Comments (8)
@bede I didn't try the instructions. I abandoned running it on OS X and I'm just running it in Linux. Everything there is working fine.
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Are you using Clang for C++ compilation? Also, did you install libomp
via brew as mentioned in the install instructions?
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Thanks Chirag. I am using Clang, but was attempting to run the OS X binary release rather than building from source.
Yes libomp
is also installed, but I don't know much about dylibs on OS X, so am likely doing something silly…
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Can you start the installation process from source in a different directory? Shouldn't take long if you already have Clang and libomp.
from fastani.
Right, I'd figured out the additonal Darwin CXXFLAGS needed to Makefile.in
and forked the repo in order to PR, only to see you'd already commited the same change to master since the last release
ifeq ($(UNAME_S),Darwin) #macOS clang
CXXFLAGS += -mmacosx-version-min=10.7 -stdlib=libc++ -Xpreprocessor -fopenmp -lomp
For me (OS 10.12.6) the process was therefore
$ ./bootstrap.sh
$ ./configure --with-gsl=/usr/local/Cellar/gsl/2.5
$ make
Perhaps you could tag a new binary and/or source release that works for Mac users : )
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I got this similar error with macOS 10.13.6 trying to use fastani-OSX64-v1.1.tar.gz
So the dependency-free binary for macOS does not appear to work. It would be really cool if it did.
fastANI -r E_coli_randomG_0001.fna -q E_coli_randomG_0002.fna -o temp.ani
>>>>>>>>>>>>>>>>>>
Reference = [E_coli_randomG_0001.fna]
Query = [E_coli_randomG_0002.fna]
Kmer size = 16
Fragment length = 3000
Threads = 1
ANI output file = temp.ani
>>>>>>>>>>>>>>>>>>
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Users/rothconrad/Downloads/ReSearch/fastani-OSX64-v1.1//./libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address
Referenced from: /Users/rothconrad/Downloads/ReSearch/fastani-OSX64-v1.1//./libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
Abort trap: 6
from fastani.
Yeah, no release has been tagged since I opened this, and the OS X bin is still broken. Do my instructions work for you @rotheconrad ? You'll need a clone or tarball of master.
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I've marked a new release (1.2) today, sorry for the delay :)
The pre-built binary is provided for linux users; mac users are recommended to build from source.
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Related Issues (20)
- Share workflow for visualizing FastANI results HOT 16
- FastANI 1.33 using more threads than allocated HOT 3
- 11
- Clustering HOT 1
- No results in output directory? HOT 3
- Error in number of mapped fragments HOT 1
- FastANI output and matrix values do not match? HOT 1
- minimizer/kmer string compression HOT 5
- #query# fastANI HOT 4
- No output given by FastANI HOT 5
- Output file is blank HOT 1
- Compilation fails on macOS 12/`conda`: c++ command problem
- parameters for viral genomes HOT 3
- What does NA mean in the result of fastANI matrix output? HOT 1
- How to get the alignment fraction value? HOT 1
- Dependency conflict when installing from bioconda along with Python 3.9 HOT 8
- libgsl.so.25 potential issue HOT 7
- Column labels of the visual output HOT 2
- Error when running Rscript HOT 1
- issues with reference list file
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