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gavinmdouglas / FuncDiv

R package for computing alpha and beta contributional diversity metrics
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Beta Diversity empty directory #10

Open gonzalofe opened 4 months ago

gonzalofe commented 4 months ago

Hello. I have succesfully ran contributional alpha diversity on my data. When I run the beta diversity script, the output generated files are empty. I ran the code using the default contributions output from picrust2, and as the phylogenetic tree i used out.tre from picrust2. This is the code i used: beta_div_contrib(metrics = c('weighted_unifrac','bray'), contrib_tab = pmip_wide_contrib, in_tree = pmip_tree, ncores = 6, samp_colname = "sample", func_colname = "function.", taxon_colname = "taxon", abun_colname = "taxon_rel_abun", write_outfiles = TRUE, outdir= "~/Documentos/pmip/contrib_div/beta_div_pmip")

gavinmdouglas commented 4 months ago

Hi @gonzalofe,

Sorry to hear you're running into this issue.

Could you let me know how many functions, taxa, and samples are in your input dataset? My first guess is that perhaps the job ran out of memory. You can see the resources requirements for the test dataset I ran in Supplementary Table 1 of the FuncDiv paper.

Thanks,

Gavin

gonzalofe commented 4 months ago

cat("Number of unique functions:", length(unique_functions), "\n") Number of unique functions: 304 cat("Number of unique taxa:", length(unique_taxa), "\n") Number of unique taxa: 690 cat("Number of unique samples:", length(unique_samples), "\n") Number of unique samples: 60

one thing to keep in my with my dataset is that the taxa column has the asv complete sequence instead of an asv id... could this be resulting in running out of memory?

gavinmdouglas commented 4 months ago

Thanks for sending those details. I wouldn't expect memory issues with a dataset of that size.

Maybe using long taxon IDs could cause a problem, but I'm not sure. Would you mind sharing your input file? My email is gmail_screenshot

gonzalofe commented 4 months ago

I shared you the data via onedrive, did it get to you? Thanks.

gavinmdouglas commented 4 months ago

I did, thanks! I'll get back to you soon.

gavinmdouglas commented 4 months ago

Hi @gonzalofe,

It looks like there's a bunch of null characters in the file (they show up like "^@" with less and vim). So it became malformed at some point, and that is likely related to your error.

Cheers,

Gavin