Hello!
I am trying to learn and run the Anacapa pipeline for my PhD project. I am using macOS Catalina with the Miniconda environment (Python 2.7) with both Conda and Homebrew installed. I also have R and RStudio already installed too.
At the moment I have managed to be able to install all the dependencies (such as fasxt toolkit, dada2, and others) run the script (the Anacapa QC, dada2 and BLCA) until the dada2 part of the pipeline. So I am using your examples and 12S example data to learn how to use it and how to manage the outputs. I manage to sort some issues regarding macOS (such as updating the Bash GCC compiler to be able to recognise the &>> code of the shell). But apparently there is a problem when the pipeline gets to the dada2 part.
Here is the Terminal code:
**Running in local mode
Using User Defined Primers
Required Arguments Given
Sun 26 Apr 2020 02:21:02 BST
Preprocessing: 1) Generate an md5sum file
Sun 26 Apr 2020 02:21:02 BST
Preprocessing: 2) Change file suffixes
Sun 26 Apr 2020 02:21:02 BST
Preprocessing: 3) Uncompress files
Sun 26 Apr 2020 02:21:02 BST
QC: 1) Run cutadapt to remove 5'sequncing adapters and 3'primers + sequencing adapters, sort for length, and quality.
Generating Primer and Primer + Adapter files for cutadapt steps. Your adapter type is nextera.
first1000reads-LSC-A-1-S19-L001 ...
forward...
check
reverse...
check
Sun 26 Apr 2020 02:21:03 BST
first1000reads-LSC-A-2-S20-L001 ...
forward...
check
reverse...
check
Sun 26 Apr 2020 02:21:03 BST
12S
Checking that Paired reads are still paired:
12S ...
12S_first1000reads-LSC-A-1-S19-L001 ...check!
12S_first1000reads-LSC-A-2-S20-L001 ...check!
Sun 26 Apr 2020 02:21:04 BST
Process metabarcode reads for with dada2
12S
Running Dada2 inline
Running dada2 on paired reads
0
moving on
Sun 26 Apr 2020 02:22:00 BST
Running dada2 on forward reads
0
moving on
Sun 26 Apr 2020 02:22:54 BST
Running dada2 on reverse reads
0
moving on
Sun 26 Apr 2020 02:23:48 BST
If a dada2 job fails you can find the run script...**
When I go to check the dada2 output it says this:
**Downloading GitHub repo benjjneb/[email protected]
checking for file ‘/private/var/folders/f9/rgzykm7d5439h5_mpc1h3lw80000gn/T/Rtmp91tC20/remotesac236df086cb/benjjneb-dada2-553008d/DESCRIPTION’ ...
✔ checking for file ‘/private/var/folders/f9/rgzykm7d5439h5_mpc1h3lw80000gn/T/Rtmp91tC20/remotesac236df086cb/benjjneb-dada2-553008d/DESCRIPTION’
─ preparing ‘dada2’:
checking DESCRIPTION meta-information ...
✔ checking DESCRIPTION meta-information
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘dada2_1.6.0.tar.gz’
- installing source package ‘dada2’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/dada2.h:7:
./../inst/include/dada2_RcppExports.h:14:14: warning: unused function 'validateSignature' [-Wunused-function]
void validateSignature(const char* sig) {
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Rmain.cpp -o Rmain.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c chimera.cpp -o chimera.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cluster.cpp -o cluster.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c error.cpp -o error.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c evaluate.cpp -o evaluate.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c filter.cpp -o filter.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c kmers.cpp -o kmers.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c misc.cpp -o misc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nwalign_endsfree.cpp -o nwalign_endsfree.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nwalign_vectorized.cpp -o nwalign_vectorized.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pval.cpp -o pval.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c strmap.cpp -o strmap.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c taxonomy.cpp -o taxonomy.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o dada2.so RcppExports.o Rmain.o chimera.o cluster.o error.o evaluate.o filter.o kmers.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o strmap.o taxonomy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-dada2/00new/dada2/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘narrow’ is not exported by 'namespace:Biostrings'
Execution halted
ERROR: lazy loading failed for package ‘dada2’
- removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dada2’
- restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/dada2’
Error: Failed to install 'dada2' from GitHub:
(converted from warning) installation of package ‘/var/folders/f9/rgzykm7d5439h5_mpc1h3lw80000gn/T//Rtmp91tC20/fileac232b86ad44/dada2_1.6.0.tar.gz’ had non-zero exit status
Execution halted**
I have made sure that dada2 is installed (along with the Bioconductor package manager for R) and being able to load it when using RStudio, but for some reason, the Anacapa script is trying to download the dada2 1.6 version for GitHub instead of working with the installed version I have. And apparently, when trying to download the dada2 1.6 version with RStudio and R I cannot do it, as it displays the same error messages as the dada2 Anacapa output file.
I am no expert on meddling with code and shells, but do you think this is still something I have to polish on my part or maybe the Anacapa pipeline is trying to use the dada2 1.6 version instead of the one I have installed (which is the latest versions from Bioconductor). Because the 1.6 version is not available anymore from GitHub or other repos, maybe this is the reason why I cannot get the pipeline running.
Do you know what can I do to address this issue, as I can't still test the other part of the Anacapa pipeline?
Thanks a lot and have a great start of the week!