I'm trying to run GGCAT on the following dataset: https://ftp.ebi.ac.uk/pub/databases/ENA2018-bacteria-661k/
I had 5T of free disk space and the following flags: -k 31 -m 32 -j 8 -s 1
However, my runs keep panicking on too many open files despite raising ulimit -n. My first two runs with ulimit -n of 1024 and 4096 crashed in the following phase:
Started phase: kmers merge prev stats:
Thread panicked at location: libs-crates/parallel-processor-rs/src/memory_fs/file/internal.rs:248:26
Error message: called `Result::unwrap()` on an `Err` value: Os { code: 24, kind: Uncategorized, message: "Too many open files" }
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Then I raised the ulimit -n to 10240, and it crashed in the following phase:
I'm trying to run GGCAT on the following dataset: https://ftp.ebi.ac.uk/pub/databases/ENA2018-bacteria-661k/ I had 5T of free disk space and the following flags:
-k 31 -m 32 -j 8 -s 1
However, my runs keep panicking on too many open files despite raisingulimit -n
. My first two runs withulimit -n
of 1024 and 4096 crashed in the following phase:Then I raised the
ulimit -n
to 10240, and it crashed in the following phase: