Hi all, I've attempted to run fragment-insertion on both the command line and in q2studio to see if I can identify why it keeps failing. Running it in the q2studio with debug finally gave me this error report: Traceback (most recent call last): File "/Users/environmentalmicrobiologyteam/minicond…

Hi @TKOneal , I am cc:ing the fragment-insertion developer @Stefan to look into this. Thanks for your patience!

Hi @TKOneal , With the caveat that your milage may vary, my experience is that SEPP is one of the few programs in QIIME 2 that assumes you're working in a specific linguistic environment. Which means that I get a similar fragment insertion failure on my Swedish machine, but not my American one. Cou…

Hi @TKOneal , reading your error report let's me first think about concurrency issues. What kind of computational environment are you using? Is it a single laptop, or are you running SEPP in a grid environment. It could be that one thread is creating a temporary directory in /var/tmp which another t…

Hi jwdebelius! Thanks for responding. Running locale shows the following:; LANG="en_US.UTF-8" LC_COLLATE="en_US.UTF-8" LC_CTYPE="en_US.UTF-8" LC_MESSAGES="en_US.UTF-8" LC_MONETARY="en_US.UTF-8" LC_NUMERIC="en_US.UTF-8" LC_TIME="en_US.UTF-8" LC_ALL=

Hi Stefan, I am running Qiime2 locally. Here are some basic system details:: MacOS Mojave v10.14.4 MacPro (late 2013) processors 2.7GHz 12-core intel xeon E5 memory 64GB 1866 MHz DDR3 I ran the fragment-insertion plugin with 20 threads of the machines 24. The following is directly from my ru…

Hi @TKOneal , Okay, so probably not the same problem Im getting! That's at least one thing

Hi Stefan, Just an update, I updated my qiime 2 version to qiime2-2019.4 and now I can't seem to get the fragment-insertion SEPP to run at all. I'm not sure if what sort of error it is but I wanted to post the report encase anyone else has the same issue. input: qiime fragment-insertion sepp…

Hi @TKOneal , I think you should at least give SEPP one thread, thus please use --p-threads 1. Inserting ~400k fragments into the 200k tips big reference tree is a heavy job. I doubt your 64 GB RAM will suffice for that. Could you please also add --p-debug to your command to get more speaking error…

Hi Stefan, Thanks for your help. I think I may have fixed part of the issue. I have been filtering my rep-seqs.qza incorrectly. It is currently running with the debug flag. I will let you know if it throws any errors. I'm also running it with 10 threads currently.

QIIME 2 Forum

Error when running insert-fragment sequences using SEPP

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q2studio, fragment-insertion

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