qiime2 OTU picking with hundreds of samples

[Nicholas_Bokulich]

@MichelaRiba,
here's another thought: maybe your tmpdir is running out of space?

this forum user mentioned uncovering an error with VSEARCH whereby it does not detect system errors correctly and just keeps running after tmpdir fills up:

Steps for taxonomy assignment on dual-indexed sequence data generated by QIIME 1.9

Hi, I am trying QIIME 2 on one of my wife's experiments that she had processed with QIIME 1.9 in 2015. She used dual-indexed primers in her experiment as published in https://doi.org/10.1186/2049-2618-2-6 (Fadrosh, D.W., Ma, B., Gajer, P. et al.). I didn't try QIIME 2 for the whole preprocessing steps because it was unclear to me whether it's easy to do. Instead, I used joined paired-ends generated by QIIME 1.9 (that is, a trimmed seqs.fna). Here's my setup: % conda --version conda 4.8.1 %…

This sounds remarkably similar to the symptoms you report.