InstallError

[B1991ing]

Dear Oskar,

I am trying to install the binny on another HPC platform now. But, I had another kind of error as shown in the screenshot.

Before asking you, I already checked the content of .condarc under my own directory (On this HPC platform, only one personal directory for each HPC user, so people can install and save everything here).
condarc.txt

envs_dirs:

• ~/conda_envs

pkgs_dirs:

• ~/conda_pkgs

I only loaded the latest version of conda in VARIABLE_CONFIG.
VARIABLE_CONFIG.txt

No change in the file config/config.init.yaml.

Looking forward for your help.

Thank you very much.

Best,

Bing

[ohickl]

Sorry Bing,
totally missed this! Ill check if I can reproduce asap!

[ohickl]

in the meantime you can also try the conda beta version.
you can install it e.g. with:
micromamba create --prefix <path/to/my>/local_tools/binny bioconda::binny.
Then you just run:

binny_path="<path/to/my>/local_tools/binny"
# Activate binny environment
micromamba activate ${binny_path}
# Ensure its all setup
binny --setup > binny_setup.log 2>&1
# Run a test
test_data_dir="${binny_path}/lib/python3.10/site-packages/binny/test"
binny --assembly ${test_data_dir}/contigs_4bins.fa \
      --bam ${test_data_dir}/*.bam \
      --outputdir ${test_data_dir}/out > binny_test.log 2>&1

[B1991ing]

Thank you very much for your reply, Oskar.

I got an error when installation --- PackageNotFoundError: Packages missing in current channels:

**Fetching package metadata .............

PackageNotFoundError: Packages missing in current channels:

• bioconda::binny

We have searched for the packages in the following channels:

• http://localhost/anaconda/pkgs/main/linux-64
• http://localhost/anaconda/pkgs/main/noarch
• http://localhost/anaconda/pkgs/free/linux-64
• http://localhost/anaconda/pkgs/free/noarch
• http://localhost/anaconda/pkgs/r/linux-64
• http://localhost/anaconda/pkgs/r/noarch
• http://localhost/anaconda/cloud/conda-forge/linux-64
• http://localhost/anaconda/cloud/conda-forge/noarch
• http://localhost/anaconda/cloud/bioconda/linux-64
• http://localhost/anaconda/cloud/bioconda/noarch**

How to solve it according to your experience?

I installed binny in the same PC but using two HPC accounts, one is successful and another is failed.

Best,

Bing

[B1991ing]

Hi Oskar,

I ran the test on the HPC account that successfully installed by me, but an error happened as shown below.

ModuleNotFoundError: No module named 'Resources.UniFunc.unifunc'

binny_setup.log
binny_test.log

Best,

Bing

[ohickl]

Hey, the setup error is strange:

fatal: unable to access 'https://github.com/PedroMTQ/UniFunc.git/': Could not resolve host: github.com

that sounds like you were lacking access to the github site/internet for some reason? maybe a temporary problem?
the error during the test was my bad, i had a typo in my example command (| instead of \ in the --bam line), i fixed it.
maybe you can just retry?

[B1991ing]

the error during the test was my bad, i had a typo in my example command (| instead of \ in the --bam line), i fixed it.
maybe you can just retry?

Oskar, can you tell me where is the typo in the --bam line ?

[B1991ing]

still not okay now.
I ran as shown below,
module load conda-mirror
conda create --prefix local_tools/binny bioconda::binny

binny_path="./local_tools/binny"

Activate binny environment

conda activate ${binny_path}

Ensure its all setup

binny --setup > binny_setup.log 2>&1

Run a test

test_data_dir="${binny_path}/lib/python3.9/site-packages/binny/test"
binny --assembly ${test_data_dir}/contigs_4bins.fa
--bam ${test_data_dir}/*.bam
--outputdir ${test_data_dir}/out > binny_test.log 2>&1

[ohickl]

the error during the test was my bad, i had a typo in my example command (| instead of \ in the --bam line), i fixed it.
maybe you can just retry?

Oskar, can you tell me where is the typo in the --bam line ?

It was this line --bam ${test_data_dir}/*.bam \ before it was --bam ${test_data_dir}/*.bam | it is already corrected in the previous response.

Regarding your new attempt, is it still the same error?

[B1991ing]

--bam ${test_data_dir}/*.bam \

Still same error. I ran using the corrected version, but not work.

binny --assembly ${test_data_dir}/contigs_4bins.fa
--bam ${test_data_dir}/*.bam
--outputdir ${test_data_dir}/out > binny_test.log 2>&1

[ohickl]

strange, i just tried again with no problems:

> micromamba activate ${binny_path}
> binny --setup
Cloning into '/mnt/lscratch/users/ohickl/local_tools/binny/lib/python3.10/site-packages/Resources/UniFunc'...
remote: Enumerating objects: 224, done.
remote: Total 224 (delta 0), reused 0 (delta 0), pack-reused 224
Receiving objects: 100% (224/224), 24.10 MiB | 20.43 MiB/s, done.
Resolving deltas: 100% (111/111), done.
...

Can you try, with the binny env activated:
mantis check or mantis db. It will probably fail at some later stage, but do you get the same error?
If so, there might be a problem with your cluster accounts/clusters internet access?

[B1991ing]

Can you try, with the binny env activated:
mantis check or mantis db. It will probably fail at some later stage, but do you get the same error?
If so, there might be a problem with your cluster accounts/clusters internet access?

The NWAFU HPC cluster which I am using now can't be connected with any internet.

I tried command lines - mantis check or mantis db with the binny env activated. Bur same error happened.

binny_path="./local_tools/binny"

Activate binny environment

conda activate ${binny_path}

mantis check

mantis db

[B1991ing]

strange, i just tried again with no problems:

I installed miniconda3 on my HPC folder, so I used conda create, conda activate.

module load conda-mirror
conda create --prefix ./local_tools/binny bioconda::binny

binny_path="./local_tools/binny"

Activate binny environment

conda activate ${binny_path}

Ensure its all setup

/storage/public/home/2023110148/local_tools/binny/bin/binny --setup > /storage/public/home/2023110148/local_tools/binny/binny_setup.log 2>&1

Run a test

test_data_dir="${binny_path}/lib/python3.10/site-packages/binny/test"
/storage/public/home/2023110148/local_tools/binny/bin/binny --assembly ${test_data_dir}/contigs_4bins.fa
--bam ${test_data_dir}/*.bam
--outputdir ${test_data_dir}/out > /storage/public/home/2023110148/local_tools/binny/binny_test.log 2>&1

[ohickl]

Can you try, with the binny env activated:
mantis check or mantis db. It will probably fail at some later stage, but do you get the same error?
If so, there might be a problem with your cluster accounts/clusters internet access?

The NWAFU HPC cluster which I am using now can't be connected with any internet.

Hm, but then can you even successfully install the binny env?

It also says you dont have the mantis Multiprocessing module for the mantis ... tests, which you definitely should have, if the environment install worked properly.

I am not sure what the problem is. Can you maybe check again with one of your sys admins? or maybe a colleague can also try the installation, to see if it is a general problem.

[B1991ing]

Hm, but then can you even successfully install the binny env?

It also says you dont have the mantis Multiprocessing module for the mantis ... tests, which you definitely should have, if the environment install worked properly.

I am not sure what the problem is. Can you maybe check again with one of your sys admins? or maybe a colleague can also try the installation, to see if it is a general problem.

One thing is that if I installed miniconda, do I need to module load conda-mirror on HPC when installing binny?

[ohickl]

i dont think so. what conda version does conda-mirror load? i would go with mamba as a much faster, still easy to use variant.