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read.accession2taxid error creating SQL file: malformed line #3
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I got |
That's good it works some places but pretty bad that it's inconsistent. I was trying to recreate the error on my side and not having much luck yet. Couple of questions:
Thanks. |
Local OS: MacOS High Sierra (Version 10.13.3), R Version 3.4.3, running as super user The warnings are all copies of:
Running just
Cheers, |
Hmm I don't call
so R will error out on the first warning and we can narrow down where the warning occurs. And just as a thought, how much space is in /tmp or wherever |
I did check the /tmp directory and it looks like it could very likely be that there's not enough free space. Here's the result of running
And here's what happened when I ran it with
|
Yeah probably not enough space in Could you try setting the temp directory to somewhere with some space when you start R? For example if you have a lot of space in whatever directory you are working in, you could start R with:
You can make sure this worked by typing Thanks for helping debug this. |
Yup, that worked perfectly. Thanks, Scott! |
Great. Thanks for debugging. Really helpful to find these edge cases. It looks like gunzip doesn't create the target file if the disk is full so I can just check if file.exists after gunzip and output a more informative error. I'll get that into the next version. |
Hi Scott,
Thanks for making this package available. I've been looking for a convenient way to convert accession numbers to UIDs to a taxonomy lineage for a while. I tried to get taxonomizr to create the .sql file to no avail. It's returning an error about a malformed line. Have you encountered this before? Any idea if I'm doing something wrong? I've attached my R logs below.
I checked the *accession2taxid.gz file checksums and they do match the md5 sums from NCBI.
MD5 sums:
Cheers,
Bryan Nguyen
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