kmdiff
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tlemane
Differential k-mer analysis
`kmdiff` by default use `std::thread::hardware_concurrency()` to get the number of available threads. in cli.cpp but, because there's a but ;-) `hardware_concurrency` returns, when possible, the underlying hardware capability to run...
Hello, I am rtying to run kmdiff on our cluster but it difficult. I notably encounter this strange behavior: kmtricks processes super kmers and counts partitions but does not write...
Hello, Would it be possible to use BAM files as input? Thanks for any insights.
Does kmdiff correct for different number of reads per sample? For example, if there are 10 million reads for one sample and 20 million reads for another, will the second...
Thanks for this very nice tool! I'm interested in doing some permutations of my groups, in order to get an impression of what a baseline number significant hits is for...
Hi, FYI, I ran into issue building with install.sh script where it couldn't find the LAPACKE library. After digging into this, I found that my environment had OpenBLAS 0.3.18 and...
``` $ \time ~/tools/kmdiff/kmdiff-v1.1.0-bin-Linux/bin/kmdiff diff --km-run kmdiff_run --output-dir kmdiff_out -s 0.01 -1 12 -2 17 [2025-02-22 13:23:11.777] [info] Process partitions [2025-02-22 13:23:12.581] [error] Killed after receive Segmentation fault:SIGSEGV(11) signal. Demangled...
Hi all, kmdiff is great! I'd love to run it on larger datasets but keep getting crashes, I assume because it's trying to run in RAM? Is there a way...
Hi all, I recently ran step 1 of the kmdiff pipeline (kmdiff count) successfully. However, when attempting Step 2 (kmdiff diff), I encountered an error. Here's the command I used:...
While running the kmdiff diff step, I encountered a repeated malloc.c:2415 assertion failure. Below is the relevant output: [2025-05-01 12:52:32.858] [info] Process partitions kmdiff: malloc.c:2415: sysmalloc: Assertion `(old_top == initial_top...