Closed beardymcjohnface closed 1 month ago
Hi,
Unfortunately, I'm not able to reproduce the error on my end.
I ran the CI on a macOS runner via GitHub to see if the problem might be OS-related. The CI passes without any issues (check it out here: CI Run). However, the GitHub macOS version is 13, which is lower than your version.
The error in your log seems to come from this line:
/bin/sh: line 1: 20164 Illegal instruction: 4 diamond blastp --outfmt 6 --max-target-seqs 1 --query test_results/temporary_files/assembly_proteins.faa -o test_results/temporary_files/diamond_result.tsv --threads 1 --db checkm2_tiny_db/checkm2_tiny_db.dmnd --query-cover 80 --subject-cover 80 --id 30 --evalue 1e-05 --block-size 2 2> test_results/temporary_files/diamond_result.log
I found this Stack Overflow question: What is the illegal instruction 4 error and why does it happen? and this GitHub issue: DIAMOND Issue #303.
It seems the issue might be related to the DIAMOND conda package not being compatible with your version of macOS.
You might want to try installing a Binette environment with a more recent version of DIAMOND. Here's how you can do it using pip within a conda environment:
First, create a conda environment with Python 3.8 and DIAMOND 2.1.9:
conda create -n binette_with_diamond2.1.9 python=3.8 diamond=2.1.9
conda activate binette_with_diamond2.1.9
Then, install Binette using pip with the main_deps
flag to ensure all dependencies are installed:
pip install binette[main_deps]
This will install all the necessary Python packages without checking the DIAMOND version, which is locked to 2.0.4 in the conda package as mentioned in #13.
Once you have everything set up, you can retry the Binette test as you did before:
git clone https://github.com/genotoul-bioinfo/Binette_TestData.git
cd Binette_TestData
binette -b binning_results/*binning --contigs all_contigs.fna --checkm2_db checkm2_tiny_db/checkm2_tiny_db.dmnd -v -o test_results
Hi Jean, That makes sense. I have not tried the instructions for installing a newer version of diamond, but Binette works perfectly on my linux system!
For review openjournals/joss-reviews/issues/6782 Hi, This is probably related to #13. I'm unable to run binette on the test dataset. I installed using the bioconda install instructions and ran the test command.
macOS Sonoma v14.5 conda 23.11.0 Python 3.8.18