DADA2 errors - return code 1 and 11

Thanks @ErikaGanda and @Dorothy!

Could you both run this command:

sysctl -a | grep machdep.cpu.leaf7_features

We’re hoping to see an entry for “AVX2”.

Thanks!

Hi @ebolyen!

This is what I got:

dhcp-morris-2820:~ ErikaGanda$ source activate qiime2-2017.12
(qiime2-2017.12) dhcp-morris-2820:~ ErikaGanda$ sysctl -a | grep machdep.cpu.leaf7_features
machdep.cpu.leaf7_features: SMEP ERMS RDWRFSGS TSC_THREAD_OFFSET BMI1 AVX2 BMI2 INVPCID
(qiime2-2017.12) dhcp-morris-2820:~ ErikaGanda$

Thanks @ErikaGanda!

Based on this and @Peris’s response, I think we can rule out missing-AVX2 as the problem. @ErikaGanda can you reproduce this problem with the moving pictures tutorial as well?

Actually I have an even better idea. Could you run this in your QIIME 2 environment:

conda install pytest
pytest --pyargs q2_dada2

It should produce a bunch of output, but you should see all the tests pass. If they don’t that gives us a really easy target while we figure out what is happening.

dhcp-morris-2820:~ ErikaGanda$ source activate qiime2-2017.12
(qiime2-2017.12) dhcp-morris-2820:~ ErikaGanda$ conda install pytest
Fetching package metadata …
Solving package specifications: .

Package plan for installation in environment /Users/ErikaGanda/miniconda3/envs/qiime2-2017.12:

The following NEW packages will be INSTALLED:

attrs:          17.3.0-py35hc219a11_0
coverage:       4.4.2-py35h36907ce_0 
hypothesis:     3.38.5-py35h843401b_0
pluggy:         0.6.0-py35hf57b818_0 
py:             1.5.2-py35h4d4d87d_0 
pympler:        0.5-py35hf41ee38_0   
pytest:         3.3.0-py35hfa6e833_0 
zope:           1.0-py35_0           
zope.interface: 4.4.3-py35hdbc5dd8_0 

Proceed ([y]/n)? pytest --pyargs q2_dada2y
Invalid choice: pytest --pyargs q2_dada2y
Proceed ([y]/n)? y

coverage-4.4.2 100% |################################| Time: 0:00:00 2.79 MB/s
pluggy-0.6.0-p 100% |################################| Time: 0:00:00 11.35 MB/s
py-1.5.2-py35h 100% |################################| Time: 0:00:00 4.35 MB/s
pympler-0.5-py 100% |################################| Time: 0:00:00 4.82 MB/s
zope-1.0-py35_ 100% |################################| Time: 0:00:00 1.44 MB/s
zope.interface 100% |################################| Time: 0:00:00 5.95 MB/s
attrs-17.3.0-p 100% |################################| Time: 0:00:00 9.21 MB/s
hypothesis-3.3 100% |################################| Time: 0:00:00 6.14 MB/s
pytest-3.3.0-p 100% |################################| Time: 0:00:00 7.20 MB/s
(qiime2-2017.12) dhcp-morris-2820:~ ErikaGanda$ pytest --pyargs q2_dada2
============================= test session starts ==============================
platform darwin – Python 3.5.4, pytest-3.3.0, py-1.5.2, pluggy-0.6.0
rootdir: /Users/ErikaGanda, inifile:
plugins: hypothesis-3.38.5
collected 11 items

miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/tests/test_denoise.py . [ 9%]
… [100%]
===================================================================== 11 passed in 181.17 seconds ======================================================================
It doesn’t look like anything failed.
Any other thoughts @ebolyen?

Hi @ebolyen, I cannot reproduce the same problem with the moving pictures tutorial.
I started running both my data and the moving pictures in two different terminals. The output of the tutorial looks fine:

Last login: Wed Jan 3 14:13:16 on ttys000
dhcp-morris-2820:~ ErikaGanda$ cd /Users/ErikaGanda/Desktop/qiime2-moving-pictures-tutorial
dhcp-morris-2820:qiime2-moving-pictures-tutorial ErikaGanda$ ls
demux.qza emp-single-end-sequences
demux.qzv sample-metadata.tsv
dhcp-morris-2820:qiime2-moving-pictures-tutorial ErikaGanda$ source activate qiime2-2017.12
(qiime2-2017.12) dhcp-morris-2820:qiime2-moving-pictures-tutorial ErikaGanda$ qiime dada2 denoise-single \

--i-demultiplexed-seqs demux.qza
--p-trim-left 0
--p-trunc-len 120
--o-representative-sequences rep-seqs-dada2.qza
--o-table table-dada2.qza
Saved FeatureTable[Frequency] to: table-dada2.qza
Saved FeatureData[Sequence] to: rep-seqs-dada2.qza
(qiime2-2017.12) dhcp-morris-2820:qiime2-moving-pictures-tutorial ErikaGanda$

My data is still running. If I get another error I will post here. I went back and my demultiplexing files look ok:
rumen-demux.qzv (283.5 KB)

A while ago I had DADA2 give me errors and @jairideout helped me in this post: DADA2 error (return code -5) - #10 by jairideout
Maybe something similar is going on this time around?

Thanks again!!

Thanks for the info @ErikaGanda!

Would you be able to share your data? We’re starting to lean towards something about the data tripping things up. If we can reproduce locally we can start actually debugging the code itself to figure out what’s going on.

Thanks!

Sure thing. Which files do you need @ebolyen?

Thanks @ErikaGanda! rumen-demux.qza would let us run your dada2 denoise-single command from above!

There you go. Let me know if there is anything else I can do!
E

Actually, it looks like the file uploads to 100% in the browser but I don’t see it on the message. Is there any other way I can send you the file? The size is 448.3 MB

Do you have the ability to create a Dropbox or Google Drive link? 450MB is too large for the forum, unfortunately.

@ErikaGanda if you are able, would you also be able to try this out:

conda create -n DONOTUSE --file  https://data.qiime2.org/distro/core/qiime2-2017.12-conda-osx-64.txt
source activate DONOTUSE
wget -qO- https://forum-qiime2-org.s3-us-west-2.amazonaws.com/original/1X/ac621debfd04f561bf1075b4efa56c0e947a1928.txt > `which run_dada_single.R`
wget -qO- https://forum-qiime2-org.s3-us-west-2.amazonaws.com/original/1X/07fa5193f904022996a35a963b12b9ac79dbb1f4.txt > `which run_dada_paired.R`

This will create a dummy environment and patch two files to behave a little differently. If you could try it out on your dataset to see if it crashes the same way, that would be awesome!

Thanks so much for all your help so far!

1 Like

https://cornell.box.com/s/nm5gik81mdp0brwsojznazxqo7ag37p5

There you go!

1 Like

Qiime2 developers: THANK YOU SO MUCH for helping me through this!

I just got an error while running DADA2 on my dataset.
Output is below:

(qiime2-2017.12) dhcp-morris-2820:Rumen ErikaGanda$ ls
Rumen-sequences.qza RumenReads rumen-demux.qzv
RumenMap.tsv rumen-demux.qza
(qiime2-2017.12) dhcp-morris-2820: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-q3jvvitx/a6d39a9d-42e3-4f5d-a135-8c762b4c1ae7/data /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmp2p4lt4re/output.tsv.biom /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmp2p4lt4re 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.

*** caught segfault ***
address 0x8, cause 'memory not mapped'

Traceback:
1: .Call("_dada2_dada_uniques", PACKAGE = "dada2", seqs, abundances, err, quals, score, gap, use_kmers, kdist_cutoff, band_size, omegaA, max_clust, min_fold, min_hamming, min_abund, use_quals, final_consensus, vectorized_alignment, homo_gap, multithread, verbose, SSE)
2: dada_uniques(names(derep[[i]]$uniques), unname(derep[[i]]$uniques), err, qi, opts[["SCORE_MATRIX"]], opts[["GAP_PENALTY"]], opts[["USE_KMERS"]], opts[["KDIST_CUTOFF"]], opts[["BAND_SIZE"]], opts[["OMEGA_A"]], if (initializeErr) { 1 } else { opts[["MAX_CLUST"]] }, opts[["MIN_FOLD"]], opts[["MIN_HAMMING"]], opts[["MIN_ABUNDANCE"]], TRUE, FALSE, opts[["VECTORIZED_ALIGNMENT"]], opts[["HOMOPOLYMER_GAP_PENALTY"]], multithread, (verbose >= 2), opts[["SSE"]])
3: dada(drps[1:i], err = NULL, selfConsist = TRUE, multithread = multithread, VECTORIZED_ALIGNMENT = FALSE, SSE = 2)
An irrecoverable exception occurred. R is aborting now ...
Traceback (most recent call last):
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 126, in denoise_single
run_commands([cmd])
File "/Users/ErikaGanda/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/ErikaGanda/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/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/qiime2-archive-q3jvvitx/a6d39a9d-42e3-4f5d-a135-8c762b4c1ae7/data', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmp2p4lt4re/output.tsv.biom', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmp2p4lt4re', '270', '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/ErikaGanda/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/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
output_types, provenance)
File "/Users/ErikaGanda/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/ErikaGanda/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.
(qiime2-2017.12) dhcp-morris-2820:Rumen ErikaGanda$

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!

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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!!