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<p class="MsoPlainText">Dear Ensembl team,</p>
<p class="MsoPlainText"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span style="color:black">I parse <a href="https://ftp.ebi.ac.uk/pub/ensemblorganisms/species.json">
https://ftp.ebi.ac.uk/pub/ensemblorganisms/species.json</a> 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.<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span style="color:black">For instance:<o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">"chromosomes.tsv.gz": "Kalanchoe_fedtschenkoi/GCA_002312845.1/genome/chromosomes.tsv.gz",</span><o:p></o:p></p>
<p class="MsoPlainText"><span style="color:black">The directory <a href="https://ftp.ebi.ac.uk/pub/ensemblorganisms/Kalanchoe_fedtschenkoi/GCA_002312845.1/genome/">
https://ftp.ebi.ac.uk/pub/ensemblorganisms/Kalanchoe_fedtschenkoi/GCA_002312845.1/genome/</a> exists but it has no chromosomes.tsv.gz file<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span style="color:black">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:<o:p></o:p></span></p>
<p class="MsoPlainText"><span style="color:black"><o:p> </o:p></span></p>
<p class="p1"><span class="apple-converted-space"> </span>
<span class="s1">"genes.gtf.gz": "Melinaea_menophilus_n_ssp_AW-2005/GCA_918358695.1/ensembl/geneset/2022_07/genes.gtf.gz",</span><o:p></o:p></p>
<p class="MsoPlainText"><span style="color:black">There is no <a href="https://ftp.ebi.ac.uk/pub/ensemblorganisms/Melinaea_menophilus_n_ssp_AW-2005/">
https://ftp.ebi.ac.uk/pub/ensemblorganisms/Melinaea_menophilus_n_ssp_AW-2005/</a><o:p></o:p></span></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">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<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Kind regards,<o:p></o:p></p>
<p class="MsoPlainText">Matthieu (he/him) <o:p></o:p></p>
<p class="MsoPlainText">-- <o:p></o:p></p>
<p class="MsoPlainText">Informatics Infrastructure Team Lead – Tree of Life programme
<o:p></o:p></p>
<p class="MsoPlainText">Wellcome Sanger Institute <o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
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