Issues with import Qiime artifacts or exported BIOM files #670
-
|
Hey, I am facing an obscure issue that I cant seem to pinpoint. I am unsure if this is a Mia issue or Qiime2 issue but desperation is setting in so gonna test my luck here aswell. I have been developing my analysis with a smaller subset of my total data. I have used Qiime2 to filter the larger cohort feature table down, and have successfully read it into a TSE with mia::importQIIME2 from the .qza artifact. The issues arise when trying to read in the full feature-table or a different larger filtered subset. Produces the error message: I have also tried to export a .biom file using Qiime2, and then using; But this also results in a similar error: The original smaller filtered subset remains functional, no issues. The problem persists between different envinroments and package versions. I am running an older version of mia in R 4.4.2 and also the devel version within the docker container provided on R 4.5.x. Sadly the data is sensitive so I can not share files, but am very grateful if someone can provide some assistance or direction on how to troubleshoot this. Feel free to remove this posting if this issue is irrelevant to Mia. I have posted the topic on Qiime2 forums aswell. |
Beta Was this translation helpful? Give feedback.
Replies: 1 comment 1 reply
-
|
Hello!
You should be able to produce the error with this:
The
and
The debugging is little bit tricky as I do not have access to the data (I think you have hdf5 file). You could try to run these functions above with We are happy to help you more, but unfortunately our options are quite limited. -Tuomas |
Beta Was this translation helpful? Give feedback.
-
|
Ok. This helps me forward. I do indeed have a hdf5 -files. I found a workaround of just using biom cli to convert the tables to .tsv -files and working from there, but it adds quite a few steps to the process of getting the data read in. I'll try to chip away at the problem with your suggestions, thank you. |
Beta Was this translation helpful? Give feedback.
Hello!
miacallsbiomformat::read_biom()function, and the error happens therehttps://github.com/joey711/biomformat/blob/0de05b1e78ea6ed42e079e07ccb13cecfd9eba6a/R/IO-methods.R#L76
You should be able to produce the error with this:
biomformat::read_biom("qiime/cohort/CC/exported-table/feature-table.biom")The
biomformat::read_biom()function tries to read the file with two different ways (BIOM-v1 is json file and BIOM-v2 is hdf5 file):jsonlite::fromJSON("qiime/cohort/CC/exported-table/feature-table.biom")and
biomformat::read_hdf5_biom("qiime/cohort/CC/exported-table/feature-table.biom")The debugging is little bit tricky as I do not have access to the data (I think you have hdf5 file).
Y…