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    could not set up reference database for DIAMOND

    Could you try to run any other program on this system that needs a couple GB of memory and reads/writes large files? Does this work?
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    could not set up reference database for DIAMOND

    This could be an indication of running out of memory. How much memory does your system have?
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    Diamond database tied to specific diamond build?

    I tried to reproduce this on a CentOS 6 system, Diamond compiled from source using GCC 4.9.4. I couldn't find any incompatibilities that shouldn't exist, i.e. databases created by v0.9.10 and v0.9.16 are compatible, as are those created by v0.9.22 and v0.9.24. Could you reproduce this using a...
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    Diamond database tied to specific diamond build?

    The build number is increased by 1 for each release, but they can't be used to discriminate between the individual commits.
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    Diamond database tied to specific diamond build?

    I think you are building two different versions of Diamond here, because database format version 3 is not created by any release version, but only the latest github commit. That can happen if you clone the repository instead of downloading a release. These other more substantial...
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    Diamond database tied to specific diamond build?

    The database format has changed twice in the past, so this is a rare occurence and should not happen regularly between different versions. Can you tell me precisely which versions are causing the problem? Could you also give me the system specs and Diamond version for which you are observing the...
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    diamond Error: Inflate error

    Please try to use the latest version of Diamond. It has the advantage that you only need to pass --taxonmap and --taxonnodes to the makedb command and it will be built into the database. Also, you don't need to decompress the nr.gz and prot.accession2taxid.gz files, Diamond can handle the...
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    Yes it has, please consult the manual for a description of the parameters.

    Yes it has, please consult the manual for a description of the parameters.
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    Problem compiling in MacOS Mojave

    Can you show me the output you are getting when trying to compile?
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    Diamond runtime + optimisation

    You can use -b5 -c1, that will help. Using -k1 will get the best hit only, and it's definitely faster than retrieving all hits. I'm not sure about the expected runtime. Diamond generally is more efficient if you use large query files (>1 million sequences).
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    Human metagenomic data, two-stage or one-stage approach?

    Feel free to share your findings! I'm not an expert on this so I'll hold off on giving a recommendation.
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    sensitivity/accuracy of fast then sensitive search

    I haven't tried this approach and don't really have any numbers for it. It should work quite well when only looking for the best hit for each query, but it also depends on the data. If say >80% of your queries have best hits with >60% identity, this should work well and improve the performance...
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    Compiling DIAMOND from source for Windows?

    You can download an executable here: https://github.com/bbuchfink/diamond/releases I compile them using MS Visual Studio.
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    species name output

    You need to use the latest commit for this. Clone the diamond repository like this: git clone https://github.com/bbuchfink/diamond Then compile from source as described in the manual.
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    species name output

    It has been added recently, please see here: https://github.com/bbuchfink/diamond/issues/256
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    --taxonlist error

    --taxonlist takes a list of numerical values (taxon ids). So for searching all bacterial proteins, use --taxonlist 2. Btw, --taxonnodes and --taxonmap need only be added to makedb.
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    taxon mapping with alternate databases?

    It is possible but requires some manual labour. You would have to create a mapping file from protein accessions to taxon ids in the same format as the NCBI file, only for Uniref50. I will put it on my todo list to provide an integrated way for this but it may take some time.
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    Joinging output blocks...seg fault error

    >M01235_52_000000000XC65VW_1_2105_13879_16114...
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    Joinging output blocks...seg fault error

    Send to buchfink@gmail.com
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    Joinging output blocks...seg fault error

    No, certainly not, unless there's nothing in there that matches the database in any way. Could you upload your data file or a small part of it so I can check it myself?
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