Hey everyone,
I am currently trying to run qiime 2 after successfully having used qiime1 and dada2 with my demultiplexed paired end samples. just a quick setting explanation: I am running the latest qiime 2 release: q2cli version 2017.11.0
conda 4.3.30
Python 3.5.4
macOS 10.9.5
my samples were run on an illumina Miseq Platform. the reads are paired end and demultiplex but still have primers in them, so I have 2 files per sample with R1 and R2. i simply want to import the files but am already stuck here.
this is my command
(qiime2-2017.11) RIMAs-MacBook-Pro:Desktop rc $ qiime tools import --type āSampleData[PairedEndSequencesWithQuality]ā --input-path qiime2_BGI/demultiplexed_BGI_sequences_gzip --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-end.qza
the error:
dyld: lazy symbol binding failed: Symbol not found: _fdopendir$INODE64
Referenced from: /Users/rc/anaconda/envs/qiime2-2017.11/lib/libpython3.5m.dylib
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: _fdopendir$INODE64
Referenced from: /Users/rc/anaconda/envs/qiime2-2017.11/lib/libpython3.5m.dylib
Expected in: /usr/lib/libSystem.B.dylib
Trace/BPT trap: 5
I am wondering if there is something else I should be installing. would otherwise running qiime 2 on the qiime2 virtual box be a solution.
any help is appreciated!
Computers DO say the darnest Things also thanks for the quick reply and the t-Rex ! I m a big fan!
I also initially thought this is what had happened. so I deactivated, removed the Environment and did a clean up and checked that it was truly removed (below is an excerpt from the command history)
I am new to qiime2 (but experienced with qiime1). I have qiime2-2017.11 installed on my Mac.
I too am trying to import data, but not reads. Just an OTU table I generated outside of qiime (clustered otus using usearch, converted txt otu table to biom format using biom convert).
Hey Colleen,
I was also initially bummed about not being able to start but until we figure this out, a good solution is working on the virtual box. I am a big fan. Just download virtual box and the qiime2 image (under install) and follow the steps, they are foolproof.
I know it s not a solution for the problem but it can help you stay motivated because you re actually getting things done.
Keep your chin up
Rima
@Drevilette, can you try out @colinbrislawnās suggestion above? I have spent some time Googling and I am starting to think this might be related to your version of macOS (this is still just a theory). Let me know how it goes, thanks!
Hi @thermokarst, I am wondering the same thing. I have a relatively old version of MacOS (10.9.5!) because our lab wonāt update due to a few dependencies for other programs we use. Iāll install qiime2 on my laptop (running High Sierra) this evening and see if this resolves the issue. Iāll ultimately need qiime2 to work on my desktop at work because it has quite a bit more RAM and processing speed than my desktop but at least this can help us narrow in on the source.
I did run
$ xcode-select ---install
but the problem persists.
When looking at the link provided by @colinbrislawn a lot of the people mentioned the had to reinstall the program that was giving them the issue. Does this mean i should remove and reinstall Miniconda2? Or just qiime2 or perhaps just update something in one of them?
I have one last question --- what do you get when you run the following?
$ pkgutil --pkg-info=com.apple.pkg.CLTools_Executables | grep version
This command should theoretically return something that looks something like this:
version: 9.1.0.0.1.1508540944
although you will probably see a different version number.
After doing a little sleuthing, I think the minimum version of macOS required is 10.10, at least according to this document. Travis CI is involved in the build process for a lot of QIIME 2's third-party dependencies, so this seems like a reasonable target.
If you have a version of XCode < 6.4 on your desktop machine, you might be able to find a 6.4 or greater version on Apple's website, but I can't really say if that is truly an option or not.
Hey there!
Thanks for the feedback and sorry I havenāt been able to reply earlier.
so i also tried downloading Xcode again (I did a quick search initially and stumbled upon that same post too), and it didnāt solve anything. So I am thinking (rudimentary physicians approach to diagnosing anything they know little aboutā¦ ) it s the macOS version and an issue of third party dependencies too.
ckellogg$ pkgutil --pkg-info=com.apple.pkg.CLTools_Executables | grep version
version: 6.2.0.0.1.1424975374
So, Iāll see if I can get my desktop up to at least 10.10 so I can get a more current version of XCode. Iāll report back about if that fixes the problem.