conda installer

[mr249]

Hello. I am using Ubuntu and I have tried python versions 3.5, 3.7, 3.9, and 2.7 and each time I get an error that my python version is wrong. I have tried to create a clean environment using: conda create -c bioconda -n flye flye=2.9 and activated it and it gave the same error. I have pasted my error messages below.

• flye -> python[version='2.7.*|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0|>=3.9,<3.10.0a0']

Your python: python=3.5

• flye -> python[version='>=3.10,<3.11.0a0|>=3.5,<3.6.0a0']

Your python: python=3.9

I was wondering if you have any suggestions. Thank you.

[jeanlain]

Hello, I had the same issue, and I resorted to downloading the right package from https://anaconda.org/bioconda/flye/files and using conda install path_to_file.tar.bz2 Note that the "i" button on the package list indicates the required python version.

But we shouldn't have to do that in the first place. It seems that conda does not detect the right version to install.

[mikolmogorov]

I would also make sure that you are running the latest version of conda (conda update -n base conda).

Also, try being explicit with the python version: conda create -n flye_29 flye=2.9 python=3.9

If it still fails, please send the full terminal output, not just last error message.

[tujiaki]

I have same problem, and attach the terminal output.

(base) aki@Linux-Tuji:~$ conda install -c bioconda flye==2.9 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: \ Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

• flye==2.9 -> python[version='>=3.10,<3.11.0a0|>=3.5,<3.6.0a0']

Your python: python=3.9

If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.

The following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.31=0
• python=3.9 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31

[mikolmogorov]

@tujiaki please check my suggestions from the post above and post the full terminal output of each command in case they fail.

[HuoJnx]

Sorry~~ I got the same issue, and here is the terminal output. Thank you very much for your kindly help.

(phages) junsheng@Alpha:~$ conda update -n base conda
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.

(phages) junsheng@Alpha:~$ conda create -n nano python=3.9
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/junsheng/BIN/anaconda3/envs/nano

  added / updated specs:
    - python=3.9


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    pkgs/main/linux-64::ca-certificates-2021.10.26-h06a4308_2
  certifi            pkgs/main/linux-64::certifi-2021.10.8-py39h06a4308_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
  libgomp            pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
  ncurses            pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
  openssl            pkgs/main/linux-64::openssl-1.1.1l-h7f8727e_0
  pip                pkgs/main/linux-64::pip-21.2.4-py39h06a4308_0
  python             pkgs/main/linux-64::python-3.9.7-h12debd9_1
  readline           pkgs/main/linux-64::readline-8.1-h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-58.0.4-py39h06a4308_0
  sqlite             pkgs/main/linux-64::sqlite-3.36.0-hc218d9a_0
  tk                 pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
  tzdata             pkgs/main/noarch::tzdata-2021e-hda174b7_0
  wheel              pkgs/main/noarch::wheel-0.37.0-pyhd3eb1b0_1
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7f8727e_4


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate nano
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(phages) junsheng@Alpha:~$ conda activate nano

(nano) junsheng@Alpha:~$ conda install flye=2.9 -c bioconda
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - flye=2.9 -> python[version='>=3.10,<3.11.0a0|>=3.5,<3.6.0a0']

Your python: python=3.9

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.23=0
  - python=3.9 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.23

[mikolmogorov]

@HuoJnx what's the output of conda create -n flye_29 flye=2.9 ?

[HuoJnx]

@fenderglass Thank you very much for your help! It works!!!

[louellette]

Hi, @fenderglass, I have the exact same issue as HuoJnx but your suggestion to solve the problem is not showing:

conda create -n flye -c bioconda flye=2.9 python=3.9

Output:

Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package python conflicts for: flye=2.9 -> python[version='>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0|>=3.9,<3.10.0a0'] flye=2.9 -> setuptools -> python[version='>=3.10,<3.11.0a0|>=3.5,<3.6.0a0'] python=3.9The following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.23=0
• feature:|@/linux-64::__glibc==2.23=0

Your installed version is: 2.23

Thanks in advance!

[jjkoehorst]

Using

conda create -n flye_29 flye=2.9
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - flye=2.9

or using

conda create -n flye -c bioconda flye=2.9 python=3.9
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: \ 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                   

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package python conflicts for:
python=3.9
flye=2.9 -> setuptools -> python[version='>=3.10,<3.11.0a0|>=3.5,<3.6.0a0']
flye=2.9 -> python[version='>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0|>=3.9,<3.10.0a0']The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.27=0
  - feature:|@/linux-64::__glibc==2.27=0

Your installed version is: 2.27

No success did a dependency change or is something else happening?

[mikolmogorov]

@jjkoehorst @louellette try conda create -n flye_29 -c bioconda flye=2.9

[druvus]

@jjkoehorst @louellette you need to set up channels according to this documentation. Alternatively, you could manually define the channels at the prompt as you did. Just make sure to also include conda-forge, i.e. conda create -n flye_29 -c conda-forge -c bioconda flye=2.9 as bioconda depends on conda-forge.

I would also recommend to take a look at mamba to handle conda installation as it it as a better dependency solver.

[carlite71]

@fenderglass I'm having this same issue with Ubuntu. Thanks in advance for your help.

conda install flye output: Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment:
Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

• flye -> python[version='>=3.5,<3.6.0a0']

Your python: python=3.9

If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.

The following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.31=0
• flye -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
• python=3.9 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31

I updated conda as suggested. Then I ran:

conda create -n flye_29 flye=2.9 python=3.9 and got this:

Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package python conflicts for: flye=2.9 -> setuptools -> python[version='>=3.5,<3.6.0a0'] flye=2.9 -> python[version='>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0'] python=3.9The following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.31=0
• python=3.9 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31

• Then I tried conda create -n flye_29 -c bioconda flye=2.9

Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError:

(it didn't actually list the error)

[Nordosa]

For those who, like me, continued to have issues with the above solutions. I found installing mamba and running the following worked:

mamba create -n flye_29 -c conda-forge -c bioconda flye=2.9

[Andreas-Bio]

(base) bio@Bio:~/Downloads$ conda install flye
Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                           

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - flye -> python[version='2.7.*|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0']

Your python: python=3.11

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.35=0
  - flye -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - python=3.11 -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.35

[touala]

Not sure this is related but I solved an install issue mentioning __glibc by adding -c conda-forge.

conda create -n flye_2.9.2
conda activate flye_2.9.2
conda install -c bioconda -c conda-forge flye=2.9.2

[RominaSSBatista]

⚠️ : I have tried several times install flye2.9.2. My last attempt was using the following approach: mamba create -n flye_29 -c conda-forge -c bioconda flye=2.9

Regardless if I use conda, maba, when I run it I get the error:

[2023-11-16 11:52:57] root: ERROR: minimap2 is not installed
[2023-11-16 11:52:57] root: ERROR: Pipeline aborted
 

If I try to follow the Local building instructions in the infrastructure I am using, I am not able. It STOUT an error regarding zlib but I have all build requirements. To install I load a module that sets the CONDA env variable ($CONDA_PREFIX/include/zlib.h and $CONDA_PREFIX/lib/libz.so.), so I assume I have all requirements.

I would appreciate if you could share your thought with me regarding these issues.

Cheers, Romina

[mikolmogorov]

DId you activate your environment using mamba activate flye_29? I think when you're running flye it pulls your local installation, rather than conda/mamba package.

[RominaSSBatista]

Dear @fenderglass it was indeed something I was doing wrong while calling Flye on my script to submit the Job. Apologies, I should have had updated it here. Fye 2.9 is running so far without issues on my HPC using the following setup/cmmds (in case it is useful for others):

1. I've allocated the job a high memory partition, otherwise it wouldn't run. I am using 20x coverage nanopore data from a non-human primate with genome size ca.2.7Gb

# ------------------------------------------------------------------------------
# SLURM Specifications
# ------------------------------------------------------------------------------

#SBATCH --partition=high-mem
#SBATCH --time=48:00:00
#SBATCH --mem=128G
#SBATCH --job-name=flye
#SBATCH --error=assemb_flye.err
#SBATCH --output=assemb_flye.out

2. I've used this commands to run Flye.

# ------------------------------------------------------------------------------
# Variables - PATH to be called & RUN FLYE
# ------------------------------------------------------------------------------

data_dir='full_path_to_rawdata_directory'
out_dir='full_path_to_output_directory'

conda activate flye_29

flye --genome-size 2.7g --threads 36 --nano-raw mysample.fastq.gz --out-dir $out_dir/

I appreciate your reply anyway. Cheers, Romina