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Snitkin-Lab-Umich / prewas

R package to perform data pre-processing for more informative bacterial GWAS
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Error: Failed to retrieve the result of MulticoreFuture (future_apply-6) #10

Open hsinjou0714 opened 3 years ago

hsinjou0714 commented 3 years ago

Hi! My Prewas wasn't able to be finished due to the following issue: image Looks like it's related to the future library? Could you please help me with it ? I also wonder if there is a way to run prewas faster if I have a large vcf file (after vcfR it's around 6GB). Thanks !

hsinjou0714 commented 3 years ago

There is another issue when I retry with anc = FALSE image However, when I looked in to my vcf, the columns and chrom positions are unique, so I'm not sure how should I fix this? code: image

I used the following to merge my vcf (snps was called by snippy): bcftools merge -i ANN:join -m both -o out_pao1_bactome_multivcf.vcf -Ov */snps.vcf.gz

Wonder if you have any suggestions?

zenalapp commented 3 years ago

Hi! Sorry we didn't respond to this earlier, I was in the middle of finishing up my PhD thesis.

  1. Some of the code we used before for future is deprecated. I removed this from the code. Could you try re-installing the GitHub version and re-running the code:

    install_github('Snitkin-Lab-Umich/prewas')

  2. If you would like to improve your performance, you can register a future plan prior to calling prewas:

    future::plan(future::multicore, workers = 2)

We used the multicore plan to split the work across 2 cores. See the future documentation for more about picking the best plan for your use case. Notably, multicore does not work inside RStudio or on Windows; you will need to use multisession instead in those cases.

I will open an issue to clarify this in the vignette.

  1. With respect to your issue with anc = FALSE, could you please provide some data that reproduces the issue so I can help troubleshoot it?