error while running DADA2 in R (return code 1),invalid permissions

Hello all, I'm still a newbie,I'm trying to use qiime2 in a miniconda3 environment, and I tried to run dada2 following this script:

time qiime dada2 denoise-paired \

--i-demultiplexed-seqs demux.qza
--p-n-threads 16
--p-trim-left-f 29 --p-trim-left-r 20
--p-trunc-len-f 0 --p-trunc-len-r 0
--o-table dada2-table.qza
--o-representative-sequences dada2-rep-seqs.qza
--o-denoising-stats denoising-stats.qza


It said this afterwards:
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-q70ufed2.log

And here's what's inside the debug file:

Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: run_dada_paired.R /tmp/tmpei0hpdw4/forward /tmp/tmpei0hpdw4/reverse /tmp/tmpei0hpdw4/output.tsv.biom /tmp/tmpei0hpdw4/track.tsv /tmp/tmpei0hpdw4/filt_f /tmp/tmpei0hpdw4/filt_r 0 0 29 20 2.0 2.0 2 independent consensus 1.0 16 1000000

R version 4.0.2 (2020-06-22)
Loading required package: Rcpp
DADA2: 1.18.0 / Rcpp: 1.0.6 / RcppParallel: 5.0.2

  1. Filtering
    *** caught segfault ***
    address 0x7f804647a000, cause 'invalid permissions'

*** caught segfault ***
address 0x7f8043044000, cause 'invalid permissions'

*** caught segfault ***
address 0x7f8048348000, cause 'invalid permissions'

*** caught segfault ***
address 0x7f804f9255c8, cause 'invalid permissions'

*** caught segfault ***
address 0x7f8046361000, cause 'invalid permissions'

I have read the other threads but I am still not sure about this. It seems nobody encountered this before. Any ideas?
Thanks in advance!

Hello @Ellwood, that is a weird one! Probably coming from the c++ runtimes. Is your data particularly large? Also, can you rerun the command with the --verbose flag and post the entire output here, please?

Thanks for helping! I think i figured it out lol. It turns out the issue lies here:
-p-n-threads 16
I changed it to -p-n-threads 10 and it worked, how silly i am, my laptop doesnt have 16 threads...

3 Likes

Yeah, that makes sense! Sounds like the c++ runtime tried to allocate resources that it wasn't allowed to in an attempt to spawn more threads.

2 Likes