Hi, The Qiime2 tutorials ran flawlessly in my mac. I'm trying to run an analysis on a large file (imported from Casava1.8 demultiplexed files) and am getting the following: (qiime2-2017.2) dhcp80ffdd4e:A05_Microbiome apzlo$ qiime dada2 denoise-paired --i-demultiplexed-seqs /Users/a pzlo/Qiime2ana…

@ebolyen Thank you for the patient and continuous support. I finally noticed that memory is an issue in this case. I have shifted all my analysis to AWS and it works fast and no error at all!! Thanks, Bing

Thanks for the update @Bing ! [image] Bing: I am just curious whether it is because I run the data analysis using an external USB rather than in local drive of my computer? Hmm, that could very well be the problem. Where are you running the analysis? Are you inside the directory that is mount…

@ebolyen Hmm, that could very well be the problem. Where are you running the analysis? Are you inside the directory that is mounted from your USB drive? I created a folder in my USB drive which is only used for the data analysis. I put all the .fastq in a folder based on the tutorial, and then a…

[image] Bing: I created a folder in my USB drive which is only used for the data analysis. I put all the .fastq in a folder based on the tutorial, and then all the analysis is running in that folder. Does that mean I need to create directory use mkdir? Nope that should work fine, mkdir doesn'…

@Bing , is it possible for you to try out this same analysis on a different USB drive? This would let us rule out hardware failure if it succeeds. If you have time/resources to do this we'd really appreciate it! We'd like to track down the source of the issue since it has affected multiple users. Al…

[image] jairideout: is it possible for you to try out this same analysis on a different USB drive? This would let us rule out hardware failure if it succeeds I will try this in another USB drive soon and will tell the results! Also I will try the command after I am back to school!

[image] jairideout: Also, what is the output from running these commands (with your USB drive plugged in)? df -h mount Here is the results: `Last login: Sun May 7 23:45:33 on console Jinbings-iMac:~ jinbingbai$ df -h Filesystem Size Used Avail Capacity iused ifree %iused M…

[image] ebolyen: Out of curiosity what does this command do inside your environment? python -c "import tempfile; print(tempfile.gettempdir())" Does that happen to be your USB drive or is it some crazy path like: /var/folder/w5/t9wf37ss1cg6s6lhtt8s33gw0000gn/T (which is what I would expect)? …

Thanks for that info @Bing ! Which volumes were you using (/Volumes/LaCie or /Volumes/LACIE SHARE) in your analyses that were failing?

@jairideout I use /Volumes/LaCie Thanks

Thanks @Bing ! Please let us know how things go when you have a chance to try a different USB drive. (The underlying issue may be related to this bug ).

QIIME 2 Forum

Dada2 "No such file or directory" and "Error in open.connection" message

User Support

dada2

show post in topic

Home
Categories
Guidelines
Terms of Service
Privacy Policy

Powered by Discourse, best viewed with JavaScript enabled