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metawrap installation and salmon question #526

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sincos2211 opened this issue Nov 25, 2023 · 1 comment
Open

metawrap installation and salmon question #526

sincos2211 opened this issue Nov 25, 2023 · 1 comment

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@sincos2211
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Hello,

I am really new to the metaWRAP, I have some issues with installation and some queries,

  1. I tried several to install as the guide, I created a new environment and used mamba to install, but it showed the error, how can I fix this error?:
    mamba install -c ursky metawrap-mg

or

mamba install -c ursky metawrap-mg=1.3.2-0

Looking for: ['metawrap-mg=1.3.2-0']

bioconda/linux-64 Using cache
bioconda/noarch Using cache
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
pkgs/main/noarch No change
pkgs/main/linux-64 No change
pkgs/r/linux-64 No change
pkgs/r/noarch No change
ursky/linux-64 No change
ursky/noarch No change

Pinned packages:

  • python 3.10.*

warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
Could not solve for environment specs
The following package could not be installed
└─ metawrap-mg 1.3.2-0** is not installable because it requires
└─ maxbin2 2.2.6.* , which conflicts with any installable versions previously reported.
(base) hemm-ws@hemmws-desktop:~$ mamba install -c ursky metawrap-mg=1.2.3-0

Looking for: ['metawrap-mg=1.2.3-0']

bioconda/linux-64 Using cache
bioconda/noarch Using cache
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
pkgs/main/linux-64 Using cache
pkgs/main/noarch Using cache
pkgs/r/linux-64 Using cache
pkgs/r/noarch Using cache
ursky/noarch No change
ursky/linux-64 No change

Pinned packages:

  • python 3.10.*

warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
Could not solve for environment specs
The following package could not be installed
└─ metawrap-mg 1.2.3-0** is not installable because it requires
└─ maxbin2 2.2.6.* , which conflicts with any installable versions previously reported.
(base) hemm-ws@hemmws-desktop:~$ conda remove maxbin2
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are missing from the target environment:

  • maxbin2
  1. In the quant_bin, there is option -a ( ASSEMBLY/final_assembly.fasta). If I do not include this option, how is it different?
  2. If I use salmon separately to find the abundances of genomes (bins), what option in the salmon tool can replace or be similar for -a option in metalwrap? In the salmon, the input is normally indexed first and then quantify, how would be different with the results can be generated using metawrap (metawrap quant_bins -b BIN_REFINEMENT/metawrap_50_10_bins -o QUANT_BINS -a ASSEMBLY/final_assembly.fasta CLEAN_READS/ERR*fastq)

I am new to this so this question might be stupid. Thank you!

@sconlan
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sconlan commented Dec 8, 2023

You may find your issue with the SOLVER is fixed by adding "--no-channel-priority" to the create command, however, I'm seeing other people with issues like: #528 so it is possible something has broken elsewhere in the install...

mamba create -y --name metawrap --channel ursky metawrap-mg=1.3.2 --no-channel-priority

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