Error message download database #83
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I was about to post the same issue. I'm getting the same error as @ELPhD. I also received the same error message with v0.2.3. This error also occurs with MentaLiST VersionUsing the latest available from Bioconda (v0.2.4, h3c2d85e_0) CommandsError MessageConda Environment (
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Same here, I'm getting the same error as rpetit3 . Installed it today. |
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Thanks for reporting @ELPhD @rpetit3 @bastian-wur. I was able to reproduce the error on my system too. I'm investigating now. |
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Ok, I think I see what went wrong. When tagging the I've deleted the old In the meantime, if the option is available to you I'd recommend grabbing an official https://julialang.org/downloads/oldreleases.html ...and add it to your https://github.com/WGS-TB/MentaLiST#macos-108 ...Then grab the MentaLiST source tarball: https://github.com/WGS-TB/MentaLiST/archive/v0.2.4.tar.gz ...and run from there (the Please let us know if this work-around will work for you, and I'll try to get the bioconda build fixed as soon as possible if that is your only installation option. |
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By the way @ELPhD, while testing the corrected I get an error as follows: It seems that the |
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@rpetit3 I've successfully built one of the databases you mentioned above, after following my proposed work-around using the official julia binary. I still get a few warning messages but the database does build successfully. |
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Thanks for the follow up Dan! |
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I've submitted a pull request to re-generate the bioconda package for |
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Hmm... The new build of The problem may be with the conda-forge |
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That's too bad :/. EDIT: Okay, I managed to install everything. Apparently another dependency called "JuMP" is missing from the description, but that's not much of an issue. |
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I've had success with using build MentaLiST VersionConda listIgnore the MentaLiST v0.2.2 below, the release for v0.2.4 was used to test. I only used v0.2.2 to install the other requirements associated with MentaLiST. |
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Good to know @rpetit3 . Thanks for testing that out. We might be able to tag the MentaLiST bioconda recipe against that specific julia build. In the long-run I think the solution will be to migrate to julia-1.0 but it may take some time to get there. |
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I'm also having this same issue. |
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@realseanla Sorry for the delay. I was using the v0.2.4 release (https://github.com/WGS-TB/MentaLiST/releases/tag/v0.2.4) from this repo not BioConda. So, This was just to verify v0.2.4 executed using the same dependencies (see below) as BioConda's v0.2.2. @dfornika Looking at the |
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Are there any updates on this issue? |
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I could create a PR on bioconda-recipes with my proposed fix above. But I'd want approval for the fix before doing so. |
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That would be great @rpetit3 . Looks good to me. |
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Submitted a PR bioconda/bioconda-recipes#13137 |
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Alright, merged into bioconda (bioconda/bioconda-recipes@f27fe11). I probably won't have a chance to test till Monday. @ELPhD @bastian-wur @realseanla Want to give it a try? |
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Sadly, I'm still getting the same error, even with Conda list |
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Hi! Having the same issue at the moment. Tried to the suggested patches and Julia versions but I'm getting the same issue. Are there any updates? :) |
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@moorembioinfo The best solution I can suggest at this point is to use one of the official julia-0.6 binaries from: https://julialang.org/downloads/oldreleases.html and to use the source code from this GitHub repo. Would that be a viable work-around for you? |
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Hi, and Could any of you check if you're also getting the same weird lines? |
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@pedrofeijao Looks similar to what I reported earlier in this thread: |
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@dfornika Oh, I don't know how I missed that, thanks for the heads up. reported above, it seems that it is fixed on the current version, based on Julia 1.1, at least for all cgmlst schemes that I've tried. I'm currently working on better detection and message for wrongly formatted FASTA files. |
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Apologies for the slow response, it took ~30 minutes (don't remember it taking that long) but I was able to successfully create a cgMLST database. I installed the latest Julia release (v1.0.3) from conda-forge and MentsLiST is a clone of the master branch. Conda list I also created a MLST DB and that only took ~1 minute. Are there plans to create a release of this version or is it still considered a work in progress? If a release is created I can submit to bioconda |
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I installed julia 1.1 along with other packages and run the mentalist github code and it downloaded but didn't construct the database for both pubmlst and cgmlst and for enterobase, I am met with this error |
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@jowong4 |
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@rpetit3 @pedrofeijao Yes, I've also been testing this out when I have time. I've just pushed an updated conda recipe to this repo: https://github.com/WGS-TB/MentaLiST/tree/master/conda It's not exactly ready for bioconda because it pulls the source code from the master branch of the repo rather than a stable tag. I also haven't really thought carefully if any of those dependencies in the I've also done a test build that's available on my personal conda channel: https://anaconda.org/dfornika/mentalist I've done some really quick testing with it, just building one cgMLST database and it worked. Personally I'd like to see a bit more testing done using the conda-supplied |
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@rpetit3 @pedrofeijao We did manage to sneak one more bugfix in. I've tagged a |
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Sorry, we've had another bug report. I'm trying to hold of on the |
Hi,
I used the following command:
mentalist download_cgmlst -o lm_cgmlst_fasta -s 690488 -k 31 --db lm_cgmlst.dbto try and download the L. mono cgmlst and but got (in addition to a load of warnings which i have ignored) an error message:
ERROR: LoadError: LoadError: LoadError: MethodError: no method matching convert(::Type{AssertionError}, ::String) Closest candidates are: convert(!Matched::Type{Any}, ::ANY) at essentials.jl:28 convert(::Type{T}, !Matched::T) where T at essentials.jl:29 AssertionError(::String) at ./coreimg.jl:14I was previously using mentalist 0.2.3 and got this error but updated to version 0.2.4 today and the problem hasnt gone away. We suspect it could be a problem with Julia which is running version 0.6.1 as downloaded with mentalist.
Thank you
Erin
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