation consists of: 33,617 gene models
[Jul 14 02:11 PM]: 34,446 protein records loaded
[Jul 14 02:11 PM]: Running HMMer search of PFAM version 35.0
[Jul 14 02:27 PM]: 38,372 annotations added
[Jul 14 02:27 PM]: Running Diamond blastp search of UniProt DB version 2022_02
[Jul 14 02:29 PM]: 1,089 valid gene/product annotations from 1,477 total
[Jul 14 02:29 PM]: Existing Eggnog-mapper results found: eggnog.emapper.annotations
[Jul 14 02:29 PM]: Parsing EggNog Annotations
[Jul 14 02:29 PM]: EggNog version parsed as 2.1.8
[Jul 14 02:29 PM]: 47,401 COG and EggNog annotations added
[Jul 14 02:29 PM]: Combining UniProt/EggNog gene and product names using Gene2Product version 1.78
[Jul 14 02:29 PM]: 10,138 gene name and product description annotations added
[Jul 14 02:29 PM]: Running Diamond blastp search of MEROPS version 12.0
[Jul 14 02:29 PM]: 1,153 annotations added
[Jul 14 02:29 PM]: Annotating CAZYmes using HMMer search of dbCAN version 10.0
[Jul 14 02:31 PM]: 731 annotations added
[Jul 14 02:31 PM]: Annotating proteins with BUSCO metazoa models
[Jul 14 02:32 PM]: 1,179 annotations added
[Jul 14 02:32 PM]: Skipping phobius predictions, try funannotate remote -m phobius
[Jul 14 02:32 PM]: Predicting secreted proteins with SignalP
[Jul 14 02:51 PM]: 4,206 secretome and 0 transmembane annotations added
[Jul 14 02:51 PM]: Parsing InterProScan5 XML file
[Jul 14 02:51 PM]: Found 0 duplicated annotations, adding 193,258 valid annotations
[Jul 14 02:51 PM]: Converting to final Genbank format, good luck!
[Jul 14 02:55 PM]: Creating AGP file and corresponding contigs file
[Jul 14 02:55 PM]: Writing genome annotation table.
[Jul 14 03:19 PM]: Funannotate annotate has completed successfully!

        We need YOUR help to improve gene names/product descriptions:
           0 gene/products names MUST be fixed, see /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/species/05.GENE_PREDICT/annotate_results/Gene2Products.must-fix.txt
           50 gene/product names need to be curated, see /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/species/05.GENE_PREDICT/annotate_results/Gene2Products.need-curating.txt
           1,003 gene/product names passed but are not in Database, see /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/species/05.GENE_PREDICT/annotate_results/Gene2Products.new-names-passed.txt

        Please consider contributing a PR at https://github.com/nextgenusfs/gene2product

Could you please provide more info concerning the last message? I understand there are 50 product names that do not fulfill the GeneBank specifications? What about the 1003 gene/product names that passed but are not in Database? What does this mean?

Thanks Alex

[nextgenusfs]

This means that in the gene2product database which lives here https://github.com/nextgenusfs/gene2product, that these 1003 names are not in the database, but they passed NCBI rules apparently. So the message is just asking users that they can improve gene names by doing a pull request at the gene2product database.