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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
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Potential issue in QUAST conda recipe - dependency minimap2 #50104

Open LiaOb21 opened 4 weeks ago

LiaOb21 commented 4 weeks ago

Hello everyone,

I am experiencing an issue with the new QUAST conda recipe. I saw the recipe was updated two months ago, even if QUAST version remains 5.2.0.

This is what is happening with the new conda recipe (installed a couple of days ago):

WARNING: Version of installed minimap2 differs from its version in the QUAST package (2.24). Please make sure that you use an actual version of software.
WARNING: Version of installed minimap2 differs from its version in the QUAST package (2.24). Please make sure that you use an actual version of software.
WARNING: Version of installed minimap2 differs from its version in the QUAST package (2.24). Please make sure that you use an actual version of software.
WARNING: Version of installed minimap2 differs from its version in the QUAST package (2.24). Please make sure that you use an actual version of software.

ERROR!   2  Failed aligning contigs asm1 to the reference (non-zero exit code). Run with the --debug flag to see additional information.

ERROR!   4  Failed aligning contigs asm2 to the reference (non-zero exit code). Run with the --debug flag to see additional information.

ERROR!   3  Failed aligning contigs asm3 to the reference (non-zero exit code). Run with the --debug flag to see additional information.

In this environment minimap2 version is 2.28-r1209.

In an older separate QUAST environment, I have the same warning about the version of minimap2, but it doesn't fail to align contigs to the reference:

WARNING: Version of installed minimap2 differs from its version in the QUAST package (2.24). Please make sure that you use an actual version of software.
WARNING: Version of installed minimap2 differs from its version in the QUAST package (2.24). Please make sure that you use an actual version of software.
WARNING: Version of installed minimap2 differs from its version in the QUAST package (2.24). Please make sure that you use an actual version of software.
WARNING: Version of installed minimap2 differs from its version in the QUAST package (2.24). Please make sure that you use an actual version of software.

Here minimap2 version is 2.26-r1175.

The data I'm analysing with the two different environments is exactly the same.

I don't know if anyone else experienced the same issue. With the older environment I get all the outputs.

Thank you in advance if you manage to look into this.

Lia

LiaOb21 commented 2 weeks ago

An update on the possible problem linked to minimap2.

I tried resolving the issue by removing minimap2 from the first environment mentioned above (the broken environment) and installing it again as minimap2=2.27 and minimap2=2.26, but I keep getting the same error message. I suspect that the problem is caused by something else.

EDIT: if I avoid the use of the -r flag with the reference genome, QUAST completes without errors (in a new just installed environment). Could it be a breakage of a dependency of minimap2?