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    Expected runtime?

    This may take a couple of hours against the NR as Diamond is not that efficient when the number of queries is small. When aligning contigs it would be useful to use the --long-reads option. If your server has a lot of memory, a good way to speed it up is to use a higher block size like this...
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    qseq and sseq in -outfmt 6 are not aligned

    Hi Romain, no problem, I will add that feature, but probably make it a new output field instead of changing the behaviour of the current ones, otherwise it will break the compatibility with previous Diamond versions. Best regards, Benjamin
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    Is it possible to get out-format 6 and out-format 102 without running Diamond twice?

    It is currently not possible without running the program twice. But this would certainly be a useful feature so I will try to get it implemented, but it may take 2-3 weeks.
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    Compiling DIAMOND from source for mac

    You can download older versions here: But it's probably better to build a new database for the latest version using the FASTA files of RefSeq etc.
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    Compiling DIAMOND from source for mac

    Hi, have you tried typing the full path: /usr/local/bin/diamond Diamond does run on a Mac if you compile it from source. P.S.: the version you are using is pretty old, I'd recommend using the latest version.
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    using Diamond for paired-end reads

    Hi Andrew, sorry but Diamond can't use paired-end information directly.
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    No command 'diamond' found Error

    For a local copy of diamond you need to prepend ./ to your call like this: wget tar xzf diamond-linux64.tar.gz ./diamond
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    DIAMOND installation error

    That is strange since I used the same compiler version to test it. Please check that you have the right commit by going to the diamond directory and running: git show. The first line should read like this: commit b6dee73c3b0deaa50187937fbff7bdbb6c5eda62 (HEAD -> master, origin/master, origin/HEAD)
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    DIAMOND installation error

    Please clone the latest version of the repository, I have just pushed a commit that should fix this.
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    DIAMOND installation error

    Hi, can you tell me your exact GCC version? Run gcc --version.
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    Feature requests

    Please use this forum to provide your ideas for missing features and possible improvements. This includes small additions and broader perspectives for future development. Diamond is an open source product of PathoVis, a bioinformatics startup focusing on software solutions for microbial...
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    Community website

    Welcome to the new community website for the popular open source protein alignment tool Diamond. Having been published in 2015, Diamond has become a widely used tool in the bioinformatics community with 881 citations in scientific literature to date. Many users have contributed to making...