Note:
Please note that this is a followup issue to @Heather_Maughan 's issue HERE.
I am opening a new issue because the above topic/issue has been locked due to inactivity. If the moderators would prefer to unlock the topic, I will gladly delete this one.
Problem
@lzgles and I are trying to run dada2 on a new computer and are running into incompatibility issues between the installed version (54.0.0) and the required/expected version (55.0.0) of r-png/png.dlyib.
Command resulting in error
qiime dada2 denoise-paired --i-demultiplexed-seqs demux_2.qza --o-table dada2_table_2 --o-representative-sequences representative_sequences_2 --p-trunc-len-f 220 --p-trunc-len-r 120 --p-trim-left-f 19 --p-trim-left-r 20 --p-n-threads 0 --p-n-reads-learn 1000000 --o-denoising-stats denoising-stats_2.qza --verbose &
stdout/stderr output
(qiime2-2022.8) [email protected] ~/Documents/Soils2 % qiime dada2 denoise-paired --i-demultiplexed-seqs demux_2.qza --o-table dada2_table_2 --o-representative-sequences representative_sequences_2 --p-trunc-len-f 220 --p-trunc-len-r 120 --p-trim-left-f 19 --p-trim-left-r 20 --p-n-threads 0 --p-n-reads-learn 1000000 --o-denoising-stats denoising-stats_2.qza --verbose &
[1] 9222
(qiime2-2022.8) [email protected] ~/Documents/Soils2 % 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.R --input_directory /var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/forward --input_directory_reverse /var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/reverse --output_path /var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/output.tsv.biom --output_track /var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/track.tsv --filtered_directory /var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/filt_f --filtered_directory_reverse /var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/filt_r --truncation_length 220 --truncation_length_reverse 120 --trim_left 19 --trim_left_reverse 20 --max_expected_errors 2.0 --max_expected_errors_reverse 2.0 --truncation_quality_score 2 --min_overlap 12 --pooling_method independent --chimera_method consensus --min_parental_fold 1.0 --allow_one_off False --num_threads 0 --learn_min_reads 1000000
R version 4.1.3 (2022-03-10)
Loading required package: Rcpp
Error: package or namespace load failed for ‘dada2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/micro/miniconda3/envs/qiime2-2022.8/lib/R/library/png/libs/png.dylib':
dlopen(/Users/micro/miniconda3/envs/qiime2-2022.8/lib/R/library/png/libs/png.dylib, 6): Library not loaded: @rpath/libpng16.16.dylib
Referenced from: /Users/micro/miniconda3/envs/qiime2-2022.8/lib/R/library/png/libs/png.dylib
Reason: Incompatible library version: png.dylib requires version 55.0.0 or later, but libpng16.16.dylib provides version 54.0.0
Execution halted
Traceback (most recent call last):
File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 308, in denoise_paired
run_commands([cmd])
File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/forward', '--input_directory_reverse', '/var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/reverse', '--output_path', '/var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/output.tsv.biom', '--output_track', '/var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/track.tsv', '--filtered_directory', '/var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/filt_f', '--filtered_directory_reverse', '/var/folders/wp/4llc60893m72l8v1y1837fph0000gn/T/tmpfka43u_g/filt_r', '--truncation_length', '220', '--truncation_length_reverse', '120', '--trim_left', '19', '--trim_left_reverse', '20', '--max_expected_errors', '2.0', '--max_expected_errors_reverse', '2.0', '--truncation_quality_score', '2', '--min_overlap', '12', '--pooling_method', 'independent', '--chimera_method', 'consensus', '--min_parental_fold', '1.0', '--allow_one_off', 'False', '--num_threads', '0', '--learn_min_reads', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__
results = action(**arguments)
File "<decorator-gen-292>", line 2, in denoise_paired
File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self._callable_executor_(scope, callable_args,
File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in _callable_executor_
output_views = self._callable(**view_args)
File "/Users/micro/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 321, in denoise_paired
raise Exception("An error was encountered while running DADA2"
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
See above for debug info.
[1] + exit 1 qiime dada2 denoise-paired --i-demultiplexed-seqs demux_2.qza --o-table
Computer and Environment/Session Info
Computer
- iMac (Retina 5K, 27-inch, 2020)
- macOS Catalina v 10.15.7
- 3.6 GHz 10-Core Intel Core i9
- 128 GB 2667 MHz DDR4
Conda and QIIME versions
Note:
- miniconda was installed according to the "regular" instructions here.
- QIIME2 was (natively) installed following the instructions here.
- homebrew/brew is not used on this machine so there should be no conflicts due to conflicts with different installed versions (as @colinbrislawn suggested might be the case)
(qiime2-2022.8) [email protected] ~ % conda --version
conda 22.11.1
(qiime2-2022.8) [email protected] ~ % qiime --version
q2cli version 2022.8.0
Run `qiime info` for more version details.
conda info
(qiime2-2022.8) [email protected] ~ % conda info
active environment : qiime2-2022.8
active env location : /Users/micro/miniconda3/envs/qiime2-2022.8
shell level : 1
user config file : /Users/micro/.condarc
populated config files : /Users/micro/.condarc
conda version : 22.11.1
conda-build version : not installed
python version : 3.9.12.final.0
virtual packages : __archspec=1=x86_64
__osx=10.15.7=0
__unix=0=0
base environment : /Users/micro/miniconda3 (writable)
conda av data dir : /Users/micro/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /Users/micro/miniconda3/pkgs
/Users/micro/.conda/pkgs
envs directories : /Users/micro/miniconda3/envs
/Users/micro/.conda/envs
platform : osx-64
user-agent : conda/22.11.1 requests/2.28.1 CPython/3.9.12 Darwin/19.6.0 OSX/10.15.7
UID:GID : 501:20
netrc file : None
offline mode : False
qiime (environment) packages
(qiime2-2022.8) [email protected] ~ % conda list
# packages in environment at /Users/micro/miniconda3/envs/qiime2-2022.8:
#
# Name Version Build Channel
_r-mutex 1.0.1 anacondar_1 conda-forge
appnope 0.1.3 pyhd8ed1ab_0 conda-forge
asttokens 2.0.8 pyhd8ed1ab_0 conda-forge
atpublic 3.0.1 pyhd8ed1ab_0 conda-forge
attrs 22.1.0 pyh71513ae_1 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
bibtexparser 1.3.0 pyhd8ed1ab_0 conda-forge
bioconductor-biobase 2.54.0 r41h3be46a4_2 bioconda
bioconductor-biocgenerics 0.40.0 r41hdfd78af_0 bioconda
bioconductor-biocparallel 1.28.3 r41hb890f52_1 bioconda
bioconductor-biostrings 2.62.0 r41h3be46a4_2 bioconda
bioconductor-dada2 1.22.0 r41hb890f52_2 bioconda
bioconductor-delayedarray 0.20.0 r41h3be46a4_2 bioconda
bioconductor-genomeinfodb 1.30.0 r41hdfd78af_0 bioconda
bioconductor-genomeinfodbdata 1.2.7 r41hdfd78af_2 bioconda
bioconductor-genomicalignments 1.30.0 r41h3be46a4_2 bioconda
bioconductor-genomicranges 1.46.1 r41h3be46a4_1 bioconda
bioconductor-iranges 2.28.0 r41h3be46a4_2 bioconda
bioconductor-matrixgenerics 1.6.0 r41hdfd78af_0 bioconda
bioconductor-rhtslib 1.26.0 r41h3be46a4_2 bioconda
bioconductor-rsamtools 2.10.0 r41hb890f52_2 bioconda
bioconductor-s4vectors 0.32.3 r41haba8685_0 bioconda
bioconductor-shortread 1.52.0 r41hb890f52_2 bioconda
bioconductor-summarizedexperiment 1.24.0 r41hdfd78af_0 bioconda
bioconductor-xvector 0.34.0 r41h3be46a4_2 bioconda
bioconductor-zlibbioc 1.40.0 r41h3be46a4_2 bioconda
biom-format 2.1.12 py38hbd87e4b_2 conda-forge
blast 2.12.0 h0370960_3 bioconda
bokeh 2.4.3 pyhd8ed1ab_3 conda-forge
bowtie2 2.4.5 py38h85b03c0_3 bioconda
brotli 1.0.9 hb7f2c08_8 conda-forge
brotli-bin 1.0.9 hb7f2c08_8 conda-forge
brotlipy 0.7.0 py38hef030d1_1005 conda-forge
bwidget 1.9.14 h694c41f_1 conda-forge
bzip2 1.0.8 h0d85af4_4 conda-forge
c-ares 1.18.1 h0d85af4_0 conda-forge
ca-certificates 2022.6.15.2 h033912b_0 conda-forge
cachecontrol 0.12.11 pyhd8ed1ab_0 conda-forge
cairo 1.16.0 h904041c_1013 conda-forge
cctools_osx-64 973.0.1 h3eff9a4_10 conda-forge
certifi 2022.6.15.2 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py38hb368cf1_3 conda-forge
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
clang 14.0.4 h694c41f_0 conda-forge
clang-14 14.0.4 default_h55ffa42_0 conda-forge
clang_osx-64 14.0.4 h3a95cd4_2 conda-forge
clangxx 14.0.4 default_h55ffa42_0 conda-forge
clangxx_osx-64 14.0.4 he1dbc44_2 conda-forge
click 8.1.3 unix_pyhd8ed1ab_2 conda-forge
colorama 0.4.5 pyhd8ed1ab_0 conda-forge
compiler-rt 14.0.4 h7fcd477_0 conda-forge
compiler-rt_osx-64 14.0.4 h6df654d_0 conda-forge
cryptography 37.0.4 py38h0f8513e_0 conda-forge
curl 7.83.1 h372c54d_0 conda-forge
cutadapt 4.1 py38h431a6f7_1 bioconda
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.32 py38h4cd09af_1 conda-forge
deblur 1.1.1 pyhdfd78af_0 bioconda
debugpy 1.6.3 py38h4cd09af_1 conda-forge
decorator 4.4.2 py_0 conda-forge
dendropy 4.5.2 pyh3252c3a_0 bioconda
dill 0.3.5.1 pyhd8ed1ab_0 conda-forge
dnaio 0.9.1 py38h431a6f7_1 bioconda
emperor 1.0.3 py38h50d1736_0 conda-forge
entrez-direct 16.2 h193322a_1 bioconda
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
executing 1.0.0 pyhd8ed1ab_0 conda-forge
expat 2.4.8 h96cf925_0 conda-forge
fastcluster 1.2.6 py38hec72209_2 conda-forge
fasttree 2.1.11 hdcdfbac_1 bioconda
flufl.lock 7.1 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.0 h5bb23bf_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.37.1 py38hef030d1_0 conda-forge
freetype 2.12.1 h3f81eb7_0 conda-forge
fribidi 1.0.10 hbcb3906_0 conda-forge
future 0.18.2 pyhd8ed1ab_6 conda-forge
gettext 0.19.8.1 hd1a6beb_1008 conda-forge
gfortran_impl_osx-64 9.5.0 h2221f41_25 conda-forge
gfortran_osx-64 9.5.0 h18f7dce_0 conda-forge
gmp 6.2.1 h2e338ed_0 conda-forge
gneiss 0.4.6 py_0 bioconda
graphite2 1.3.13 h2e338ed_1001 conda-forge
gsl 2.7 h93259b0_0 conda-forge
h5py 2.10.0 nompi_py38h9a16e60_106 conda-forge
harfbuzz 5.1.0 h00bb2c2_0 conda-forge
hdf5 1.10.6 nompi_hc5d9132_1114 conda-forge
hdmedians 0.14.2 py38hbd87e4b_3 conda-forge
hmmer 3.1b2 3 bioconda
htslib 1.15.1 hc057d7f_0 bioconda
icu 70.1 h96cf925_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
ijson 3.1.3 pyhd3deb0d_0 conda-forge
importlib-metadata 4.11.4 py38h50d1736_0 conda-forge
importlib_resources 5.9.0 pyhd8ed1ab_0 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
iow 1.0.5 py38hb139fc8_1 bioconda
ipykernel 6.15.2 pyh736e0ef_0 conda-forge
ipython 8.5.0 pyhd1c38e8_1 conda-forge
ipywidgets 8.0.2 pyhd8ed1ab_1 conda-forge
iqtree 2.2.0.3 h135ad0d_1 bioconda
isa-l 2.30.0 h0d85af4_4 conda-forge
isl 0.22.1 hb1e8313_2 conda-forge
jedi 0.18.1 pyhd8ed1ab_2 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9e hac89ed1_2 conda-forge
jsonschema 4.15.0 pyhd8ed1ab_0 conda-forge
jupyter_client 7.3.5 pyhd8ed1ab_0 conda-forge
jupyter_core 4.11.1 py38h50d1736_1 conda-forge
jupyterlab_widgets 3.0.3 pyhd8ed1ab_0 conda-forge
kiwisolver 1.4.4 py38h98b9b1b_1 conda-forge
krb5 1.19.3 hb49756b_0 conda-forge
lcms2 2.12 h577c468_0 conda-forge
ld64_osx-64 609 h1e06c2b_10 conda-forge
lerc 3.0 he49afe7_0 conda-forge
libblas 3.9.0 16_osx64_openblas conda-forge
libbrotlicommon 1.0.9 hb7f2c08_8 conda-forge
libbrotlidec 1.0.9 hb7f2c08_8 conda-forge
libbrotlienc 1.0.9 hb7f2c08_8 conda-forge
libcblas 3.9.0 16_osx64_openblas conda-forge
libclang-cpp14 14.0.4 default_h55ffa42_0 conda-forge
libcurl 7.83.1 h372c54d_0 conda-forge
libcxx 14.0.6 hccf4f1f_0 conda-forge
libdeflate 1.10 h0d85af4_0 conda-forge
libedit 3.1.20191231 h0678c8f_2 conda-forge
libev 4.33 haf1e3a3_1 conda-forge
libffi 3.4.2 h0d85af4_5 conda-forge
libgfortran 5.0.0 11_3_0_h97931a8_27 conda-forge
libgfortran-devel_osx-64 9.5.0 hc2d6858_27 conda-forge
libgfortran5 11.3.0 h082f757_27 conda-forge
libglib 2.72.1 hfbcb929_0 conda-forge
libiconv 1.16 haf1e3a3_0 conda-forge
libidn2 2.3.3 hac89ed1_0 conda-forge
liblapack 3.9.0 16_osx64_openblas conda-forge
liblapacke 3.9.0 16_osx64_openblas conda-forge
libllvm10 10.0.1 h009f743_3 conda-forge
libllvm13 13.0.1 h64f94b2_2 conda-forge
libllvm14 14.0.4 h41df66c_0 conda-forge
libnghttp2 1.47.0 h7cbc4dc_1 conda-forge
libopenblas 0.3.21 openmp_h429af6e_3 conda-forge
libpng 1.6.37 h5481273_4 conda-forge
libsodium 1.0.18 hbcb3906_1 conda-forge
libsqlite 3.39.3 ha978bb4_0 conda-forge
libssh2 1.10.0 h7535e13_3 conda-forge
libtiff 4.4.0 hfca7e8f_0 conda-forge
libunistring 0.9.10 h0d85af4_0 conda-forge
libwebp-base 1.2.4 h775f41a_0 conda-forge
libxcb 1.13 h0d85af4_1004 conda-forge
libxml2 2.9.14 hea49891_4 conda-forge
libxslt 1.1.35 heaa0ce8_0 conda-forge
libzlib 1.2.12 hfd90126_4 conda-forge
llvm-openmp 14.0.4 ha654fa7_0 conda-forge
llvm-tools 14.0.4 h41df66c_0 conda-forge
llvmlite 0.36.0 py38h872f124_0 conda-forge
lockfile 0.12.2 py_1 conda-forge
lxml 4.9.1 py38h0dd4459_0 conda-forge
lz4 4.0.0 py38h10aaa5c_3 conda-forge
lz4-c 1.9.3 he49afe7_1 conda-forge
mafft 7.505 ha5712d3_0 bioconda
make 4.3 h22f3db7_1 conda-forge
markupsafe 2.1.1 py38hef030d1_2 conda-forge
matplotlib 3.5.3 py38h50d1736_2 conda-forge
matplotlib-base 3.5.3 py38hae485fc_2 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mpc 1.2.1 hbb51d92_0 conda-forge
mpfr 4.1.0 h0f52abe_1 conda-forge
msgpack-python 1.0.4 py38h98b9b1b_1 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
natsort 8.2.0 pyhd8ed1ab_0 conda-forge
nbformat 5.4.0 pyhd8ed1ab_0 conda-forge
ncurses 6.3 h96cf925_1 conda-forge
nest-asyncio 1.5.5 pyhd8ed1ab_0 conda-forge
networkx 2.8.6 pyhd8ed1ab_0 conda-forge
nose 1.3.7 py_1006 conda-forge
numba 0.53.1 py38h5b9a75a_1 conda-forge
numpy 1.23.2 py38h84cd246_0 conda-forge
openjdk 17.0.3 hbc0c0cd_2 conda-forge
openjpeg 2.5.0 h5d0d7b0_1 conda-forge
openssl 1.1.1q hfd90126_1 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.4.4 py38h5e0dbaf_0 conda-forge
pango 1.50.9 hc8ec20f_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
patsy 0.5.2 pyhd8ed1ab_0 conda-forge
pbzip2 1.1.13 h9d27c22_1 conda-forge
pcre 8.45 he49afe7_0 conda-forge
pcre2 10.37 h3f55489_1 conda-forge
perl 5.32.1 2_h0d85af4_perl5 conda-forge
perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge
perl-compress-raw-bzip2 2.201 pl5321h775f41a_0 conda-forge
perl-compress-raw-zlib 2.202 pl5321h775f41a_0 conda-forge
perl-encode 3.19 pl5321hb7f2c08_0 conda-forge
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge
perl-extutils-makemaker 7.64 pl5321hd8ed1ab_0 conda-forge
perl-io-compress 2.106 pl5321h9722bc1_1 bioconda
perl-io-zlib 1.11 pl5321hdfd78af_0 bioconda
perl-json 4.09 pl5321hdfd78af_0 bioconda
perl-json-xs 2.34 pl5321hcd10b59_5 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321ha5712d3_1 bioconda
perl-parent 0.238 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321h775f41a_0 conda-forge
perl-scalar-list-utils 1.63 pl5321h775f41a_0 conda-forge
perl-storable 3.15 pl5321h775f41a_0 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pigz 2.6 h5dbffcc_0 conda-forge
pillow 9.2.0 py38h7bff4d5_2 conda-forge
pip 22.2.2 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 hbcb3906_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 pyhd8ed1ab_5 conda-forge
prompt-toolkit 3.0.31 pyha770c72_0 conda-forge
psutil 5.9.2 py38hef030d1_0 conda-forge
pthread-stubs 0.4 hc929b4f_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
py 1.11.0 pyh6c4a22f_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.13.0 pyhd8ed1ab_0 conda-forge
pynndescent 0.5.7 pyh6c4a22f_0 conda-forge
pyopenssl 22.0.0 pyhd8ed1ab_1 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyrsistent 0.18.1 py38hef030d1_2 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytest 7.1.3 py38h50d1736_0 conda-forge
python 3.8.13 h394c593_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.16.1 pyhd8ed1ab_0 conda-forge
python-isal 1.0.1 py38h35d34b1_0 conda-forge
python_abi 3.8 3_cp38 conda-forge
pytz 2022.2.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 py38hef030d1_5 conda-forge
pyzmq 23.2.1 py38hde384ec_0 conda-forge
q2-alignment 2022.8.0 py38_0 qiime2/label/r2022.8
q2-composition 2022.8.0 py38_0 qiime2/label/r2022.8
q2-cutadapt 2022.8.0 py38_0 qiime2/label/r2022.8
q2-dada2 2022.8.0 py38_0 qiime2/label/r2022.8
q2-deblur 2022.8.0 py38_0 qiime2/label/r2022.8
q2-demux 2022.8.0 py38_0 qiime2/label/r2022.8
q2-diversity 2022.8.0 py38_0 qiime2/label/r2022.8
q2-diversity-lib 2022.8.0 py38_0 qiime2/label/r2022.8
q2-emperor 2022.8.0 py38_0 qiime2/label/r2022.8
q2-feature-classifier 2022.8.0 py38_0 qiime2/label/r2022.8
q2-feature-table 2022.8.1 py38_0 qiime2/label/r2022.8
q2-fragment-insertion 2022.8.0 py38_0 qiime2/label/r2022.8
q2-gneiss 2022.8.0 py38_0 qiime2/label/r2022.8
q2-longitudinal 2022.8.0 py38_0 qiime2/label/r2022.8
q2-metadata 2022.8.0 py38_0 qiime2/label/r2022.8
q2-mystery-stew 2022.8.0 py38_0 qiime2/label/r2022.8
q2-phylogeny 2022.8.0 py38_0 qiime2/label/r2022.8
q2-quality-control 2022.8.0 py38_0 qiime2/label/r2022.8
q2-quality-filter 2022.8.0 py38_0 qiime2/label/r2022.8
q2-sample-classifier 2022.8.0 py38_0 qiime2/label/r2022.8
q2-taxa 2022.8.0 py38_0 qiime2/label/r2022.8
q2-types 2022.8.0 py38_0 qiime2/label/r2022.8
q2-vsearch 2022.8.0 py38_0 qiime2/label/r2022.8
q2cli 2022.8.0 py38_0 qiime2/label/r2022.8
q2galaxy 2022.8.1 py38_0 qiime2/label/r2022.8
q2templates 2022.8.0 py38_0 qiime2/label/r2022.8
qiime2 2022.8.3 py38_0 qiime2/label/r2022.8
r-backports 1.4.1 r41h815d134_1 conda-forge
r-base 4.1.3 h85fa70c_2 conda-forge
r-bh 1.78.0_0 r41hc72bb7e_1 conda-forge
r-bitops 1.0_7 r41h815d134_1 conda-forge
r-brio 1.1.3 r41h815d134_1 conda-forge
r-callr 3.7.2 r41hc72bb7e_1 conda-forge
r-cli 3.4.0 r41h49197e3_0 conda-forge
r-cluster 2.1.3 r41h1e4e481_1 conda-forge
r-colorspace 2.0_3 r41h815d134_1 conda-forge
r-crayon 1.5.1 r41hc72bb7e_0 conda-forge
r-deldir 1.0_6 r41h1e4e481_1 conda-forge
r-desc 1.4.2 r41hc72bb7e_1 conda-forge
r-diffobj 0.3.5 r41h815d134_1 conda-forge
r-digest 0.6.29 r41h49197e3_1 conda-forge
r-ellipsis 0.3.2 r41h815d134_1 conda-forge
r-evaluate 0.16 r41hc72bb7e_0 conda-forge
r-fansi 1.0.3 r41h815d134_1 conda-forge
r-farver 2.1.1 r41h49197e3_1 conda-forge
r-formatr 1.12 r41hc72bb7e_1 conda-forge
r-fs 1.5.2 r41h49197e3_2 conda-forge
r-futile.logger 1.4.3 r41hc72bb7e_1004 conda-forge
r-futile.options 1.0.1 r41hc72bb7e_1003 conda-forge
r-getopt 1.20.3 r41ha770c72_3 conda-forge
r-ggplot2 3.3.6 r41hc72bb7e_1 conda-forge
r-glue 1.6.2 r41h815d134_1 conda-forge
r-gtable 0.3.1 r41hc72bb7e_1 conda-forge
r-hwriter 1.3.2.1 r41hc72bb7e_1 conda-forge
r-interp 1.1_3 r41h49197e3_1 conda-forge
r-isoband 0.2.5 r41h9951f98_0 conda-forge
r-jpeg 0.1_9 r41h815d134_1 conda-forge
r-jsonlite 1.8.0 r41h0f1d5c4_0 conda-forge
r-labeling 0.4.2 r41hc72bb7e_2 conda-forge
r-lambda.r 1.2.4 r41hc72bb7e_2 conda-forge
r-lattice 0.20_45 r41h815d134_1 conda-forge
r-latticeextra 0.6_30 r41hc72bb7e_1 conda-forge
r-lifecycle 1.0.1 r41hc72bb7e_0 conda-forge
r-magrittr 2.0.3 r41h815d134_1 conda-forge
r-mass 7.3_58.1 r41h815d134_1 conda-forge
r-matrix 1.4_1 r41hce01bf1_1 conda-forge
r-matrixstats 0.62.0 r41h815d134_1 conda-forge
r-mgcv 1.8_40 r41h40f944a_1 conda-forge
r-munsell 0.5.0 r41hc72bb7e_1005 conda-forge
r-nlme 3.1_159 r41h1e4e481_1 conda-forge
r-optparse 1.7.3 r41hc72bb7e_1 conda-forge
r-permute 0.9_7 r41hc72bb7e_1 conda-forge
r-pillar 1.8.1 r41hc72bb7e_1 conda-forge
r-pkgconfig 2.0.3 r41hc72bb7e_2 conda-forge
r-pkgload 1.3.0 r41hc72bb7e_1 conda-forge
r-plyr 1.8.7 r41h49197e3_1 conda-forge
r-png 0.1_7 r41h815d134_1005 conda-forge
r-praise 1.0.0 r41hc72bb7e_1006 conda-forge
r-processx 3.7.0 r41h815d134_1 conda-forge
r-ps 1.7.1 r41h815d134_1 conda-forge
r-r6 2.5.1 r41hc72bb7e_1 conda-forge
r-rcolorbrewer 1.1_3 r41h785f33e_1 conda-forge
r-rcpp 1.0.9 r41h49197e3_2 conda-forge
r-rcppeigen 0.3.3.9.2 r41h4f1a15b_1 conda-forge
r-rcppparallel 5.1.5 r41h49197e3_1 conda-forge
r-rcurl 1.98_1.8 r41h67d6963_0 conda-forge
r-rematch2 2.1.2 r41hc72bb7e_2 conda-forge
r-reshape2 1.4.4 r41h49197e3_2 conda-forge
r-rlang 1.0.5 r41h49197e3_0 conda-forge
r-rprojroot 2.0.3 r41hc72bb7e_1 conda-forge
r-scales 1.2.1 r41hc72bb7e_1 conda-forge
r-snow 0.4_4 r41hc72bb7e_1 conda-forge
r-stringi 1.7.8 r41h7183e51_1 conda-forge
r-stringr 1.4.1 r41hc72bb7e_1 conda-forge
r-testthat 3.1.4 r41h8619c4b_0 conda-forge
r-tibble 3.1.8 r41h815d134_1 conda-forge
r-utf8 1.2.2 r41h815d134_1 conda-forge
r-vctrs 0.4.1 r41hc4bb905_0 conda-forge
r-vegan 2.6_2 r41h63324e3_1 conda-forge
r-viridislite 0.4.1 r41hc72bb7e_1 conda-forge
r-waldo 0.4.0 r41hc72bb7e_1 conda-forge
r-withr 2.5.0 r41hc72bb7e_1 conda-forge
raxml 8.2.12 ha5712d3_4 bioconda
readline 8.1.2 h3899abd_0 conda-forge
requests 2.28.1 pyhd8ed1ab_1 conda-forge
samtools 1.15.1 h9f30945_0 bioconda
scikit-bio 0.5.7 py38hbe852b5_0 conda-forge
scikit-learn 0.24.1 py38hfd19401_0 conda-forge
scipy 1.8.1 py38hfb8b963_3 conda-forge
seaborn 0.12.0 hd8ed1ab_0 conda-forge
seaborn-base 0.12.0 pyhd8ed1ab_0 conda-forge
sepp 4.3.10 py38h3252c3a_2 bioconda
setuptools 65.3.0 pyhd8ed1ab_1 conda-forge
sigtool 0.1.3 h57ddcff_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sortmerna 2.0 h5c9b4e4_4 bioconda
sqlite 3.39.3 h9ae0607_0 conda-forge
stack_data 0.5.0 pyhd8ed1ab_0 conda-forge
statsmodels 0.13.2 py38hc1426ef_0 conda-forge
tapi 1100.0.11 h9ce4665_0 conda-forge
tbb 2020.2 h940c156_4 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tk 8.6.12 h5dbffcc_0 conda-forge
tktable 2.10 h49f0cf7_3 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.2 py38hef030d1_1 conda-forge
tqdm 4.64.1 pyhd8ed1ab_0 conda-forge
traitlets 5.3.0 pyhd8ed1ab_0 conda-forge
typing_extensions 4.3.0 pyha770c72_0 conda-forge
tzlocal 2.1 pyh9f0ad1d_0 conda-forge
umap-learn 0.5.3 py38h50d1736_0 conda-forge
unicodedata2 14.0.0 py38hef030d1_2 conda-forge
unifrac 1.1.1 py38h6da613f_0 bioconda
unifrac-binaries 1.1.1 h8c74715_4 bioconda
urllib3 1.26.11 pyhd8ed1ab_0 conda-forge
vsearch 2.21.1 h1a264f4_1 bioconda
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
wget 1.20.3 h52ee1ee_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.3 pyhd8ed1ab_0 conda-forge
xopen 1.6.0 py38h50d1736_1 conda-forge
xorg-libxau 1.0.9 h35c211d_0 conda-forge
xorg-libxdmcp 1.1.3 h35c211d_0 conda-forge
xz 5.2.6 h775f41a_0 conda-forge
yaml 0.2.5 h0d85af4_2 conda-forge
zeromq 4.3.4 he49afe7_1 conda-forge
zipp 3.8.1 pyhd8ed1ab_0 conda-forge
zlib 1.2.12 hfd90126_4 conda-forge
zstd 1.5.2 hfa58983_4 conda-forge
Attempts to correct the issues
I've tried a number of things to try to get this fixed.
Attempt 1: Could R be corrected? Reinstall png r package.
R executable outside of the conda environment is located here:
[email protected] ~ % which R
/usr/local/bin/R
While the R executable within the QIIME environment is at:
(qiime2-2022.8) [email protected] ~ % which R
/Users/micro/miniconda3/envs/qiime2-2022.8/bin/R
So there should be no issues due to different R installations, conda is doing its job at keeping track of the paths to be used.
Asking (QIIME envt) R to load the png package results in an error:
(qiime2-2022.8) [email protected] ~ % R
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library("png")
Error: package or namespace load failed for ‘png’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/micro/miniconda3/envs/qiime2-2022.8/lib/R/library/png/libs/png.dylib':
dlopen(/Users/micro/miniconda3/envs/qiime2-2022.8/lib/R/library/png/libs/png.dylib, 6): Library not loaded: @rpath/libpng16.16.dylib
Referenced from: /Users/micro/miniconda3/envs/qiime2-2022.8/lib/R/library/png/libs/png.dylib
Reason: Incompatible library version: png.dylib requires version 55.0.0 or later, but libpng16.16.dylib provides version 54.0.0
Re-installing png and opening a new terminal instance (and R) allows me to load png, but attempting to execute the problematic qiime command (under "Problem") still results in an error.
Conclusion: this approach does not solve the issue.
Attempt 2: delete and remake the qiime environment
Following @Oddant1 's suggestion, I deleted the qiime2-2022.8 conda environment, and recreated it following the native install instructions on the QIIME website. This did not solve the issue.
Attempt 3: clean install of miniconda and qiime
@ebolyen indicated that this behavior might be related to the version of png on cran. They later commented/replied (on here) QIIME forum comment that the issue may have been fixed with an update to a new build on conda-forge; a link to the issue @ebolyen opened on conda-forge's github is here. Following all of this, I deleted miniconda completely (including the qiime environment) and did a clean install of both miniconda and qiime.
the problem still persists:
(qiime2-2022.8) [email protected] ~ % conda list r-png
# packages in environment at /Users/micro/miniconda3/envs/qiime2-2022.8:
#
# Name Version Build Channel
r-png 0.1_7 r41h815d134_1005 conda-forge
? Potential Solution ? As yet untested: specifically updating r-png
There are many versions of r-png available thorugh the terminal search feature:
[email protected] ~ % conda search r-png
Loading channels: done
# Name Version Build Channel
r-png 0.1_7 mro350_0 pkgs/r
r-png 0.1_7 r3.1.3_0 pkgs/r
r-png 0.1_7 r3.1.3_0a pkgs/r
r-png 0.1_7 r3.2.0_1 pkgs/r
r-png 0.1_7 r3.2.0_1a pkgs/r
r-png 0.1_7 r3.2.1_1 pkgs/r
r-png 0.1_7 r3.2.1_1a pkgs/r
r-png 0.1_7 r3.2.2_1 pkgs/r
r-png 0.1_7 r3.2.2_1a pkgs/r
r-png 0.1_7 r3.3.1_2 pkgs/r
r-png 0.1_7 r3.3.2_2 pkgs/r
r-png 0.1_7 r3.3.2_3 pkgs/r
r-png 0.1_7 r3.4.1_3 pkgs/r
r-png 0.1_7 r342hfd481a1_0 pkgs/r
r-png 0.1_7 r343h157672f_0 pkgs/r
r-png 0.1_7 r350h459e2dc_0 pkgs/r
r-png 0.1_7 r351h6402f54_0 pkgs/r
r-png 0.1_7 r36h46e59ec_0 pkgs/r
And version 0.1_8 is available. I am going to try to figure out a way to manually update or specify this in the qiime environment, but I'm not sure how successfull I'll be.
Conclusion
We ran into the same problem that @Heather_Maughan experienced when trying to run dada2 on our data, which resulted from a version conflict of png. I unsuccessfully tried to remedy the situation as outlined above. We would like to use QIIME (specifically with dada2) to perform our analysis to have consistent bioinformatics pipelines between successive datasets. Unfortunately I'm not familliar enough with python and this level of computer science to problem solve this particular issue. Any input you'd be able to provide would be greatly appreciated.
Jake Price