Beta Diversity empty directory
Opened this issue · 6 comments
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")
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
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?
I shared you the data via onedrive, did it get to you? Thanks.
I did, thanks! I'll get back to you soon.
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