DADA2 errors - return code 1 and 11

Hi @ebolyen! It looks like whatever magic you worked on creating this new environment is the solution.

I have been running it with --verbose since yesterday and so far I did not get an error.
I didn’t get past the first sample before, and now I am up to sample 14.

Will post whatever output I get when it finishes running.

THANKS!

We have just released a patched update to q2-dada2 that appears to fix this :crossed_fingers: . Please follow the instructions here to get your hands on the patch, and please let us know how it goes! Thanks so much for all the support while we were debugging this! :t_rex:

Hi @thermokarst!
I updated my qiime2-2017.12 and ran DADA2, but I got an error towards the end.

Any thoughts?

(qiime2-2017.12) Erikas-MacBook-Pro:Rumen ErikaGanda$ qiime dada2 denoise-single \

--i-demultiplexed-seqs rumen-demux.qza
--p-trim-left 0
--p-trunc-len 270
--o-representative-sequences rumen-rep-seqs-dada2.qza
--o-table rumen-table-dada2.qza
--verbose

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 /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/qiime2-archive-8fqc85zl/a6d39a9d-42e3-4f5d-a135-8c762b4c1ae7/data /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpb2ns3arx/output.tsv.biom /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpb2ns3arx 270 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.
    Sample 1 - 91807 reads in 56092 unique sequences.
    Sample 2 - 64987 reads in 44507 unique sequences.
    Sample 3 - 67539 reads in 47125 unique sequences.
    Sample 4 - 108200 reads in 65596 unique sequences.
    Sample 5 - 64163 reads in 41787 unique sequences.
    Sample 6 - 67642 reads in 42793 unique sequences.
    Sample 7 - 52144 reads in 36422 unique sequences.
    Sample 8 - 65922 reads in 43672 unique sequences.
    Sample 9 - 67666 reads in 44921 unique sequences.
    Sample 10 - 36152 reads in 27625 unique sequences.
    Sample 11 - 141572 reads in 89293 unique sequences.
    Sample 12 - 62983 reads in 42869 unique sequences.
    Sample 13 - 91496 reads in 61123 unique sequences.
    Sample 14 - 85505 reads in 54316 unique sequences.
    selfConsist step 2
    selfConsist step 3
    selfConsist step 4
    selfConsist step 5
    selfConsist step 6
    selfConsist step 7
    selfConsist step 8
    selfConsist step 9
    selfConsist step 10
    Self-consistency loop terminated before convergence.

  3. Denoise remaining samples .................

  4. Remove chimeras (method = consensus)

  5. Report read numbers through the pipeline
    input filtered denoised non-chimeric
    jess1_12_L001_R1_001.fastq.gz 118107 91807 91807 50573
    jess10_6_L001_R1_001.fastq.gz 76066 64987 64987 46560
    jess11_20_L001_R1_001.fastq.gz 79398 67539 67539 48116
    jess12_24_L001_R1_001.fastq.gz 136854 108200 108200 60975
    jess13_29_L001_R1_001.fastq.gz 76034 64163 64163 39502
    jess14_31_L001_R1_001.fastq.gz 81867 67642 67642 42706

  6. Write output
    shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
    Traceback (most recent call last):
    File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/bin/qiime", line 11, in
    sys.exit(qiime())
    File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py", line 722, in call
    return self.main(*args, **kwargs)
    File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
    File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
    File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
    File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
    File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
    File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 237, in call
    path = result.save(output)
    File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/result.py", line 143, in save
    self._archiver.save(filepath)
    File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 341, in save
    self.CURRENT_ARCHIVE.save(self.path, filepath)
    File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 161, in save
    allowZip64=True) as zf:
    File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/zipfile.py", line 1009, in init
    self.fp = io.open(file, filemode)
    FileNotFoundError: [Errno 2] No such file or directory: 'rumen-table-dada2.qza'
    (qiime2-2017.12) Erikas-MacBook-Pro:Rumen ErikaGanda$
    (qiime2-2017.12) Erikas-MacBook-Pro:Rumen ErikaGanda$

It looks like qiime is there, but not listed as a directory:

Erikas-MacBook-Pro:~ ErikaGanda$ cd /Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/bin
Erikas-MacBook-Pro:bin ErikaGanda$ pwd
/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/bin
Erikas-MacBook-Pro:bin ErikaGanda$ ls
2to3 llvm-cvtres
2to3-3.5 llvm-cxxdump
FastTree llvm-cxxfilt
FastTree.c llvm-diff
FastTreeMP llvm-dis
R llvm-dlltool
Rscript llvm-dsymutil
aclocal.bak llvm-dwarfdump
activate llvm-dwp
appletviewer llvm-extract
autoheader.bak llvm-lib
autom4te.bak llvm-link
automake.bak llvm-lto
autopoint llvm-lto2
autoreconf.bak llvm-mc
autoscan.bak llvm-mcmarkup
autoupdate.bak llvm-modextract
biom llvm-mt
blast_formatter llvm-nm
blastdb_aliastool llvm-objdump
blastdbcheck llvm-opt-report
blastdbcmd llvm-pdbutil
blastn llvm-profdata
blastp llvm-ranlib
blastx llvm-readelf
bokeh llvm-readobj
bugpoint llvm-rtdyld
c-index-test llvm-size
c_rehash llvm-split
cairo-trace llvm-stress
captoinfo llvm-strings
chardetect llvm-symbolizer
cjpeg llvm-tblgen
clang llvm-xray
clang++ lzcat
clang-5.0 lzcmp
clang-check lzdiff
clang-cl lzegrep
clang-cpp lzfgrep
clang-format lzgrep
clang-import-test lzless
clang-offload-bundler lzma
clang-rename lzmadec
clear lzmainfo
compile_et lzmore
conda mafft
convert2blastmask mafft-distance
coverage mafft-einsi
curl mafft-fftns
curl-config mafft-fftnsi
cutadapt mafft-ginsi
cygdb mafft-homologs.rb
cython mafft-linsi
cythonize mafft-nwns
deactivate mafft-nwnsi
deblur mafft-profile
deltablast mafft-qinsi
derb mafft-sparsecore.rb
djpeg mafft-xinsi
doesitcache make_emperor.py
dustmasker makeblastdb
easy_install makeconv
einsi makembindex
envsubst makeprofiledb
extcheck msgattrib
f2py msgcat
fax2ps msgcmp
fax2tiff msgcomm
fc-cache msgconv
fc-cat msgen
fc-list msgexec
fc-match msgfilter
fc-pattern msgfmt
fc-query msggrep
fc-scan msginit
fc-validate msgmerge
fftns msgunfmt
fftnsi msguniq
freetype-config native2ascii
futurize natsort
gapplication ncurses5-config
gdbus ncursesw5-config
gdbus-codegen ngettext
genbrk nosetests
gencfu nwns
gencnval nwnsi
gendict obj2yaml
genrb openssl
gettext opt
gettext.sh orbd
gettextize pack200
gif2h5 pal2rgb
ginsi pandoc
gio pandoc-citeproc
gio-querymodules pango-view
git-clang-format pasteurize
glib-compile-resources pcre-config
glib-compile-schemas pcregrep
glib-genmarshal pcretest
glib-gettextize pigz
glib-mkenums pip
gobject-query pkgdata
gresource png-fix-itxt
gsettings pngfix
gsl-config policytool
gsl-histogram ppm2tiff
gsl-randist psiblast
gss-client py.test
gtester pydoc
gtester-report pydoc3
h52gif pydoc3.5
h5c++ pygmentize
h5cc pytest
h5copy python
h5debug python3
h5diff python3-config
h5dump python3.5
h5fc python3.5-config
h5import python3.5m
h5jam python3.5m-config
h5ls pyvenv
h5mkgrp pyvenv-3.5
h5perf_serial qiime
h5redeploy raw2tiff
h5repack rdjpgcom
h5repart recode-sr-latin
h5stat reset
h5unjam rmic
hb-ot-shape-closure rmid
hb-shape rmiregistry
hb-view rpsblast
iconv rpstblastn
icu-config run_dada_paired.R
icuinfo run_dada_single.R
idle3 sancov
idle3.5 sanstats
idlj scan-build
ifnames.bak scan-view
indexdb_rna schemagen
infocmp sclient
infotocap segmasker
iptest serialver
iptest3 servertool
ipython set-xcode-analyzer
ipython3 sim_client
jar sortmerna
jarsigner sqlite3
java ssu
javac tab-qiime
javadoc tabs
javah tblastn
javap tblastx
jcmd tclsh
jconsole tclsh8.5
jdb tic
jdeps tiff2bw
jhat tiff2pdf
jinfo tiff2ps
jjs tiff2rgba
jmap tiffcmp
jpegtran tiffcp
jps tiffcrop
jrunscript tiffdither
jsadebugd tiffdump
jsonschema tiffinfo
jstack tiffmedian
jstat tiffset
jstatd tiffsplit
jupyter tnameserv
jupyter-bundlerextension toe
jupyter-kernel tput
jupyter-kernelspec tset
jupyter-migrate unlzma
jupyter-nbconvert unpack200
jupyter-nbextension unpigz
jupyter-notebook unxz
jupyter-run update_blastdb.pl
jupyter-serverextension uuclient
jupyter-troubleshoot verify-uselistorder
jupyter-trust vsearch
k5srvutil wget
kadmin wheel
kdestroy windowmasker
keytool wish
kinit wish8.5
klist wrjpgcom
kpasswd wsgen
krb5-config wsimport
kswitch xgettext
ktutil xjc
kvno xml2-config
legacy_blast.pl xmlcatalog
libpng-config xmllint
libpng16-config xz
linsi xzcat
llc xzcmp
lli xzdec
llvm-ar xzdiff
llvm-as xzegrep
llvm-bcanalyzer xzfgrep
llvm-c-test xzgrep
llvm-cat xzless
llvm-config xzmore
llvm-cov yaml2obj
Erikas-MacBook-Pro:bin ErikaGanda$ cd qiime
-bash: cd: qiime: Not a directory
Erikas-MacBook-Pro:bin ErikaGanda$

Hi @ErikaGanda!

That's a new one. I think you may have gotten bitten by the OS X limitation of 3-days walltime before it starts deleting files. How long was the process running for? If that's the case, then you could try the steps in this post to deal with that for now.

Does the moving pictures tutorial work? Does re-running work?

That is expected, so I think everything is ok there.

Thanks for your patience and help!

2 Likes

Hi @ebolyen! Thanks for following up.
The run took about 3 days. I looked around and couldn’t find the proper way to ask to run DADA2 multi thread. Is that an option?

I have a MAC with 4 processors, if I could use 2 or 3 that would make things better, no?

If that is a possibility where in the command should I write it?

Thanks!!

That would help! You can use --p-threads to add more CPUs to the task (it can be added anywhere). Since you made it to basically the end result, you shouldn't have any issue if you add --p-threads (you can run --help to see a full description of that parameter).

For larger analysis you will need to set your TMPDIR elsewhere (or use linux which is better suited to very long jobs anyhow).

Awesome! Thanks!
I’ll try again.
E

1 Like

It worked!
Thank you so much for guiding me through this.
You guys from the developer team are awesome!

Happy QIIMEing!

2 Likes

Hello, I was getting the return code -11 error so I did the native reinstall and I’m still getting this message:

Plugin error from dada2:

An error was encountered while running DADA2 in R (return code -11), please inspect stdout and stderr to learn more.
Debug info has been saved to /var/folders/8s/s3hc01bn0hq8_x8q4p_bcz5m0000gp/T/qiime2-q2cli-err-oh4_vmf4.log

the debug file says:
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 /var/folders/8s/s3hc01bn0hq8_x8q4p_bcz5m0000gp/T/qiime2-archive-_1z0nz6f/136dce20-b3ec-48ef-8a95-1060d3865983/data /var/folders/8s/s3hc01bn0hq8_x8q4p_bcz5m0000gp/T/tmpv274aw7k/output.tsv.biom /var/folders/8s/s3hc01bn0hq8_x8q4p_bcz5m0000gp/T/tmpv274aw7k 200 0 2.0 2 consensus 1.0 1 1000000

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

*** caught segfault ***
address 0x18, cause ‘memory not mapped’

Traceback:
1: dyn.load(file, DLLpath = DLLpath, …)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ attr(package, “LibPath”) <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else “” msg <- gettextf(“package or namespace load failed for %s%s:\n %s”, sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste(“Error:”, msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(dada2)
11: withCallingHandlers(expr, warning = function(w) invokeRestart(“muffleWarning”))
12: suppressWarnings(library(dada2))
An irrecoverable exception occurred. R is aborting now …
Traceback (most recent call last):
File “/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 126, in denoise_single
run_commands([cmd])
File “/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 35, in run_commands
subprocess.run(cmd, check=True)
File “/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_single.R’, ‘/var/folders/8s/s3hc01bn0hq8_x8q4p_bcz5m0000gp/T/qiime2-archive-_1z0nz6f/136dce20-b3ec-48ef-8a95-1060d3865983/data’, ‘/var/folders/8s/s3hc01bn0hq8_x8q4p_bcz5m0000gp/T/tmpv274aw7k/output.tsv.biom’, ‘/var/folders/8s/s3hc01bn0hq8_x8q4p_bcz5m0000gp/T/tmpv274aw7k’, ‘200’, ‘0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’]’ returned non-zero exit status -11

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py”, line 224, in call
results = action(**arguments)
File “”, line 2, in denoise_single
File “/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 228, in bound_callable
output_types, provenance)
File “/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 363, in callable_executor
output_views = self._callable(**view_args)
File “/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 137, in denoise_single
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code -11), please inspect stdout and stderr to learn more.

Please help.

Hi @bmillerlab, can you please provide the output for the following command?

$ qiime info

Thanks!

Sorry for the delay. Info that I I got is:

$ qiime info
System versions
Python version: 3.5.4
QIIME 2 release: 2017.12
QIIME 2 version: 2017.12.1
q2cli version: 2017.12.0

Installed plugins
alignment 2017.12.0
composition 2017.12.0
cutadapt 2017.12.0
dada2 2017.12.1
deblur 2017.12.0
demux 2017.12.0
diversity 2017.12.0
emperor 2017.12.0
feature-classifier 2017.12.0
feature-table 2017.12.0
gneiss 2017.12.0
longitudinal 2017.12.0
metadata 2017.12.0
phylogeny 2017.12.0
quality-control 2017.12.0
quality-filter 2017.12.0
sample-classifier 2017.12.0
taxa 2017.12.0
types 2017.12.0
vsearch 2017.12.0

Application config directory
/Users/Paige/Library/Application Support/q2cli

Getting help
To get help with QIIME 2, visit https://qiime2.org

Citing QIIME 2
If you use QIIME 2 in any published work, you should cite QIIME 2 and the plugins that you used. To display the citations for QIIME 2 and all installed plugins, run:

qiime info --citations

Hmm, that looks like the right version of QIIME 2 is installed (the one with the patched DADA2), however you are the only user we have heard back from that this patch didn’t work for. Maybe it is worth cleaning up your existing environments and trying to reinstall fresh?

$ conda env remove -n qiime2-2017.12
$ conda clean --all

Then, follow the install directions to reinstall the latest. Please let us know how that goes for you! If it still fails, would you be willing to share your data with us so that we can reproduce the error locally? If so, please upload to a service like Dropbox or Google Drive and share a direct link in a private message to one of us. Thanks! :t_rex:

Hello, Unfortunately this did not help. I’m getting the same error. Whom should receive the shared link?

Feel free to send to me. Thanks!

Here is the link. I put the .gza file in box, since I was able to make that with no problem.

https://ucsb.box.com/s/cuyq6t368swzy471780iljy0s1rk2007

@bmillerlab, I just ran the following:

$ qiime dada2 denoise-single \
  --i-demultiplexed-seqs MOCKN-demux.qza \
  --p-trunc-len 200 \
  --p-trim-left 0 \
  --output-dir dada2-output-2 \
  --verbose
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 /var/folders/kv/fmn2vtxn5pq0c3tl9wv7cbqh0000gn/T/qiime2-archive-p5b1od_0/dd8b7ed3-f333-46ea-8111-ca6d7c2fc0c8/data /var/folders/kv/fmn2vtxn5pq0c3tl9wv7cbqh0000gn/T/tmpwuynbvo9/output.tsv.biom /var/folders/kv/fmn2vtxn5pq0c3tl9wv7cbqh0000gn/T/tmpwuynbvo9 200 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.
Sample 1 - 20628 reads in 11443 unique sequences.
Sample 2 - 10668 reads in 6508 unique sequences.
Sample 3 - 16981 reads in 10001 unique sequences.
Sample 4 - 29777 reads in 16382 unique sequences.
Sample 5 - 18720 reads in 8059 unique sequences.
Sample 6 - 19114 reads in 8096 unique sequences.
Sample 7 - 18022 reads in 7521 unique sequences.
Sample 8 - 21626 reads in 9447 unique sequences.
Sample 9 - 72772 reads in 26514 unique sequences.
   selfConsist step 2
   selfConsist step 3
   selfConsist step 4
Convergence after  4  rounds.

3) Denoise remaining samples
4) Remove chimeras (method = consensus)
5) Report read numbers through the pipeline
                                    input filtered denoised non-chimeric
MOCK-1_XS96_L001_R1_001.fastq.gz    30369    20628    20628        19760
MOCK-2_S191_L001_R1_001.fastq.gz    16821    10668    10668        10375
MOCK-4_S381_L001_R1_001.fastq.gz    26255    16981    16981        16624
MOCK-5_X413_L001_R1_001.fastq.gz    45490    29777    29777        28349
NEG-CON-1_XS95_L001_R1_001.fastq.gz 20517    18720    18720        18328
NEG-CON-2_S192_L001_R1_001.fastq.gz 32987    19114    19114        19081
6) Write output
Saved FeatureTable[Frequency] to: dada2-output-2/table.qza
Saved FeatureData[Sequence] to: dada2-output-2/representative_sequences.qza

As you can see, dada2 successfully ran, at least with those settings.

Can you provide the following information:

  • What was the exact command you ran? Copy and paste please.
  • What are the names of the installed conda environments on your system - run conda env list?
  • After activating your QIIME 2017.12 environment, please run conda list, to show all of the installed packages in that environment.

Thanks! :t_rex:

Hello, Ok, it is my computer because I installed everything on another computer and everything works fine. I'm answering your questions in hopes you can point me in the direction I need to fix this problem. I did not have it with the QIIME 2017.10.

Exact commands I ran in repeat of test with output:
(qiime2-2017.12) miller3:~ Paige$ qiime dada2 denoise-single \

--i-demultiplexed-seqs /Users/Paige/MOCK-NEGCON-ASV/MOCKN-demux.qza
--p-trim-left 0
--p-trunc-len 200
--o-representative-sequences /Users/Paige/MOCK-NEGCON-ASV/MOCKN-repseqs-demux.qza
--o-table /Users/Paige/MOCK-NEGCON-ASV/MOCKN-table-demux.qza
--verbose
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 /var/folders/8s/s3hc01bn0hq8_x8q4p_bcz5m0000gp/T/qiime2-archive-ghk6f6bj/dd8b7ed3-f333-46ea-8111-ca6d7c2fc0c8/data /var/folders/8s/s3hc01bn0hq8_x8q4p_bcz5m0000gp/T/tmpjvf3xmma/output.tsv.biom /var/folders/8s/s3hc01bn0hq8_x8q4p_bcz5m0000gp/T/tmpjvf3xmma 200 0 2.0 2 consensus 1.0 1 1000000

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

*** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(dada2)
11: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
12: suppressWarnings(library(dada2))
An irrecoverable exception occurred. R is aborting now ...
Traceback (most recent call last):
File "/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 126, in denoise_single
run_commands([cmd])
File "/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands
subprocess.run(cmd, check=True)
File "/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_single.R', '/var/folders/8s/s3hc01bn0hq8_x8q4p_bcz5m0000gp/T/qiime2-archive-ghk6f6bj/dd8b7ed3-f333-46ea-8111-ca6d7c2fc0c8/data', '/var/folders/8s/s3hc01bn0hq8_x8q4p_bcz5m0000gp/T/tmpjvf3xmma/output.tsv.biom', '/var/folders/8s/s3hc01bn0hq8_x8q4p_bcz5m0000gp/T/tmpjvf3xmma', '200', '0', '2.0', '2', 'consensus', '1.0', '1', '1000000']' returned non-zero exit status -11

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 224, in call
results = action(**arguments)
File "", line 2, in denoise_single
File "/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
output_types, provenance)
File "/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 363, in callable_executor
output_views = self._callable(**view_args)
File "/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 137, in denoise_single
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code -11), please inspect stdout and stderr to learn more.

Plugin error from dada2:

An error was encountered while running DADA2 in R (return code -11), please inspect stdout and stderr to learn more.

See above for debug info.

Additional info requested:
miller3:~ Paige$ conda env list

conda environments:

base * /Users/Paige/miniconda3
qiime1 /Users/Paige/miniconda3/envs/qiime1
qiime2-2017.12 /Users/Paige/miniconda3/envs/qiime2-2017.12

(qiime2-2017.12) miller3:~ Paige$ conda list

packages in environment at /Users/Paige/miniconda3/envs/qiime2-2017.12:

appnope 0.1.0 py35_0 conda-forge
asn1crypto 0.22.0 py35_0 conda-forge
backports 1.0 py35_1 conda-forge
backports.functools_lru_cache 1.4 py35_1 conda-forge
bioconductor-biobase 2.38.0 r3.4.1_0 bioconda
bioconductor-biocgenerics 0.24.0 r3.4.1_0 bioconda
bioconductor-biocparallel 1.12.0 r3.4.1_0 bioconda
bioconductor-biostrings 2.46.0 r3.4.1_0 bioconda
bioconductor-dada2 1.6.0 r3.4.1_0 bioconda
bioconductor-delayedarray 0.4.1 r3.4.1_0 bioconda
bioconductor-genomeinfodb 1.14.0 r3.4.1_0 bioconda
bioconductor-genomeinfodbdata 1.0.0 r3.4.1_1 bioconda
bioconductor-genomicalignments 1.14.0 r3.4.1_0 bioconda
bioconductor-genomicranges 1.30.0 r3.4.1_0 bioconda
bioconductor-iranges 2.12.0 r3.4.1_0 bioconda
bioconductor-rsamtools 1.30.0 r3.4.1_0 bioconda
bioconductor-s4vectors 0.16.0 r3.4.1_0 bioconda
bioconductor-shortread 1.36.0 r3.4.1_0 bioconda
bioconductor-summarizedexperiment 1.8.0 r3.4.1_0 bioconda
bioconductor-xvector 0.18.0 r3.4.1_0 bioconda
bioconductor-zlibbioc 1.24.0 r3.4.1_0 bioconda
biom-format 2.1.6 py35_8 qiime2
blas 1.1 openblas conda-forge
blast 2.6.0 boost1.64_2 bioconda
bleach 2.0.0 py35_0 conda-forge
bokeh 0.12.13 py35_0 conda-forge
ca-certificates 2017.11.5 0 conda-forge
cachecontrol 0.12.3 py35_0
cairo 1.14.6 4 conda-forge
certifi 2017.11.5 py35_0 conda-forge
cffi 1.11.2 py35_0 conda-forge
chardet 3.0.4 py35_0 conda-forge
clangdev 5.0.0 default_0 conda-forge
click 6.7 py_1 conda-forge
cryptography 2.1.4 py35_0 conda-forge
curl 7.54.1 0 conda-forge
cutadapt 1.15 py35_0 bioconda
cycler 0.10.0 py35_0 conda-forge
cython 0.27.3 py35_0 conda-forge
deblur 1.0.3 py35h7f3a046_0 biocore
decorator 4.1.2 py35_0 conda-forge
emperor 1.0.0beta13 py35_1 conda-forge
entrypoints 0.2.3 py35_1 conda-forge
fastcluster 1.1.24 py35_0 conda-forge
fasttree 2.1.10 0 bioconda
fontconfig 2.12.1 6 conda-forge
freetype 2.7 1 conda-forge
future 0.16.0 py35_0 conda-forge
gettext 0.19.8.1 0 conda-forge
glib 2.51.4 0 conda-forge
gneiss 0.4.2 py35hd262515_6 biocore
graphite2 1.3.10 0 conda-forge
gsl 2.1 2 conda-forge
h5py 2.7.0 np112py35_0 conda-forge
harfbuzz 1.4.3 0 conda-forge
hdf5 1.8.17 11 conda-forge
html5lib 1.0.1 py_0 conda-forge
icu 58.2 0 conda-forge
idna 2.6 py35_1 conda-forge
ijson 2.3 py35_0 qiime2
intel-openmp 2018.0.0 h8158457_8
ipykernel 4.7.0 py35_0 conda-forge
ipython 6.2.1 py35_1 conda-forge
ipython_genutils 0.2.0 py35_0 conda-forge
ipywidgets 7.1.0 py35_0 conda-forge
jedi 0.10.2 py35_0 conda-forge
jinja2 2.10 py35_0 conda-forge
jpeg 9b 2 conda-forge
jsonschema 2.6.0 py35_0 conda-forge
jupyter_client 5.2.1 py35_0 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
krb5 1.14.2 0 conda-forge
libcxx 5.0.0 0 conda-forge
libffi 3.2.1 3 conda-forge
libgcc 4.8.5 hdbeacc1_10
libgfortran 3.0.1 h93005f0_2
libiconv 1.15 0 conda-forge
libpng 1.6.28 1 conda-forge
libsodium 1.0.15 1 conda-forge
libssh2 1.8.0 1 conda-forge
libtiff 4.0.7 0 conda-forge
libxml2 2.9.5 0 conda-forge
llvmdev 5.0.0 default_0 conda-forge
lockfile 0.12.2 py35_0 conda-forge
mafft 7.310 0 bioconda
markupsafe 1.0 py35_0 conda-forge
matplotlib 2.1.1 py35_0 conda-forge
mistune 0.8.3 py_0 conda-forge
mkl 2018.0.1 hfbd8650_4
msgpack-python 0.4.8 py35_0 conda-forge
natsort 5.0.2 py35_0 conda-forge
nbconvert 5.3.1 py_1 conda-forge
nbformat 4.4.0 py35_0 conda-forge
ncurses 5.9 10 conda-forge
nose 1.3.7 py35_2 conda-forge
notebook 5.2.2 py35_1 conda-forge
numpy 1.12.1 py35_blas_openblas_200 [blas_openblas] conda-forge
openblas 0.2.19 2 conda-forge
openjdk 8.0.121 zulu8.20.0.5_0 conda-forge
openssl 1.0.2n 0 conda-forge
pandas 0.22.0 py35_0 conda-forge
pandoc 2.1 0 conda-forge
pandocfilters 1.4.1 py35_0 conda-forge
pango 1.40.4 0 conda-forge
patsy 0.5.0 py35_0 conda-forge
pcre 8.39 0 conda-forge
pexpect 4.3.1 py35_0 conda-forge
pickleshare 0.7.4 py35_0 conda-forge
pigz 2.3.4 0 conda-forge
pip 9.0.1 py35_1 conda-forge
pixman 0.34.0 1 conda-forge
prompt_toolkit 1.0.15 py35_0 conda-forge
psutil 5.4.0 py35_0 conda-forge
ptyprocess 0.5.2 py35_0 conda-forge
pycparser 2.18 py35_0 conda-forge
pygments 2.2.0 py35_0 conda-forge
pyopenssl 17.4.0 py35_0 conda-forge
pyparsing 2.2.0 py35_0 conda-forge
pysocks 1.6.7 py35_0 conda-forge
python 3.5.4 0 conda-forge
python-dateutil 2.6.1 py35_0 conda-forge
pytz 2017.3 py_2 conda-forge
pyyaml 3.12 py35_1 conda-forge
pyzmq 16.0.2 py35_3 conda-forge
q2-alignment 2017.12.0 py35_0 qiime2/label/r2017.12
q2-composition 2017.12.0 py35_0 qiime2/label/r2017.12
q2-cutadapt 2017.12.0 py35_0 qiime2/label/r2017.12
q2-dada2 2017.12.1 py35_0 qiime2/label/r2017.12
q2-deblur 2017.12.0 py35_0 qiime2/label/r2017.12
q2-demux 2017.12.0 py35_0 qiime2/label/r2017.12
q2-diversity 2017.12.0 py35_0 qiime2/label/r2017.12
q2-emperor 2017.12.0 py35_0 qiime2/label/r2017.12
q2-feature-classifier 2017.12.0 py35_0 qiime2/label/r2017.12
q2-feature-table 2017.12.0 py35_0 qiime2/label/r2017.12
q2-gneiss 2017.12.0 py35_0 qiime2/label/r2017.12
q2-longitudinal 2017.12.0 py35_0 qiime2/label/r2017.12
q2-metadata 2017.12.0 py35_0 qiime2/label/r2017.12
q2-phylogeny 2017.12.0 py35_0 qiime2/label/r2017.12
q2-quality-control 2017.12.0 py35_0 qiime2/label/r2017.12
q2-quality-filter 2017.12.0 py35_0 qiime2/label/r2017.12
q2-sample-classifier 2017.12.0 py35_0 qiime2/label/r2017.12
q2-taxa 2017.12.0 py35_0 qiime2/label/r2017.12
q2-types 2017.12.0 py35_0 qiime2/label/r2017.12
q2-vsearch 2017.12.0 py35_0 qiime2/label/r2017.12
q2cli 2017.12.0 py35_0 qiime2/label/r2017.12
q2templates 2017.12.0 py35_0 qiime2/label/r2017.12
qiime2 2017.12.1 py35_0 qiime2/label/r2017.12
r-base 3.4.1 0 conda-forge
r-bh 1.65.0_1 r3.4.1_0 conda-forge
r-bitops 1.0_6 r3.4.1_0 conda-forge
r-colorspace 1.3_2 r3.4.1_0 conda-forge
r-data.table 1.10.4 r3.4.1_0 conda-forge
r-dichromat 2.0_0 r3.4.1_0 conda-forge
r-digest 0.6.12 r3.4.1_0 conda-forge
r-futile.logger 1.4.3 r3.4.1_0 conda-forge
r-futile.options 1.0.0 r3.4.1_0 conda-forge
r-ggplot2 2.2.1 r3.4.1_0 conda-forge
r-gtable 0.2.0 r3.4.1_0 conda-forge
r-hwriter 1.3.2 r3.4.1_0 conda-forge
r-labeling 0.3 r3.4.1_0 conda-forge
r-lambda.r 1.1.9 r3.4.1_0 conda-forge
r-lattice 0.20_34 r3.4.1_0 conda-forge
r-latticeextra 0.6_28 r3.4.1_0 conda-forge
r-lazyeval 0.2.0 r3.4.1_0 conda-forge
r-magrittr 1.5 r3.4.1_0 conda-forge
r-mass 7.3_45 r3.4.1_0 conda-forge
r-matrix 1.2_7.1 r3.4.1_0 conda-forge
r-matrixstats 0.52.2 r3.4.1_0 conda-forge
r-munsell 0.4.3 r3.4.1_0 conda-forge
r-plyr 1.8.4 r3.4.1_0 conda-forge
r-rcolorbrewer 1.1_2 r3.4.1_0 conda-forge
r-rcpp 0.12.13 r3.4.1_0 conda-forge
r-rcppparallel 4.3.20 r3.4.1_0 conda-forge
r-rcurl 1.95_4.8 r3.4.1_0 conda-forge
r-reshape2 1.4.2 r3.4.1_0 conda-forge
r-rlang 0.1.2 r3.4.1_0 conda-forge
r-scales 0.4.1 r3.4.1_0 conda-forge
r-snow 0.4_2 r3.4.1_0 conda-forge
r-stringi 1.1.5 r3.4.1_0 conda-forge
r-stringr 1.2.0 r3.4.1_0 conda-forge
r-tibble 1.3.3 r3.4.1_0 conda-forge
readline 6.2 0 conda-forge
requests 2.18.4 py35_1 conda-forge
scikit-bio 0.5.1 py35_0 qiime2
scikit-learn 0.19.1 py35_blas_openblas_200 [blas_openblas] conda-forge
scipy 0.19.1 py35_blas_openblas_202 [blas_openblas] conda-forge
seaborn 0.8.1 py35_0 conda-forge
setuptools 38.4.0 py35_0 conda-forge
simplegeneric 0.8.1 py35_0 conda-forge
six 1.11.0 py35_1 conda-forge
sortmerna 2.0 1 bioconda
sqlite 3.13.0 1 conda-forge
statsmodels 0.8.0 py35_0 conda-forge
terminado 0.8.1 py35_0 conda-forge
testpath 0.3.1 py35_0 conda-forge
tk 8.5.19 2 conda-forge
tornado 4.5.2 py35_0 conda-forge
traitlets 4.3.2 py35_0 conda-forge
tzlocal 1.3 py35_0 qiime2
unifrac 0.9.2 py35h1806a49_1 biocore
urllib3 1.22 py35_0 conda-forge
vsearch 2.6.0 0 bioconda
wcwidth 0.1.7 py35_0 conda-forge
webencodings 0.5 py35_0 conda-forge
wget 1.18 0
wheel 0.30.0 py35_2 conda-forge
widgetsnbextension 3.1.0 py35_0 conda-forge
xopen 0.3.2 py35_0 bioconda
xz 5.2.3 0 conda-forge
yaml 0.1.7 0 conda-forge
zeromq 4.2.1 1 conda-forge
zlib 1.2.8 3 conda-forge

@bmillerlab, is the impacted computer a Linux machine or a Mac machine? Can you provide some details, what model of computer, what version operating system, anything else worth noting…

If it is linux computer, can you please run the following command:

$ grep avx /proc/cpuinfo

If it is a Mac, please run:

$ sysctl -a | grep machdep.cpu.leaf7_features

Please copy and paste the output. Thanks!

Thanks for trying to help.

It is a macbook pro running OS High Sierra 10.13.2. It works with qiime 1 and it ran qiime 2 through version .10 using these same commands.
Here is the output requested:
$ sysctl -a | grep machdep.cpu.leaf7_features
machdep.cpu.leaf7_features: SMEP ERMS RDWRFSGS TSC_THREAD_OFFSET BMI1 HLE AVX2 BMI2 INVPCID RTM SMAP RDSEED ADX IPT SGX FPU_CSDS MPX CLFSOPT