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Activity
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    davelopez (David López): I can confirm that after clearing the cached data for usegalaxy.eu everything behaves as it should and I can scroll through my histories.
    Bérénice Batut
    @bebatut:matrix.org
    [m]
    same for me
    tingting081
    @tingting081
    Hi there. My data upload job doesn't run. How can I fix this problem?
    Are we experiencing downtime now? How long does it take?
    tingting081
    @tingting081
    Thank you and waiting for your feedback.
    Surbhigrewal
    @Surbhigrewal
    Hi, any idea how long will the current down time be for?
    2 replies
    Lada Jovović
    @LadushkaY_twitter
    @bgruening:matrix.org any update on my bug report for Trinity?
    1 reply
    Yvan Le Bras
    @yvanlebras
    Hi @LadushkaY_twitter . I see you encounter issues with RNAseq analysis. You mentionned 4 weeks of running jobs? Seems to be quite big... Do you think this is "normal" (ie, you have big input files ?) or maybe not and maybe "just" trying rerunning the jobs can be ok ? If you have big files, maybe it can be of interest to look at reducing it but not sure this is relevant / possible
    Lada Jovović
    @LadushkaY_twitter
    Hi @yvanlebras I am pretty much new in bioinformatics so I am not sure whether my data are too big for Galaxy - I made a collection of 16 trimmed pairs, each approx 20M reads, and when I look at my trimmed data size it is 42,0 GB. Is it too much? If that's the case shouldn't I receive some kind of message which confirms that - something like this -> https://training.galaxyproject.org/training-material/faqs/galaxy/#understanding-exceeds-memory-allocation-error-messages
    gmauro
    @gmauro:matrix.org
    [m]
    Currently, we have some issues with our web processes and we are working to fix them. Sorry for the inconvenience
    sncgbrl
    @sncgbrl
    thank you very much. Good luck
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    is there a status page for usegalaxy.eu at the moment?
    gmauro
    @gmauro:matrix.org
    [m]
    have a look at https://status.galaxyproject.org/
    Our own stats website is currently down
    proteomics
    @proteomics_twitter
    usegalaxy.eu seems to be down for training
    https://usegalaxy.eu/join-training/quant-meta/status/
    gmauro
    @gmauro:matrix.org
    [m]
    We fixed the issues with the web interface and upload jobs.
    Everything should work properly now.
    proteomics
    @proteomics_twitter
    It failed again - can you have a look?
    bgruening
    @bgruening:matrix.org
    [m]
    @proteomics_twitter: did you get an error message?
    gmauro
    @gmauro:matrix.org
    [m]
    There is still a problem with the web processes. We are looking for a solution, meanwhile could happen the website will be occasionally unreachable for a few minutes
    proteomics
    @proteomics_twitter
    Sounds good
    proteomics
    @proteomics_twitter
    @bgruening - An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1.
    https://usegalaxy.eu/u/pratikjagtap/h/imported-inputs-for-metaproteomics-gtn
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Not an expert for the tool, but the error message says "Data must be aligned to block boundary in ECB mode", which sounds like an input data issue to me?
    tingting081
    @tingting081
    Thank you so much. Last night I figured out now the server is downtime by visiting status page. It clearly shows operational status. Thank you so much.
    irisbeirith
    @irisbeirith_twitter
    Hi all, does anyone know how to download the data contained in DEXseq results file? there is no download button below and too much data to copy paste
    bgruening
    @bgruening:matrix.org
    [m]
    There is no download button in the history?
    Can you sent me a screenshot maybe?
    tingting081
    @tingting081
    hello there. I see the operation system is now good. However, it still does not work when I upload data. Can you help me fix it?
    Does that mean, we are still having downtime now?
    davelopez (David López)
    @davel0pez:matrix.org
    [m]
    There is currently high load in the uploads, we are investigating
    tingting081
    @tingting081
    Thanks. Does that mean we need to wait for a while before the issue is fixed?
    davelopez (David López)
    @davel0pez:matrix.org
    [m]
    You should be able to continue :) but uploads or some jobs could take some more time to catch up
    tingting081
    @tingting081
    ok, thanks. I will try to continue. Those jobs haven been waiting for running for a few hours. Just no idea about when it will start running.
    thank you so much for your help.
    gmauro
    @gmauro:matrix.org
    [m]
    We have currently, ~2000 uploads jobs running and ~3000 waiting in the queue. We are trying some tuning to speed up the queue
    tingting081
    @tingting081
    Got it. Much appreciated for your help and consideration.
    Surbhigrewal
    @Surbhigrewal
    Hi Is there any way to upload using a URL from Microsoft Sharepoint?
    bgruening
    @bgruening:matrix.org
    [m]
    is the URL public accessible?
    daikez
    @daikez
    any problems with usegalaxy.eu? couldn't load up data since yesterday.
    irisbeirith
    @irisbeirith_twitter
    no, all good for me with usegalaxy.eu. However, I do regularly open the page in a new tab again to access all.
    ZhouHY-77
    @ZhouHY-77
    Hi guys, I uploaded some FASTA files, but they are always grey in history. Do you know how to make them available? Thank you a lot!
    irisbeirith
    @irisbeirith_twitter
    Hi guys, anyone knowing the tool for SRA data import in FASTA format? I can only find the one for FASTQ. Thanks in advance
    bgruening
    @bgruening:matrix.org
    [m]
    You want to have reads in FASTA format? I don't think they store it that way. But you can convert fastq to fasta.
    irisbeirith
    @irisbeirith_twitter
    I tired to convert from Fastq to Fasta. however, the result is not matching with Mirdeep ( I'm trying to follow galaxy tutorial for miRNA analysis). SRA does provide an option to directly download in Fasta, but I can't find an option here, unfortunately.
    Patrick Bovio
    @pbovio
    @bgruening:matrix.org Hi Björn, I get an "Internal Server Error" when trying to export a history into a workflow. Any insides? I would like to export all tools and settings to the workflow to publish it alongside a Revised Manuscript.
    there used to be a simple .xml format for this
    bgruening
    @bgruening:matrix.org
    [m]
    @pbovio: can you try again, but let me know when you hit the button?
    Patrick Bovio
    @pbovio
    hitting in 5 sec
    again in 5 sec @bgruening:matrix.org