ariba

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problems with resfinder and vfdb

2

Hi! I have some problems when I try to download resfinder and vfdb_full. In the case of resfinder this is the following error when I run ariba prepareref: ariba.reference_data.Error: Sequence...

fedeserral

mpileup: invalid option -- 't'

1

Hello, I want to use the last version of ARIBA (2.14.6) but an error occured when I ran ariba test or directly my samples. Here all the error messages (with...

Mx-Chpl

Hello, I want to use the last version of ARIBA (XXX) but an error occured when I ran ariba test or directly my samples. Here all the error messages (with...

Mx-Chpl

A cluster failed !! Any help would be great

1

I am running ariba as follows ariba run ../get_prep_ref/resfinder/out.resfinder.prepareref ../../preprocessing/K13657/K13657_R1_filtered.fastq.gz ../../preprocessing/K13657/K13657_R2_filtered.fastq.gz K13657/out.resfinderK13657run And I get the above error ariba.clusters.error: at least one cluster failed! stopping...

MariaPerezVazquez

Hi there, Hope you're well. I noticed there is a bug in ariba that occurs when insertions or deletions are multiples of three and do not start at the first...

pirale

NCBI Database Download Error

4

Im trying to download the NCBI reference database and keep getting this error. I did force Biopython 1.76 to deal with the BioAlphabet issue, but that is the only modification...

EmmaMills101

hi if the single-end data can be used for ariba ？i have single-end data to deal with. thank you.

daoerxianqiao

Conda package support for Python 3.7+

4

Is there support for Python3.7+? I am trying to install ariba into my conda environment following the guide on [this page](https://anaconda.org/bioconda/ariba). I tried using the first command there which is...

zmunro

Skip whole genome records

1

In order to prepare the NCBI acquired gene database, the records that are whole genome as determined by a prefix of 'AP' should be skipped

antunderwood

Currently, when using the `getref vfbd_full (...)` command downloading the full VFDB dataset, it is not possible to proceed with `ariba preparef (...)` using the resulting reference data without manual...

lknegendorf