[ensembl-dev] Missing files on the FTP

[Matthieu Muffato]

Dear Ensembl team,



I parse https://ftp.ebi.ac.uk/pub/ensemblorganisms/species.json to find out what can be retrieved the FTP. I would like to report that among the ~65k files referenced, ~3.5k don't seem to exist.



For instance:

                "chromosomes.tsv.gz": "Kalanchoe_fedtschenkoi/GCA_002312845.1/genome/chromosomes.tsv.gz",

The directory https://ftp.ebi.ac.uk/pub/ensemblorganisms/Kalanchoe_fedtschenkoi/GCA_002312845.1/genome/ exists but it has no chromosomes.tsv.gz file



I see that across a variety of files (cdna.fa.gz, genes.embl.gz, regulation.gff, variation.vcf.gz, etc). Sometimes the entire species directory is missing:



                        "genes.gtf.gz": "Melinaea_menophilus_n_ssp_AW-2005/GCA_918358695.1/ensembl/geneset/2022_07/genes.gtf.gz",

There is no https://ftp.ebi.ac.uk/pub/ensemblorganisms/Melinaea_menophilus_n_ssp_AW-2005/



I’d like to understand if the files are genuinely missing and may be added later, or perhaps species.json was malformed in the first place. I also wonder if the opposite may happen: files present on the FTP but not listed in species.json



Kind regards,

Matthieu (he/him)

--

Informatics Infrastructure Team Lead – Tree of Life programme

Wellcome Sanger Institute




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