Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
    bgruening
    @bgruening:matrix.org
    [m]
    I have installed this one
    and you can now run your pangolin with this version instead of latest version from web
    but this version does not seem to have Omicron included yet
    :(
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Uh, really weird cause I got B.1.1.529 annotated with latest from web until Wednesday last week.
    Going to dive into changelogs later today.
    Marius
    @mvdbeek:matrix.org
    [m]
    I guess you saw it, but the tests for pe-wgs-ivar-analysis.ga_0 also started failing at the pangolin step
    pangolearn updated to 2021-11-25
    constellations updated to v0.0.29
    pango-designation updated to v1.2.110
    Job stats:
    job                     count    min threads    max threads
    --------------------  -------  -------------  -------------
    add_failed_seqs             1              1              1
    align_to_reference          1              1              1
    all                         1              1              1
    generate_report             1              1              1
    get_constellations          1              1              1
    hash_sequence_assign        1              1              1
    pangolearn                  1              1              1
    scorpio                     1              1              1
    total                       8              1              1
    
    Warning: couldn't parse the following string: # nuc:G11287T - ignoring
    [Sun Dec 12 17:00:19 2021]
    Error in rule get_constellations:
        jobid: 7
        output: /tmp/tmp3gwbt4h9/get_constellations.txt
        shell:
    
            scorpio list         --constellations /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.429.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cAY.4.2.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cP.2.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.617.1.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.617.2+K417N.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cP.3.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.525.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cA.23.1+E484K.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cBA.2.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.617.3.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.621.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.1.529.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cBA.1_probable.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cA.23.1.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cBA.1.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cAY.4.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.617.2.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.351.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.427.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.526.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.1.318.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cAV1.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cP.1.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cC.37.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.1.7+E484K.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.1.7.json         --pangolin > /tmp/tmp3gwbt4h9/get_constellations.txt
    
            (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    
    
    Exiting because a job execution failed. Look above for error message
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Yeah, investigating currently, but this multi-component architecture of pangolin doesn't make debugging easy :(
    bgruening: could you find out, which version of scorpio the .eu installed pangolin is using? That's the only version info I don't have.
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Seems you can run pangolin --all-versions to find out (I guess we should include that command in the wrapper and print the result so that things are more transparent)
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Not sure yet, but this seems like a very good candidate for the problem (scorpio v0.3.15 release notes):
    Allows comments in constellation files
    The latest from web functionality updates constellations, but not scorpio
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Well, yes, upgrading scorpio locally from 0.3.14 to 0.3.15 fixes it.
    otoh, cov-lineages/constellations@564121a is the last commit that made it into constellations 0.0.29
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Puh, it's the warning in the output above:
    Warning: couldn't parse the following string: # nuc:G11287T - ignoring
    bgruening
    @bgruening:matrix.org
    [m]
    scorpio 0.3.14 pyhdfd78af_0 bioconda
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    If you remove the # it starts working again
    This line is in the new definitions/cBA.1.json and now we only need to find out if it's there on purpose or just a typo.
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    cov-lineages/constellations#48 lets see what they say.
    bgruening
    @bgruening:matrix.org
    [m]
    I update the scorpio version
    maybe it works now
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Yes, it's "fixed".
    However, that strange line will parse as an empty string in scorpio 0.3.15 and I don't believe that's the intention
    So I still have hopes that it'll get fixed upstream in constellations, and then things would work again everywhere, not just on .eu
    bgruening
    @bgruening:matrix.org
    [m]
    this warning we also had in 0.3.14
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    The thing is the warning doesn't happen with 0.3.15 (that's why I imagine nobody noticed what I think is a typo)
    Marius
    @mvdbeek:matrix.org
    [m]
    Would a new mulled build fix this ?
    I guess scorpio is not pinned in the pangolin package
    I'll trigger a new build, that would fix it at least for the container usage
    ah, that fix was only applied for version 3.1.17
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    So my issue got addressed (they removed the line completely and https://github.com/cov-lineages/constellations/releases/tag/v0.0.30 is out
    That means that pangolin latest from web should simply work again.
    As for the pangolin 3.1.17 update, I don't know for sure yet. I guess it'll be fine, and dependency-pinning is sth I was looking forward to.
    So why not try and see.
    Marius
    @mvdbeek:matrix.org
    [m]
    At least we won't have to rush this now
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Yes, that's good
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Marius: pangolin is still at 3.1.14 on usegalaxy.org, btw. Definitely deserves an update to 3.1.16.
    Marius
    @mvdbeek:matrix.org
    [m]
    Gonna run the update now
    bwlang
    @bwlang:matrix.org
    [m]
    i can confirm that the fix is live - i did not have to update pangolin to get the database fix. thanks wm75 (Wolfgang Maier) for getting this to the right place upstream!
    i should say - working properly for me now on our internal galaxy server as well as usegalaxy.eu
    bwlang
    @bwlang:matrix.org
    [m]
    I've just noticed that the ivar-based fast workflow seem to be missing the S insertion at 22204.
    It is picked up by wm75 (Wolfgang Maier) 's workflow.
    NC_045512.2    22204    .    T    TGAGCCAGAA    10152    PASS    AF=0.603814;DP=472;DP4=92,104,118,167;HRUN=1;SB=5;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||gat/gaGCCAGAAGAt|D215EPED|1273|S|protein_coding|CODING|GU280_gp02|1|TGAGCCAGAA|INFO_REALIGN_3_PRIME)
    pvanheusden: FYI ^^ - Ill try to have a look as soon as I can get my head above water.
    Marius
    @mvdbeek:matrix.org
    [m]
    We're tracking the people that want to be part of the workflow working group (I guess at this point that's just the synonym for the IWC) and that will be available to do some work over the next few months in an internal spreadsheet. So far we've got John, Wolfgang, Simon and me, but if you want to be part of the group and you don't have access / don't know about the spreadsheet let me know and I'll make sure you're added
    F. H.
    @heylf
    @mvdbeek:matrix.org please include me in it as well
    Marius
    @mvdbeek:matrix.org
    [m]
    Excellent @heylf, I've added you to the spreadsheet ... and if I can figure out how to share the meeting calendar I'll drop a link. The next meeting is Monday the 17th, at 4pm CET
    https://calendar.google.com/calendar/u/0?cid=NWw2bzBtc2ZkdW9pcjU5aHJhYjBqbGtvY2NAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ is the calendar for all the WG meetings, not sure how to limit that to just the IWC meetings though
    Marius
    @mvdbeek:matrix.org
    [m]
    Quick reminder, we'll have a meeting in 75 minutes, hope y'all can join: meet.google.com/myu-vozy-bsj. Tentative topics could be workflow default files, conditionals and tutorials that we could / should write