I’m trying to install PICRUSt2 and am using qiime2-2019.1 in VirtualBox.
Apologies if this seems really basic but I have been struggling with this for literally weeks now and have finally admitted defeat and come to ask for help!
First of all I tried to follow the tutorial, which states “These instructions assume you have a conda environment named qiime2-2019.10 installed.” I don’t - I have 2019.1 and I’m not keen on changing it because then I would need to update VirtualBox and I would have to contact my IT department to get them to do that for me, plus I’m worried about how it might affect my existing VMs. I have seen a thread on this forum where someone used PICRUSt2 in qiime-2019.1 so I assume it’s possible? If not then fair enough!
This is what I initially ran:
conda install q2-picrust2=2019.1 -c conda-forge -c bioconda -c gavinmdouglas
In the tutorial it actually has “conda install q2-picrust2=2019.10…” but I changed the version to “2019.1” because the tutorial said “Note that the plugin version for qiime2-2019.10 is specified.” I figured, specify it for my qiime2-2019.1 environment. That didn’t work and this is the error message I got:
Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: - q2-picrust2=2019.1 Current channels: - https://conda.anaconda.org/conda-forge/linux-64 - https://conda.anaconda.org/conda-forge/noarch - https://conda.anaconda.org/bioconda/linux-64 - https://conda.anaconda.org/bioconda/noarch - https://conda.anaconda.org/gavinmdouglas/linux-64 - https://conda.anaconda.org/gavinmdouglas/noarch - https://repo.anaconda.com/pkgs/main/linux-64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/linux-64 - https://repo.anaconda.com/pkgs/r/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page.
So then I tried again, this time leaving the version as qiime2-2019.10. The output/error message I got from this was so gigantic that it wouldn’t all fit in my terminal window, so I can’t actually copy and paste the whole thing, but I’ve attached as much as possible (from the bottom half) in a word document. q2-picrust2 error.txt (590.3 KB)
So then I tried to install from source, as instructed in the tutorial. What an ordeal that was!! It took days and got so messy that I can’t even say what I eventually did to get it to work, but I finally got it. However, this didn’t work either:
(picrust2) [email protected]:~/Documents/PICRUSt$ picrust2_pipeline.py -s rep-seqs.qza/dna-sequences.fasta -i table-no-23-24-63-64-69-70-minsample5-minfreq50-no-ctrls-no-chloroplasts-BIOM-format/feature-table.biom -o picrust2_out_pipeline -p 1 Error running this command: place_seqs.py --study_fasta rep-seqs.qza/dna-sequences.fasta --ref_dir /home/qiime2/picrust2-2.3.0-b/picrust2/default_files/prokaryotic/pro_ref --out_tree picrust2_out_pipeline/out.tre --processes 1 --intermediate picrust2_out_pipeline/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 Standard error of the above failed command: Error running this command: epa-ng --tree /home/qiime2/picrust2-2.3.0-b/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --ref-msa picrust2_out_pipeline/intermediate/place_seqs/ref_seqs_hmmalign.fasta --query picrust2_out_pipeline/intermediate/place_seqs/study_seqs_hmmalign.fasta --chunk-size 5000 -T 1 -m /home/qiime2/picrust2-2.3.0-b/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model -w picrust2_out_pipeline/intermediate/place_seqs/epa_out --filter-acc-lwr 0.99 --filter-max 100 Standard output of the above failed command: INFO Selected: Output dir: picrust2_out_pipeline/intermediate/place_seqs/epa_out/ INFO Selected: Query file: picrust2_out_pipeline/intermediate/place_seqs/study_seqs_hmmalign.fasta INFO Selected: Tree file: /home/qiime2/picrust2-2.3.0-b/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre INFO Selected: Reference MSA: picrust2_out_pipeline/intermediate/place_seqs/ref_seqs_hmmalign.fasta INFO Selected: Filtering by accumulated threshold: 0.99 INFO Selected: Maximum number of placements per query: 100 INFO Selected: Automatic switching of use of per rate scalers INFO Selected: Preserving the root of the input tree INFO Selected: Specified model file: /home/qiime2/picrust2-2.3.0-b/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model INFO Rate heterogeneity: GAMMA (4 cats, mean), alpha: 0.453141 (user), weights&rates: (0.25,0.0250674) (0.25,0.220229) (0.25,0.782933) (0.25,2.97177) Base frequencies (user): 0.229585 0.22008 0.298596 0.251739 Substitution rates (user): 1.00319 2.79077 1.5301 0.87441 3.83966 1 INFO Selected: Reading queries in chunks of: 5000 INFO Selected: Using threads: 1 INFO ______ ____ ___ _ __ ______ / ____// __ \ / | / | / // ____/ / __/ / /_/ // /| | ______ / |/ // / __ / /___ / ____// ___ |/_____// /| // /_/ / /_____//_/ /_/ |_| /_/ |_/ \____/ (v0.3.6) INFO Output file: picrust2_out_pipeline/intermediate/place_seqs/epa_out/epa_result.jplace
From what I’ve read, I think this is a RAM issue, so I have requested an upgrade but in the meantime, I wanted to use the q2-picrust2 plugin because I know you can use the alternative pipeline to reduce the RAM requirements.
Sorry for the length of this post. If anybody can help me out here I would be really appreciative.
(Edited to move file upload text!)