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    Diamond tblastx

    No, I'm afraid that feature is not available at this time.
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    v2.0.4 released

    Fixed a bug that could cause the --max-target-seqs/-k, --ext-chunk-size and --file-buffer-size options not to function correctly on macOS.
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    v2.0.3 released

    Added a new sensitivity mode that is between the default mode and the sensitive mode in sensitivity (option --mid-sensitive). Added counters for total number of reference blocks, shapes and index chunks to the status messages. Fixed a bug (persisting since v2.0.2) that could cause secondary HSPs...
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    --unal (0,1) question

    The feature does work for me, can you show me your full command line?
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    out of memory

    Try using a smaller block size, like -b1. It is not that simple to know the memory use in advance, and it can increase under certain circumstances.
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    Memory cost problem in makedb

    That should be ok, makedb does not necessarily use all CPU cores.
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    Memory cost problem in makedb

    This looks like you are running the native Windows version (diamond.exe). So you should try building the database again using the same call.
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    Memory cost problem in makedb

    Try running it from the Windows command promt (cmd.exe) and just click run anyway if that message appears.
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    Memory cost problem in makedb

    You seem to be using cygwin under Windows, have you tried using the native Windows version of Diamond instead?
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    Memory cost problem in makedb

    32 GB should be plenty enough (no guarantee though, I have not tested it).
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    diamond blastp produce longer alignments with lower identity than ncbi blast

    Yes, you need to change the scoring matrix for this.
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    Memory cost problem in makedb

    The memory use of makedb with taxonomy can be higher than 16 GB unfortunately. It's a known issue and I will try to provide a solution in the future, but it may take some time.
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    diamond blastp produce longer alignments with lower identity than ncbi blast

    Diamond does not use a xdrop-like algorithm for extension, so you can't really make it prefer shorter alignments that way. You would have to tweak the scoring matrix and set higher penalties for mismatches. Support for custom scoring matrices and ungapped-only alignments is not officially...
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    Question about --taxonlist

    It should not happen that the sensitivity is reduced using very-sensitive. Are you using the latest Diamond version? Could you send me your query file so I can take a closer look? (Email: buchfink@gmail.com) For repeat masking, Diamond uses the tantan method...
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    Question about --taxonlist

    It is probably a question of sensitivity, so you should try the more sensitive modes of Diamond like --sensitive or --very-sensitive. Another reason could be repeat masking, so you can try again with --masking 0.
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    v2.0.2 released

    Fixed a bug (persisting since v2.0.0) that could cause incomplete results in blastx mode. Reduced the use of temporary disk space. Fixed an issue that could cause long runtimes when using the --taxon-list option.
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    v2.0.1 released

    Added feature for using the tool in a distributed computing environment. (See here for details: http://www.diamondsearch.org/index.php?pages/distributed_computing/) Fixed an issue that could cause increased memory usage and runtimes in certain cases. Fixed a bug that could cause a crash when...
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    v2.0.0 released

    Added the sensitivity modes --very-sensitive and --ultra-sensitive. Both modes are designed for finding distant hits of <40% identity with a sensitivity similar to BLAST, with the ultra-sensitive mode being the slightly more sensitive mode. The --block-size/-b parameter is set to 0.4 and the...
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    v0.9.36 released

    Fixed a bug that could cause makedb to produce invalid database files when using taxonomy features. Fixed a bug that could cause a crash when running in query-indexed mode.
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    Hectic operation under WinServer 2019 / NVRAM / AMD Epyc config

    Hi Blaize, no idea about this error unfortunately. Could you maybe run diamond using the --log option and show me the output, that might help me narrow down things a bit.
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