Has anyone had trouble with installing QIIME2 on a Mac running Catalina? The new OS system removed QIIME1.9 from my system as a security threat. 
Cheers
Becks
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Hi @BecksHawaii,
No issue with QIIME 2, but I haven’t tried a QIIME 1 installation in over 12 months. It’s been deprecated for at least 18, so it might just be time to move over and fully embrace QIIME 2?
Best,
Justine
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Hello Becks,
I’m having the exact same problems too as I also have Catalina OSX and the system refuses to download the program. I’m trying to work through it and I’m wondering if you ever came by a solution.
Cheers,
Veronica
Welcome to the forum @veronica_rodriguez!
Just to clarify: you cannot download QIIME 2 on Catalina? Or QIIME 1?
Since QIIME 1 is no longer maintained, there is unlikely to be a solution if Catalina does not like QIIME 1.
I’m trying to download QIIME2 on Catalina natively with miniconda
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Thanks for clarifying and giving the install details! (it sounded like @BecksHawaii’s problem was qiime1, so just wanted to make sure)
We will attempt to replicate. Could you please provide the error message you are receiving and more specific system info? Thanks!
A friend of mine recently did this (recently like 1-2 months ago). She told me it was a bit of an arduous process to get QIIME1 and QIIME2 running again. I will ask her some of those details.
I did invite her to come onto the forum, but she hasn’t accepted yet. Ben
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So, my friend told me:
This was the website the worked for QIIME1:
http://www.metagenomics.wiki/tools/16s/qiime/install/packagesnotfounderror
Apparently to get QIIME2 to run, she had to re-install everything into a new Python Environment. She stressed that when she installed it, she had to create a new environment separate from the one that QIIME1 was installed in (this makes sense to me).
She also stressed that nay plug-ins that you use will have to be installed in the new environment as well (e.g., Songbird etc.). ’
Her ultimate recommendation though, she told me not to update to Catalina. Sorry if you have already.
Ben
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You should be running a QIIME 1.9.1 environment separately from any of your QIIME 2 environments: the requirements are totally different and they won’t work together. This is one of the benefits and drawbacks of conda: you can have multiple environments, like multiple rooms in your house. We might have a sink in your laundry room, kitchen, bathroom1 and bathroom2 but they’re different versions of the base release “sink” which slightly different behavior. Like, my kitchen sink is slightly more feature complete because the head pops off. (However, this is Europe so its not entirely feature complete. I miss my garbage disposal.) Environments can take on slightly different features/behaviors, and its important to keep them self contained and separate.
Best,
Justine
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I hear you, I didn’t know exactly which part or why she installed it in conflcting/overlapping environments. I wasn’t present when she installed it so I can only assume there was some issue regarding when and how she installed QIIME1 and QIIME2.
Although, to her benefit, she is quite good w/ conda and I may be understating the issues she encountered.
Ben
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Sorry, I don’t mean to be difficult . Environment management can be hard and it’s been a weird week for it here. I apologize if I came off as condescending or just rude.
Best,
Justine
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Aloha, I started this post, and I actually gave up on using QIIME at all for awhile, and not sure where things stand with QIIME 1 on latest Catalina version (or QIIME2 for that matter). Right now, I have been running QIIME2 through a third party platform. Until the next workshop.
Do the QIIME developers/helpers (Justine and others): love you guys and I know you work incredibly hard to answer all of our questions. I do want to stress though that being able to use QIIME 1, especially when you have not attended a QIIME 2 workshop, is very helpful. I know the scripts, so I need to manipulate a table, etc…, if I don’t know how to do it in QIIME2, I can do it QIIME1. I think its important to recognize that many of us that use QIIME are not “scripters” and there is a learning curve with QIIME2. You guys changed the language used! Not just the available tools. Now there are “features” and ASVs to learn. So its not simple. I have been using QIIME since 2010, and I had to learn QIIME on my own - a supervisor gave me a set of scripts and said “follow that” and I had never worked in command line before in my life. So, although I appreciate that we should “embrace” QIIME2, please also be understanding that those of us that are trying to do this on our own, figure out ways around a problem to make it work. Hence the QIIME 1 install question.
Maybe offering more workshops would help?? I do those myself for genomic science, so I know they are a pain and loads of work.
Thanks for all the help!!
Cheers
Becks
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Hi @BecksHawaii,
Im sorry if i made you feel unwelcome or uncomfortable. It is absolutely a transition and a learning curve. thank you for being patient with us and I will work on being more patient in the future.
My guess would be qiime 1.9.1 is probably easiest to run out of a virtual machine because I dont think there’s much support anymore. Python 2.7 is almost fully deprecated and so it will likely get harder to install and maintain. @thermokarst may have some better ideas for you, he’s the chief installation expert I know and all around good guy.
It is hard and can be overwhelming and scary! I’m not sure if its helpful or not, but the moving picture tutorial is a direct port from QIIME 1 if you worked with the illumina tutorial there, so maybe that would be helpful to make you feel more comfortable translating the script you’ve got in your head?
As far as, workshops go, we have our first online workshop in October. it’s a little bit experimental, so there maybe some hiccups. But, most of the lectures come from really brilliant people and there will be hands on support. It’s hopefully the first of more.
Best,
Justine
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Thanks @jwdebelius!
@BecksHawaii, maybe the VirtualBox installation would help get you moving?
https://docs.qiime2.org/2020.8/install/virtual/virtualbox/
I will say, I have been using Catalina for a while now, and it all seems to be smooth sailing... 
Certainly! We work extremely hard to ensure that we make things as "accessible" as possible. Sometimes you just have to challenge yourself, though, and work through things that are difficult. Luckily you've got a great resource here on the QIIME 2 forum - we are happy to help! This is also why we have put in so much effort to build an "interface-agnostic" platform, that way GUI interfaces can be supported. We are hard at work on a new q2Galaxy interface that hopefully should launch some time in 2021 (
).
While I appreciate the sentiment, I don't think we are really responsible for changing the language of microbiome science, we are just trying to keep up with the state of the field! Things change - ASVs replacing OTUs is a really great example. I think that is just part of academic/scientific progress.
Regarding QIIME 1 - I think maybe the best way to think of it is as a completely different software package when compared to QIIME 2. Just like mothur is totally different from QIIME 1, you know? As for QIIME 1 support, we announced our plans for ending QIIME 1 support back in 2016, and provided a year-long transition plan for helping people transition to QIIME 2 in as seamless a manner as possible. Change is rough, but the QIIME 2 team is 100% committed to building up the QIIME 2 platform in a way that is easy-to-use, and up-to-date with the latest methods and techniques. This means you might need to put in a little bit of work, too, to get caught up on the latest-and-greatest. Like I said, we are happy to help, just come find us here on the forum! As well, we have assembled a significant amount of written resources at docs.qiime2.org, with tutorials and docs for multiple skill-levels and backgrounds!
As @jwdebelius mentioned, we have announced a workshop (CZI-CABANA Microbiome Bioinformatics with QIIME 2 Workshop (our first-ever online QIIME 2 workshop!)) a few weeks ago, and we are gearing up for several more online workshops in the coming months (announcements soon !).
Thanks so much! 
Aloha, I appreciate all the above, and your suggestions. I don’t need the virtual box for QIIME 1 - solved those problems. But thank you very much. I do “power through” all the time - with metagenomics, HMMs, QIIME2, ASVs, etc…I know that the announcement regarding QIIME 1 came out awhile ago - believe me! We are all trying to use QIIME2 now, and doing the best we can. I do understand that you personally (and the QIIME team) did not change the language. My apologies if it came across that way. I am familiar with the literature, and understand that the field moves along and you are following that. I think my point was more general - that all of us have to use the skills we have to solve our problems, regardless of its the latest version of anything. So pushing “just change to QIIME2” may not be that helpful.
thanks about the workshops! Not trying to be critical at all - I am aware of the upcoming workshop and glad that is being offered online. I was unable to attend the last one in Maryland. I know they are heaps of work, so greatly appreciated.
No need for a response, I am not trying to argue with you guys. I do really appreciate all that you do.
Cheers
Becks
I think maybe you misread - I provided a link to the QIIME 2 virtualbox.
I don't think that is what we are suggesting here, though. What we are saying is that you're here on the QIIME 2 forum asking for help, we can only provide help for QIIME 2. The QIIME 1 team no longer exists, so asking for help with QIIME 1 here isn't really something we can help with. As I mentioned above, we provided a multi-year transition plan for active QIIME 1 users. Now, if you missed that window, we are certainly happy to help you with transitioning, we just can't provided QIIME 1 support.
I didn't think you were being critical, I just wanted to let you know what are current workshop plans are, since you asked above about offering more workshops.
No worries, I didn't think you were arguing, I just want to make sure you get what you need, but also keep in mind the limitations of what we can and can't help with here on this support forum.
Thanks so much!