TypeError: sample_counts.biom does not appear to be a BIOM file!

[palomo11]

Hi,

First of all thanks for the nice pipeline.

I've running the pipeline without problems until Part 3, when it has called for the folowing error:

biom convert -i sample_counts.biom -o sample_counts.tab --to-tsv "TypeError: sample_counts.biom does not appear to be a BIOM file!"

Here I attach the file:

I got that file by doing:

library(biomformat) ... seqtab_biom <- t(seqtab.nochim) seqtab_biom <- seqtab_biom[rownames(seqtab_biom)%in%db_out_filt$seqs,] rownames(seqtab_biom) <- db_out_filt[db_out_filt$seqs%in%rownames(seqtab_biom),"ids"] biom_object <- make_biom(data = seqtab_biom) write_biom(biom_object, biom_file = "sample_counts.biom")

sample_counts.biom.zip

I hope you can help me with this.

Thanks in advance.

[vmaffei]

Hey, palomo11, make sure to use library(biom) by Joey instead of library(biomformat)

Specifically, use the latest dev version of biom

# install
library(devtools)
install_github("joey711/biom")

You only need to regenerate the sample_counts.biom file in Part 1 (so don't delete anything if you've already run everything else). Let me know if that works!

[palomo11]

Yes, it works! Thanks!

I had used biomformat because the first time I tried to install biom, it did not work. But now it is fine.

[vmaffei]

Good to hear! Let me know if you run into any further issues!