Nehal Adel issues

Results 9 issues of


                                            Nehal Adel

card database update: ERROR: Helicobacter pylori rdxA mutation conferring resistance to metronidazole has {model_param}{snp}

Hi, I am trying to update the CARD database through abricate `abricate-get_db --db card --force` but I get this error `ERROR: Helicobacter pylori rdxA mutation conferring resistance to metronidazole has...

macOS: Solving environment: failed with initial frozen solve. Retrying with flexible solve.

Hi! conda environments are giving me hard time trying to install any new package. Mostly I use the bioconda channel. Operating system is macOS Catalina. It does not resolve environments...

Does Phylophlan support genome multiple alignment of samples as multiple contigs?

Hi, I have samples assembled to multiple contigs. I would like to construct a phylogenomic tree based on contigs of the samples. Does Phylophlan support this? Thank You

Running RagTag on bacterial short-read assemblies

Hi! I have short read assemblies from bacterial genomes that I am trying to improve using RagTag. My question is about how I can use RagTag for bacterial genomes considering...

Question: Why one gene can be present more than once in annotation?

Hello, I used prokka to annotate draft asssemblies followed by Roary for presence/absence matrix. Interestingly, I find the same gene sometimes or same gene_number (geneX_1,geneX_2) with different abundancies! One time...

PackagesNotFoundError: The following packages are not available from current channels: - sibeliaz

Hello, I am trying to install SibeliaZ on a conda environment using the following codes: `conda install -c bioconda sibeliaz` and `conda install sibeliaz ` but I keep getting the...

Creating Locus References Database

Hi, I am new to Kaptive. I wonder if there is an argument to help me create locus references database through Kaptive or if that you can add this input...

line 487: syntax error near unexpected token `>'

Hi, I installed plasmidID using bioconda in a separate conda environment and I tried to run it using the below command in which I supplied file names with their directory...

sort: Broken pipe

Hi! I tried to run Plascad on plasmid assemblies and also on the example file here in the repo, both returned `Warning: [blastp] Number of threads was reduced to 8...