argweaver
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mdrasmus
Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)
Hello, I try to use this script, but nothing happen when I put the commands, can you help me please, or maybe give some advice for use this script. Thanks
Hello, I have a problem running arg-sample, I hope you can help me with that. **The parameters are:** `../bin/arg-sample \ --fasta h3a_phased_haplotypes_johnsoni_phoenix.fas \ -N 10000 \ --recombrate 1.6e-8 \ --mutrate...
Hi @mdrasmus , I tried to use arg-sample to generate my smc files, while I got an error like this: `arg-sample: src/argweaver/sample_thread.cpp:444: void argweaver::arghmm_forward_alg(const argweaver::LocalTrees*, const argweaver::ArgModel*, const argweaver::Sequences*, argweaver::ArgHmmMatrixIter*,...
My species (non-model) does not have phased haplotypes (less than 5 individuals sequenced till now). So i am trying to use the --unphased option in arg-sample. However, it says it...
With some OSes / libraries (but not all) I get the following message when running the attached .sites file (here saved as .txt to allow github uploading). ``` arg-sample --sites...
By adding the sequence/chromosome name to each row, these file formats will be easier to index with tabix. Also bgzip should be an optional compression format.
Programs/functions that use tabix and bgzip should check for the presence of these programs and if not present fail with a useful error message. Some example programs: - arg-layout -...
pip install argweaver throws this error ```bash $ pip install argweaver Collecting argweaver Using cached argweaver-0.8.1.tar.gz (1.1 MB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error × python setup.py egg_info did...
Surprised to get the following error with what does not seem like a huge amount of data. Halved the number of samples (and tried separate runs with both halves) and...
Hi, I have successfully run the function arg-sample on 63 out of 64 genomic windows (2 MB windows of a single chromosome). For some reason, I have a stubborn window...
