Example cc_variants.sqlite dataset trouble

Mark Sfeir

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Apr 27, 2022, 12:03:12 PM4/27/22

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Working through the examples in the R/qtl2 user guide on Kbroman.com, I received an error when attempting to set up (by downloading the necessary files in the target directory) and use the query_variants function shown there to query the cc_variants.sqlite data. I had no such issue using the query_genes function to query the mouse_genes.sqlite data, in a similar way.

Here is the error message I got in RStudio:

> variants_2_97.5 = query_variants(2,97,98)
Error: database disk image is malformed
In addition: Warning message:
Couldn't set synchronous mode: database disk image is malformed
Use `synchronous` = NULL to turn off this warning.

Any guidance on what may be happening here, or what I should do? Maybe this file has been corrupted somehow in a way that isn't isolated to my computer?

I would appreciate any help,

Mark Sfeir at the UNC Nutrition Research Institute

Karl Broman

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Apr 27, 2022, 12:06:27 PM4/27/22

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My guess is that the download was incomplete, so I would try again with that.

karl

Mark Sfeir

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Apr 28, 2022, 10:52:28 AM4/28/22

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I tried downloading again, adjusting the default "timeout" option to try to support a larger file size in the following way:

> options(timeout = 1000)

> download.file(url="https://figshare.com/ndownloader/files/18533342",destfile = "cc_variants.sqlite")

trying URL 'https://figshare.com/ndownloader/files/18533342'

Content type 'application/octet-stream' length 4159954944 bytes (3967.2 MB)

downloaded 3967.2 MB

As shown above, it appeared to me that the file was downloaded in its entirety in this way, though I still went on to get the same error when creating and using my query_variant function.

Do I need to increase the timeout option even more, or is there anything else I should try next?

-Mark

Karl Broman

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Apr 28, 2022, 10:57:45 AM4/28/22

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I’m not sure what’s going on. Could you show me all the rest of the code, leading up to the error?

karl

Mark Sfeir

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Apr 28, 2022, 11:08:10 AM4/28/22

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And amid that .Rhistory session I sent, I deleted the previous version of cc_variants.sqlite manually in my Windows file explorer system to make room for the new attempt. :/

Mark Sfeir

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Apr 28, 2022, 11:21:59 AM4/28/22

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Karl Broman

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Apr 28, 2022, 11:23:00 AM4/28/22

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Maybe try download.file() again using mode = "wb"

karl

Mark Sfeir

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Apr 28, 2022, 11:24:39 AM4/28/22

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Thank you, I'll try that, though I may need to pick this back up another day.

Mark Sfeir

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Apr 28, 2022, 12:02:54 PM4/28/22

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It looks like using mode = 'wb', the download worked as intended! I'm not sure if the 'wb' mode is worth using every time on Windows, especially since I hadn't specified it before when I successfully downloaded and use the "query_genes" function from the same part of the R/qtl2 user guide. It is good to know though, and I should be set for following the rest of the example for now.