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    mira_miracoli
    @mira_miracoli:matrix.org
    [m]
    It should be a bit better now. Please tell if it's still slow for you
    Dr. Ewa Chrostek
    @EwaChrostek_twitter
    Still slow. I have been running FastQC on 2KB file (4 reads) for the last 5h, and it is not quite done yet :(
    Dr. Ewa Chrostek
    @EwaChrostek_twitter
    It actually finished... trying to align my 4 reads now!
    Dr. Ewa Chrostek
    @EwaChrostek_twitter
    Ok, sorry, it is better now :)
    Dr. Ewa Chrostek
    @EwaChrostek_twitter
    Thank you for sorting this out!
    1 reply
    JayanthiGangiredla
    @JayanthiGangiredla
    Hi, can someone please update this toolset : suite_enasearch
    A Python library for interacting with ENA's
    AttributeError: 'HTTPError' object has no attribute 'encode'
    3 replies
    Cristóbal Gallardo
    @gallardoalba:matrix.org
    [m]
    Did you try to increase the option "Level of search result details"? @JayanthiGangiredla
    2 replies
    I mean, to use --verbosiy 3
    Cristóbal Gallardo
    @gallardoalba:matrix.org
    [m]
    Yes, I think you can use as input the SRR accession number in the Accession number option (In the Advanced options section)
    5 replies
    Then you need to increase the lever of verbosity in order to include the information about the bioproject in the report.
    Sara Monzón
    @saramonzon
    @mira_miracoli It is still being slow for us, the job queue reserved for the course is slower than the normal usegalaxy.eu queue
    image.png
    image.png
    just me in the queue now and the jobs are in queue for over 10 minutes, in the usual usegalaxy queue is working:
    the problem is that most of the students have already joined the virologist_isciii, is there a way to choose which queue to use? So they can change it? Or they have to create a new user?
    mira_miracoli
    @mira_miracoli:matrix.org
    [m]
    I checked the queue and it has something to do with pulsar, all other jobs are running normal, as you said. I will try to find the problem as fast as possible
    Sara Monzón
    @saramonzon
    thanks!!
    mira_miracoli
    @mira_miracoli:matrix.org
    [m]
    You should be queued to the usual usegalaxy.eu queue now
    Sara Monzón
    @saramonzon
    perfect! I don't see any students registered in the status page, so it should be fine, thanks!
    Dr. Ewa Chrostek
    @EwaChrostek_twitter
    Hi, I am running the workshop atm as well, and it is unexpectedly slow. Is there anything I can do to make it faster?
    We are mostly running STAR RNA now.
    bgruening
    @bgruening:matrix.org
    [m]
    @EwaChrostek_twitter: are your tools yellow or grey?
    2 replies
    mira_miracoli
    @mira_miracoli:matrix.org
    [m]
    If you set pulsar endpoints in your user preferences, the jobs will still be scheduled there, even if you are in a training group. To use the training group resources, please remove the endpoints from your preferences temporarily.
    Dr. Ewa Chrostek
    @EwaChrostek_twitter
    image.png
    Sorry, that was meant to be pasted in the thread above about it being slow.
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    Last minute request for help from a UseGalaxy.eu admin: could you please update the lotus2 tool ( https://toolshed.g2.bx.psu.edu/view/earlhaminst/lotus2/a3d31a68f291 ) to version 2.21+galaxy2 which contains a minor bugfix that would help for a training course in 2 hours? 🙏
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Just installed it now. mira_miracoli can you restart things so that it gets picked up?
    bgruening
    @bgruening:matrix.org
    [m]
    done
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    Thanks both!
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    Mmmh, the tool is installed and I can find it fine in the tool menu, but the tool search returns "No results found!"
    (only for lotus)
    bgruening
    @bgruening:matrix.org
    [m]
    is it better now?
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    💯
    maaryaam-gh
    @maaryaam-gh
    Hello, I have a very large table file (with about 1400000 rows and 1307 columns) and I want to make changes in it.
    For example, I want to delete some of its rows and put some at the beginning of the file and some at the end of the file.
    I don't even know in which column or row are the items that I want to delete or move
    How do I make these changes?
    bgruening
    @bgruening:matrix.org
    [m]
    @maaryaam-gh: there are a ton of text manipulation tools in Galaxy. You can filter by row, by column, sort them etc. For all functionality there is a separate tool.
    Try them out and explore your data.
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    maaryaam-gh
    @maaryaam-gh
    @wm75:matrix.org @bgruening:matrix.org Thanks for your guidance
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    if you want to investigate - dataset 65 in history 41c0e6d221451102 has been stuck since yesterday (downloading a file from EBI). might be one of the I/O problems that show up from time to time.
    mira_miracoli
    @mira_miracoli:matrix.org
    [m]
    yes, we have a storage problem with the NFS currently, we are working on it. Downloading data from other servers might not work as expected, while uploading data directly from local filesystem should work.
    Cristóbal Gallardo
    @gallardoalba:matrix.org
    [m]
    It sees to work fine if you use the bioproject ID In the query field, but also you need to enable the option: Genetic material recovered directly from environmental or clinical samples @JayanthiGangiredla
    1 reply
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    hey folks - did you get the request for a TiaaS from Danielle Brites for the M. tuberculosis workshop in January?
    Chen Huiping
    @Huipingis_gitlab
    Hi, Mira, I uploaded my fastq files yesterday, but still running today. I wonder how I can do to speed up? Thanks.
    bgruening
    @bgruening:matrix.org
    [m]
    We had some upload problems in the last week
    Let me try to recover your upload today. If this does not work, please restart it
    Chen Huiping
    @Huipingis_gitlab
    Thanks!
    Chen Huiping
    @Huipingis_gitlab
    Hi, Bgruening, I wonder if you tried to recover my upload? Thanks.
    bgruening
    @bgruening:matrix.org
    [m]
    please have a look, I tried my best
    Chen Huiping
    @Huipingis_gitlab
    It was done, many thanks.