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'Failed to limit memory to' error on Mac M3 Max, while SPAdes runs normally via a virtual Linux machine on the same computer. #1324
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The error in log is completely unrelated to that warning. First of all, starting from Monterey it is not possible to really limit the used memory in many circumstances unless one is not running under root. So, we demoted error and produce a warning here:
Going back to the error, it is an I/O error: SPAdes is unable to open one of its intermediate files. So, I'd suppose you to check system log & free disk space available. |
The system has 4TB free space. Error is reproducible. |
Check system limits on number of open files? E.g. via |
I've increased to 1,000,000 |
Did it really increase the limit? Have you checked via |
Yes, I've checked by |
Description of bug
The same FASTQ files are processed normally in a virtual Linux machine (Ubuntu 22.04.02 ARM64) on a Mac M3 Max with macOS Sonoma, but fail with a 'failed to limit memory' error when executed purely in macOS.
spades.log
spades.log
params.txt
params.txt
SPAdes version
v4.0.0
Operating System
macOS Sonoma 14.1
Python Version
3.9.6
Method of SPAdes installation
binaries
No errors reported in spades.log
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