Wrong paper auto-downloaded - how to report?

Hi there,

I’m a long time user and I found a problem with this paper (10.1038/s41564-023-01558-w) i wanted to report.

I don’t have access to this journal, but auto-download finds, and downloads the incorrect article every time I try. It should give me an error that it is not found.

I can report other errors, but I don’t see any way to report incorrect downloads (which is a serious problem, as you might not notice depending on how similar it is).

I thought this might be the best way.


Welcome to the forum @Nathan_Johnson. You can report these issues like this one here, via the in app chat, or by emailing support@paperpile.com. The team could not reproduce the error you reported. Can you share the JSON of the article with us by selecting the reference in your library and hitting Cmd-J/Ctrl-J so that the team can investigate it further?

Sure! Weird that it is only happening on my machine.

I can’t see where the article it keeps pulling is referenced in the JSON.

For clarity, the reference is: 10.1038/s41564-023-01558-w
and it keeps pulling the article pdf for: 10.1038/s41576-019-0159-6

In my connection, the paper I want is behind a paywall and I probably cannot access it - this is how I spotted that it was grabbing the wrong file.

    "dup_sha1": "8590ef6814fe5993b5c48180feff3d83ffccd822",
    "issue": "1",
    "pdf_restricted": 0,
    "incomplete": 0,
    "duplicates": [],
    "url": [
    "updated": 1711027329.25252,
    "doi": "10.1038/s41564-023-01558-w",
    "autocompleted": 1,
    "id_list": [
    "published": {
        "month": "1",
        "year": "2024"
    "affiliation": "Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA. ibrito@cornell.edu.",
    "abstract": "Bacteria respond to environmental stimuli through precise regulation of transcription initiation and elongation. Bulk RNA sequencing primarily characterizes mature transcripts, so to identify actively transcribed loci we need to capture RNA polymerase (RNAP) complexed with nascent RNA. However, such capture methods have only previously been applied to culturable, genetically tractable organisms such as E. coli and B. subtilis. Here we apply precision run-on sequencing (PRO-seq) to profile nascent transcription in cultured E. coli and diverse uncultured bacteria. We demonstrate that PRO-seq can characterize the transcription of small, structured, or post-transcriptionally modified RNAs, which are often absent from bulk RNA-seq libraries. Applying PRO-seq to the human microbiome highlights taxon-specific RNAP pause motifs and pause-site distributions across non-coding RNA loci that reflect structure-coincident pausing. We also uncover concurrent transcription and cleavage of CRISPR guide RNAs and transfer RNAs. We demonstrate the utility of PRO-seq for exploring transcriptional dynamics in diverse microbial communities.",
    "title": "Precision run-on sequencing (PRO-seq) for microbiome transcriptomics",
    "pages": "241-250",
    "folders": [],
    "journalfull": "Nature microbiology",
    "sha1": "d192d26995773269fd4e99c0101b29ca55769252",
    "collection_timestamps": {},
    "issn": "2058-5276",
    "author": [
            "initials": "AC",
            "first": "Albert C",
            "formatted": "Vill AC",
            "_id": "da8e209f-d1d2-0ceb-9634-80fe15dfd04e",
            "last": "Vill"
            "initials": "EJ",
            "first": "Edward J",
            "formatted": "Rice EJ",
            "_id": "14cd1e66-cdc6-0d6a-902e-f58cd24d9233",
            "last": "Rice"
            "initials": "I",
            "first": "Iwijn",
            "formatted": "De Vlaminck I",
            "_id": "eece2851-6281-032e-a1e6-d571134c8e84",
            "last": "De Vlaminck"
            "initials": "CG",
            "first": "Charles G",
            "formatted": "Danko CG",
            "_id": "7697fb97-9b23-0544-89db-3b118667dd27",
            "last": "Danko"
            "initials": "IL",
            "first": "Ilana L",
            "orcid": "0000-0002-2250-3480",
            "formatted": "Brito IL",
            "_id": "237223a7-6e0a-0fab-8745-570037bb9efd",
            "last": "Brito"
    "citedByLink": "http://scholar.google.com/scholar?hl=en&lr=&num=30&cites=http://dx.doi.org/10.1038/s41564-023-01558-w",
    "kind": "Research Article",
    "pubtype": "PP_ARTICLE",
    "pmc": "6858503",
    "crawl_urls": [
    "labels": [],
    "citekey": "Vill2024-gl",
    "journal": "Nat Microbiol",
    "imported": 1,
    "owner": "FD2D6CBE320A11E4BE47B4CFBF9F7527",
    "attachments": [
            "article_pdf": 1,
            "_id": "2a47cd96-aafa-0d8f-a326-20eac18bfa96",
            "hasUpdates": 1,
            "pub_trashed": 0,
            "pub_id": "a8462500-ad88-0f95-a576-12643a036f07",
            "source_filename": "[article_pdf].pdf",
            "s3_md5": "aa2865ed5b6ed62a14f9e16a34f3a7f8",
            "updated": 1711027350.044,
            "owner": "FD2D6CBE320A11E4BE47B4CFBF9F7527",
            "gdrive_id": "16NeHvecTq9ZM7E6LoaNLLaXQb562cMTL",
            "filesize": 1624877,
            "created": 1711027329.40961,
            "md5s": [
            "filename": "Vill et al. 2024 - Precision run-on sequencing (PRO-seq) for microbiome transcriptomics.pdf",
            "gdrive_needs_sync": 0,
            "subfolders": [
                "All Papers/V"
            "mimeType": "application/pdf",
            "md5": "aa2865ed5b6ed62a14f9e16a34f3a7f8"
    "volume": "9",
    "language": "en",
    "pii": "10.1038/s41564-023-01558-w",
    "journal_checked": 1,
    "created": 1711024423.59686,
    "subfolders": [
        "All Papers/V"
    "pmid": "38172625",
    "autoCleaned": 1

Thank you for your help!

Ahh, i see the problem in the URLs.

The PMID 38172625 is correct, but PMC6858503 is not. Perhaps this is an NCBI problem…

Thank you for following up, @Nathan_Johnson! Can you recall how you added the reference to your library? If so, can you share with us one of:

  • The URL from which you added the paper to your library if you used the P button in your browser
  • The file if you imported it from a bibliographic file
  • If you searched by title or DOI in Search online in the web app.

If you could let us know how you added it to library, then the team can try to reproduce and understand why there is an incorrect PMC in the reference data.

Sure! I can’t actually remember exactly how I downloaded it, but I’m sure it was by adding entry through the paperpile extension on a webpage (either google, or the actual paper’s website). It may have failed to find the paper, and I clicked the autodownload function in the paperpile interface.

Just on a lark, I tried to reproduce the problem entirely. I did the following:

  1. Trash the paperpile entry for this paper.
  2. Go to the DOI for the paper (on nature microbiology)
  3. Re-add the paper with the browser add-on (I am using Brave-browser).

Following these steps, paperpile added the entry, and downloaded (again) the incorrect file. I’m not sure how it got a PMC ID for this paper, as it is not in the PMC and is not publicly available.

This JSON looks to be identical as before.

Thank you for sharing, @Nathan_Johnson! The team has made a bug for the issue and it’ll be fixed in a future release of the extension.