Hi there, I'm facing exactly the same problem as the one introduced in this post . Interestingly, I ran the same code chunk both on my laptop and on the server, and the result is that in the laptop run no error occurred, while in the server one the comand was killed. I also tried the solution propos…

Hi @iptz1 ! Can you rerun with the following: qiime fragment-insertion sepp \ --i-representative-sequences outputs/rep-seqs.qza \ --i-reference-database sepp-refs-gg-13-8.qza \ --p-threads 4 \ --o-tree outputs/insertion-tree.qza \ --o-placements outputs/insertion-placements.qza \ --p-de…

Hi @thermokarst , I attach the log file here. Thank you for your kind help! err_sepp.txt (2.4 MB)

Thanks @iptz1 ! I see a ton of errors in this log, but I need some help making sense of it - @Stefan , can you lend a hand? Thanks!

Hi @iptz1 , to me, it looks like each and every invocation of the pplacer program fails. Unfortunately, I don't know what exit code -11 stands for. Typically, pplacer fails due to exceeding main memory. May I ask about the characteristics of your input? How many fragments and how long are they on av…

what just came to my mind is this issue report about pplacer. Looks like a kernel option might cause errors. What happens on the server if you manually invoke /opt/conda/envs/qiime2-2020.2/bin/pplacer ?

Hi @Stefan , thank you for the help. You're right, my OS/Kernel are the "problematic" ones highlighted in the post (Operating System: Debian GNU/Linux 10 (buster), Kernel: Linux 4.19.0-6-amd64). And yes, the same input went through on my laptop, but not on the server, despite having the same memory…

Hi there, the system manager finally found the problem: vsyscall was disabled and this caused sepp process to die instead of performing a "normal" system call. Hope this will help others if detecting the same issue. Thank you for the kind help!

QIIME 2 Forum

Non-zero exit status when performing fragment-insertion sepp

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sepp, fragment-insertion

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