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I'm trying to download PubMed Central Open Access articles from ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk. However, I am not able to decompress the archives without errors.

tar always gives me the error:

gzip: data stream error
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now

Does PubMed provide corrupted archives or does downloading corrupt the archive?

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  • $\begingroup$ Have you tried to decompress it in the past few days since it's been updated? Picking a smaller file, tar -zxvf non_comm_use.A-B.xml.tar.gz works fine. $\endgroup$
    – Michael
    Jun 11, 2021 at 10:12
  • $\begingroup$ I was eventually able to do it on Linux. It didn't work on MacOS for me (not even with gnu-tar). $\endgroup$
    – TomTom
    Jun 19, 2021 at 19:18
  • $\begingroup$ The download attempt might be caused by an attempt to download the files while these files are being updated by the NCBI server. Try downloading on other days and make sure you have a strong connectivity. $\endgroup$
    – venrey
    Oct 28, 2021 at 6:06

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