Error (return code -6) in feature table construction by DADA2

HI, everyone.
I was using qiime2 to run full length amplicon sequencing data analysis, and a R errors occurred, when using the following command,
(qiime2-2018.2) $ qiime dada2 denoise-single --i-demultiplexed-seqs dps-fl-demux_180422.qza --p-trim-left 0 --p-trunc-len 0 --output-dir dada2-notrunc_output --verbose
And the errors were shown below.

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_single.R /tmp/qiime2-archive-0i8rvny9/a7c518a5-6687-4350-ab5c-55a3606a7c50/data /tmp/tmp3b2xqirg/output.tsv.biom /tmp/tmp3b2xqirg 0 0 2.0 2 consensus 1.0 1 1000000

R version 3.4.1 (2017-06-30)
Loading required package:Rcpp
DADA2 R package version: 1.4.0

  1. Filtering …
  2. Learning Error Rates
    Initializing error rates to maximum possible estimate.
    *** Error in `/home/dps/miniconda3/envs/qiime2-2018.2/lib/R/bin/exec/R’: free(): invalid pointer: 0x000000000f844a58 ***
    Plugin error from dada2:

An error was encountered while running DADA2 in R (return code -6), please inspect stdout and stderr to learn more.

What should I do next to solve the problem? Thank you so much!

Hey there @dpsh! Do you happen to have RStudio installed? I ask, because I noticed this little tidbit:

The version of DADA2 deployed with QIIME 2 2018.2 is version 1.6.0, not 1.4.0. We usually see this kind of version mismatch whenever RStudio is around. If that is the case, check out this post for suggestions on how to fix:

https://forum.qiime2.org/t/rprofile-and-libpaths-with-dada2-exit-code-11/1519/5

Let us know how it goes, and if you’re still stuck we can come up with some additional ideas!

Thanks! :t_rex:

Thinks a lot @thermokarst !
I have installed dada2_1.6.0 from the Bioconductor, and execute the same commands. But there was the same error as following:

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_single.R /tmp/qiime2-archive-z6xabghu/a7c518a5-6687-4350-ab5c-55a3606a7c50/data /tmp/tmpuq0od7pm/output.tsv.biom /tmp/tmpuq0od7pm 0 0 2.0 2 consensus 1.0 1 1000000

R version 3.4.1 (2017-06-30)
Loading required package:Rcpp
DADA2 R package version: 1.6.0

  1. Filtering …
  2. Learning Error Rates
    Initializing error rates to maximum possible estimate.
    *** Error in `/home/dps/miniconda3/envs/qiime2-2018.2/lib/R/bin/exec/R’: free(): invalid pointer: 0x0000000011a98ec8 ***
    Plugin error from dada2:

An error was encountered while running DADA2 in R (return code -6), please inspect stdout and stderr to learn more.

Well, should I change another data sequencing from V4 to test?

Hi @dpsh!

I don’t think that will work - you will either need to try the fix I suggested above, or, uninstall RStudio, or whatever the offending R-tool is (sorry, pain in the butt, I know).

The next release of QIIME 2 (2018.4) should include some built-in workarounds for this issue, so stay tuned!

Keep us posted! :t_rex:

Hi @thermokarst, you are right, my other data also had the same error in dada2. But I can’t uninstall RStudio, others need to use it. So, I look forward to a new version, and thanks to your work and attention!

Did you try the fix I pointed out above? That approach will allow you to keep Rstudio installed.

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