is it possible to resume an interrupted run of UnifiedGenotyper?

glowgooseglowgoose University of Texas at AustinMember

..so is it possible?

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    No. But if you use Queue to scatter-gather UG jobs, it will automatically resume/retry any jobs that fail or get interrupted for whatever reason.

  • pdexheimerpdexheimer Member ✭✭✭✭

    Resume? No. Restart with a different interval (i.e., "last logged location before interruption" - "end of genome")? Sure.

  • pdexheimerpdexheimer Member ✭✭✭✭

    I'm going to perform a minor threadjack here, but I have a question about the auto-resume feature you mention with Queue, Geraldine.

    Queue absolutely tracks the individual jobs, and will pick up where it left off if you restart a failed run. But in my experience, it will not automatically resubmit a failed job in the middle of a run. I do remember seeing code somewhere in Queue (possibly in the example scripts?) that would auto-resubmit jobs that failed because they ran out of memory, and increment the requested memory each time. I never got around to playing with that, but it looked cool. Did something like that end up in the main Queue engine and I missed it? Or am I just being ridiculously picky about your response?

  • glowgooseglowgoose University of Texas at AustinMember

    Thanks for your prompt responses, people! Clearly, my problems are rooted in my ignorance of the Queue. I would love to use it to run UG split by contig - I am sure this will dramatically shorten my runs and get rid of the "run interrupted" problem - but I am hopeless with those QScripts, it feels like I need to budget a week to learn this stuff. In the meantime, can anyone please share a UG Qscript that allows multiple BAM files (I have 132 of those) on the input, and splits the UG job by contig? I would tremendously appreciate that!..

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @pdexheimer, it's a useful thread-jack, my wording was unintentionally misleading. The basic "resume" behaviour in Queue does indeed NOT resume jobs mid-run; as you point out you have to relaunch the script to make it retry failed jobs. There are indeed some cool automagic tricks but they're a little cryptic; I'll try to document them for our upcoming workshop.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @glowgoose, if you hang on a couple of days I will send you the draft presentations that we plan to present at our upcoming workshop. You can be our guinea pig and hopefully it will clarify a lot of things for you. But right now I can't take the time to give you the info in detail here because I'm behind schedule on making the slide decks...

  • glowgooseglowgoose University of Texas at AustinMember

    This sounds absolutely awesome, Geraldine!
    standing by...

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