Tag: QIIME2

Quality-filter “‘NoneType’ object is not subscriptable” – Technical Support

Hello, I’m trying to use q2 quality-filter on the Mockrobiota ‘Extreme’ data (mock-12) before denoising with deblur, using the command qiime quality-filter q-score –i-demux demuxed_sequences.qza –o-filtered-sequences quality_filtered_seqs.qza –o-filter-stats quality_filtered_stats.qza –verbose However, I get the following error when I try to run it on my data: Traceback (most recent call last):File…

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qiime2/q2cli – githubmate

A click-based command line interface for QIIME 2. Installation and getting help Visit qiime2.org to learn more about q2cli and the QIIME 2 project. Enabling tab completion Bash To enable tab completion in Bash, run the following command or add it to your .bashrc/.bash_profile: ZSH To enable tab completion in…

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An error about using DADA2 in QIIME2 – Community Plugin Support

Hi everyone,I analyzed my pacbio data according to this PR, but an error was happened: Error in h(simpleError(msg, call)) : Error: invalid class “SRFilterResult” object: superclass “Mnumeric” no t defined in the environment of the object’s class stop Traceback (most recent call last): File “/home/xxx/miniconda3/envs/qiime2-2021.4/lib/python3.8/site- packages/q2_dada2/_denoise.py”, line 361, in denoise_ccs…

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Bioenv diversity error with qiime version 2021.4, but not with 2020.2 – Technical Support

203967.metadata.tsv (702 Bytes) table-trim55126.qza (58.4 KB) rooted-tree.qza (76.7 KB) I have qiime 2020.2 and qiime 2021.4 installed via conda. Using the attached files, I ran the following command which succeeded in both qiime version 2020.2 and version 2021.4: qiime diversity core-metrics-phylogenetic –verbose –i-phylogeny rooted-tree.qza –i-table table-trim55126.qza –m-metadata-file 203967.metadata.tsv –p-sampling-depth 300…

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How to differenciate between 16s hypervariables regions using QIIME2 ? – User Support

M_F: May i search the sequences on ncbi for example correponding to v4 domain No, NCBI probably would not have such sequences in an easily indexed form but I could be wrong. Rather, grab some reference sequences (can be a random subsample, do not need all of them) and use…

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Import problem: Not a(n) QIIME1DemuxFormat file – Technical Support

Hi @emiliomastriani, Did you download the sequences form sra?This previous question may give you some help: Hi there, I am familiar with QIIME1 but relatively new with QIIME2. I have gotten my raw file in the past from a facility in the CASAVA pair ended demultiplexed format and I had…

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qiime2-import data from non-working directory – User Support

Hello, qiime2 users community! I have the following set-up: a huge collection of .fastq files which I would like to process with the dada2 pipeline a remote cluster of servers with the separated storage where those files are stored, and the working machines for computing. Question: Is it possible to…

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q2-krona: Plugin for creating Krona plots – Plugins

Hello everyone, I’ve finally got time from work and finished the plugin. Special thanks to @Nicholas_Bokulich for suggesting making my own plugin, and @thermokarst for revision. The plugin is available at my github page (see: github.com/kaanb93/q2-krona). Simply, Krona is a tool to create interactive multi-layered pie charts. Here is an…

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Issue with installing QIIME2 2021.11 on Windows 10 – Technical Support

Hi QIIME support team, I’m attempting to install QIIME2 on my Windows 10 machine. I installed Anaconda3, then set up conda to run in Git Bash: echo “. ${PWD}/conda.sh” >> ~/.bashrc Once I restarted Git Bash and activated Conda, I installed python-wget because installation of wget kept getting the following…

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Still Not Use QIIME2 for Amplicon Analysis? You’re OUT!

I want to share with you a powerful tool named QIIME 2. It’s handy for Amplicon analysis. What is QIIME 2? The Quantitative Insights Into Microbial Ecology (QIIME) microbiome bioinformatics platform has supported many microbiome studies and gained a broad user and developer community. QIIME 2™(qiime2.org) is a new version…

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how to demultiplex paired end reads when R1 and R2 are identified by two different substrings?

I am struggling with finding a solution to a problem which seems easy but it’s not. I found many many questions that seems to be related (and I believe they are) but they are confusing and you never know which one fits your case. So there we go. I’ll try…

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