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Hello! This is a bit of a strange request, but I am running into a strange error when running dockerized versions of CoverM. It is related to this somehow, I am not entirely sure why it only fails on a collaborators machine, but CoverM fails when attempting to find the Minimap2 executable using the bash -c 'which minimap2' command, which is here.
When running this manually (not via CoverM), I get the following:
docker run ghcr.io/vdblab/coverm:0.6.1 bash -c "which minimap2"
/opt/conda/bin/minimap2
So far so good. When run on my institute's HPC via singularity, I get
singularity run docker://ghcr.io/vdblab/coverm:0.6.1 bash -c "which minimap2"
INFO: Using cached SIF image
/opt/conda/bin/minimap2
which is good as well. However, when my collaborator attempts on their cluster, they get
Illegal option --
That results in their CoverM calls failing with the following error:
[2024-03-13T18:11:22Z ERROR bird_tool_utils::external_command_checker] Could not find an available minimap2 executable.
[2024-03-13T18:11:22Z ERROR bird_tool_utils::external_command_checker] The STDERR was: "Illegal option --\n"
[2024-03-13T18:11:22Z ERROR bird_tool_utils::external_command_checker] Cannot continue without minimap2. Testing for presence with `which minimap2` failed
thread 'main' panicked at 'Failed to find installed minimap2: "Cannot continue without minimap2. Testing for presence with `which minimap2` failed"', src/external_command_checker.rs:9:10
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
We think that somehow Singularity is getting mixed up between system and container versions of which.
Would you be willing to switch to a different method of executable checking? I don't know Rust, but it looks like there is a pretty popular package for this: https://crates.io/crates/which
Thanks in advance!
The text was updated successfully, but these errors were encountered:
I encountered the same "ERROR bird_tool_utils::external_command_checker] Could not find an available minimap2 executable" when running a coverM.sif container built using apptainer, even though minimap2 was successfully installed in the container.
Amazing, thank you so much!! I just pushed an image with these changes, and I'll ask our collaborator if it works on their system now! @microjishuai, would you be willing to try as well?
docker run ghcr.io/vdblab/coverm:0.7.0-dev
# or
singularity run docker://ghcr.io/vdblab/coverm:0.7.0-dev
Hello! This is a bit of a strange request, but I am running into a strange error when running dockerized versions of CoverM. It is related to this somehow, I am not entirely sure why it only fails on a collaborators machine, but CoverM fails when attempting to find the Minimap2 executable using the
bash -c 'which minimap2'
command, which is here.When running this manually (not via CoverM), I get the following:
So far so good. When run on my institute's HPC via singularity, I get
which is good as well. However, when my collaborator attempts on their cluster, they get
That results in their CoverM calls failing with the following error:
We think that somehow Singularity is getting mixed up between system and container versions of
which
.Would you be willing to switch to a different method of executable checking? I don't know Rust, but it looks like there is a pretty popular package for this: https://crates.io/crates/which
Thanks in advance!
The text was updated successfully, but these errors were encountered: