ariba

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Hi, nose has been deprecated long back, and has not received an update in years, it's official page says so as well, see [here](https://nose.readthedocs.io/en/latest/index.html) It is advised to switch to...

nileshpatra

Incompatible Biopython version in Ariba Docker image

1

I got an error when running 'ariba getref ncbi out.ncbi' in Docker. The error is: **_ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be...

KuangXY3

Support for downloading cgMLST schemes?

1

I was curious if ariba could download a cgMSLT scheme from pubMLST or do I have to create a custom database for all 1.5K loci?

slvrshot

NCBI Data Download Error

1

```javascript E-fetching 6055 genbank records from BioProject PRJNA313047 and writing to. This may take a while. Parsing genbank records. 'NG_074760.1' Processing record 1 of 6055 (accession NG_074760.1) 'NG_074759.1' ..... Processing...

hackerzone85

Try to understand the report column 27 and 29

1

Hi, When I looked at the `report.tsv` file, I found that the sum of the column 29 `smtls_nts_depth` is not equal to column 27 `smtls_total_depth`. May I know why?

pixuenan

Problem interpreting 'gene' + 'var_only' columns

1

From the wiki: ``` 3. gene | 1=gene, 0=non-coding (same as metadata column 2) 4. var_only | 1=variant only, 0=presence/absence (same as metadata column 3) ``` From my understanding, if...

ghost

Biopython 1.78 not compatible because of Alphabet missing

3

Using ARIBA for gene detection, I tried to download the ncbi database with the following line `ariba getref ncbi out.ncbi ` ``` E-fetching 5795 genbank records from BioProject PRJNA313047 and...

besnarda

WARNING: I tried to get the version of spades with: "/extra_storage1/miniconda3/envs/[email protected]/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9\.]+)" Exception ignored in: BrokenPipeError: [Errno 32] Broken pipe WARNING....

ajkarloss

Unable to download Escherichia coli#1 and Escherichia coli#2

2

Traceback (most recent call last): File "/usr/local/bin/ariba", line 4, in __import__('pkg_resources').run_script('ariba==2.14.4', 'ariba') File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 658, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1438, in run_script exec(code, namespace, namespace) File...

RotimiDada

Hi there, I keep on obtaining an error when running ARIBA and VFDB information. From 96 samples, ARIBA failed in 2 samples given the same log details: > Error making...

JFsanchezherrero