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    pvanheus
    @pvanheus
    Thanks for the explanation though. I think it is most appropriate that we have our explanation on the GTN this afternoon :)
    Helena Rasche
    @erasche
    Expect a temporary interruption in service
    a DNS change did not go as planned
    ugh
    Helena Rasche
    @erasche
    should be fixed now.
    Milad Miladi
    @mmiladi
    Dear admins, could you please upgrade the SRA downloader version in the server. Thanks in advance
    Helena Rasche
    @erasche
    It should be installed automatically on saturday morning
    Milad Miladi
    @mmiladi
    Thanks Helena.
    Milad Miladi
    @mmiladi
    The issue I face is not because of the sra-tools version. Using the same version and input the download succeeds on usegalaxy.org
    Björn Grüning
    @bgruening
    But this is US and the SRA is in the US
    We got a timeout isn't it?
    Milad Miladi
    @mmiladi
    Well just tested again.
    Now succeed. Sorry so ignore previous one.
    This one is still valid though: galaxyproject/tools-iuc#2105
    fastq-dump filters out all reads
    Having fastq-dump --table SEQUENCE would fix the filtering.
    Björn Grüning
    @bgruening
    Will try to add the --table option as soon as I can
    Milad Miladi
    @mmiladi
    Merc :+1:
    David Twesigomwe
    @twesigomwedavid
    Hello, Are there any standard databases integrated for kraken on https://usegalaxy.eu/?
    Björn Grüning
    @bgruening
    @twesigomwedavid we don't
    which one do you need?
    David Twesigomwe
    @twesigomwedavid
    @bgruening I would like to use the one for bacteria
    amitpande74
    @amitpande74
    Hi...I want tools to be added on qiime
    Björn Grüning
    @bgruening
    @amitpande74 you mean complete new tools?
    @twesigomwedavid working on this. Please check in a few days
    amitpande74
    @amitpande74
    qiime quality-filter q-score (version 2018.4)
    this tool is not installed
    its here
    - Quality filter based on sequence quality scores
    Björn Grüning
    @bgruening
    and we probably need to update them
    can you create an issue
    that you want to have version 2.0
    amitpande74
    @amitpande74
    ok
    done
    David Twesigomwe
    @twesigomwedavid
    @bgruening Thank you
    Milad Miladi
    @mmiladi
    Hello, do you have an expectation when extra high-memory nodes will be available for the server?
    Helena Rasche
    @erasche
    at least a week to get more nodes into the cloud
    which jobs/tools?
    Milad Miladi
    @mmiladi
    I have a couple of Spades and Unicycler mapping waiting jobs
    Helena Rasche
    @erasche
    we can redirect to SGE in the meantime
    by redirect I mean you'll need to restart the jobs
    Milad Miladi
    @mmiladi
    That would be nice. Alternatively it should be fine to reduce the requested memory. It's Bacteria genome, so 180GB would be likely not needed.
    Krzysztof Poterlowicz
    @kpoterlowicz
    Hi Helena, just to confirm are you restarting handlers now on usegalaxy.eu ?
    Helena Rasche
    @erasche
    Hi @kpoterlowicz nope, we aren't doing anything.
    any reason?
    Krzysztof Poterlowicz
    @kpoterlowicz
    just two of my students have waiting status for while :)
    but other got yellow now so we will be patient