ibe-uw / tiara Goto Github PK

Here is the file where this occurred: [ attached in zip ]

Here is the command:

tiara -i $FP --probabilities --threads 16 -o tiara_output/${FP}.tiara.tsv

I'm using Tiara v1.0.2

Here's my error (I replace $HOME)

$HOME/anaconda3/envs/tiara_env/lib/python3.7/site-packages/tiara/src/transformations.py:195: RuntimeWarning: invalid value encountered in true_divide   result = result / np.linalg.norm(result, axis=1).reshape((-1, 1))

Is Tiara supposed to be the same for each run or is there a degree of randomness?

Hi.

From your docs/paper I assume that this size discrepancy is alarming?

grep euk whokaryote_predictions_T.tsv | wc -l
220366

grep euk tiara_pred.txt | wc -l
3161

This seems like an essential tool to have in metagenomics environments and would be (a little) easier to install in one-liner commands with more careful dependency checks. Having pip is ok too but it would make it that much more accessible so when I package up tools that depend on this I can just add this to the recipe.

Tiara lacks an option to spit out its version number when requested. It would be useful to have this to track the version automatically when writing e.g. a Nextflow pipeline.

It would be great to be able to run tiara directly on fastq files (including gzipped ones) without having to convert them first to fasta. Also, this would allow users to run assemblers that need quality values on sets of reads selected using tiara.

Currently, I have to merge all of my fasta files into a temporary file to run but it would be extremely helpful if I could just do :

zcat *.fa.gz | tiara -o test.tsv --predictions --threads 16