-
Hi! I am trying to run the pipeline for 12 samples, with the following parameters:
`nextflow run EBI-Metagenomics/emg-viral-pipeline --fasta "./contigs_rnaSpades/*.fasta" --cores 8 -profile local,d…
-
Hi,
I have run the `GCF_009025895.1.fna` as the input fasta file.
When I looked at the `GCF_009025895.1_find_proviruses/GCF_009025895.1_provirus.tsv`,
```
seq_name source_seq start …
-
Phigaro currently uses the GC score in a way that prophages are more likely to be GC-rich (i.e. genes have high GC content) than GC-poor. Although the benchmarking suggests this is a good approach it …
-
This is a very interesting and useful tool, but I have a question, which is the bed file in the output results, some of which have the following display
(phigaro) [kxy@zju Phigaro]$ cd /data/users/kx…
-
**Describe the bug**
Phables fails at Koverage step with error. I installed the latest version of phables using mamba, the install appears to work and the test is fine. The run fails when it reaches …
-
Hi Fmalmeida,
I am getting the following error as I try to resume my pipeline analysis.
`Pulling fmalmeida/bacannot ...
Remote origin did not advertise Ref for branch refs/heads/116-integron_finder…
-
Hi!
I am trying to run VIRify in an HPC cluster using nextflow (22.10.4.5836), slurm and singularity (3.4.2).
This is the command in my sbatch script
`nextflow run /CCAS/home/cpavloudi/.nextf…
-
Tool Name: Phispy (or the equivalent, to identify prophages in bacterial genomes)
Tool Link:
Available on [Bioconda](https://anaconda.org/bioconda/phispy)
Available on [nf-core/modules](ht…
-
Hello,
I try to run the virify pipeline using slurm singularity on our cluster, but I get : annotate:checkV failed.
At first , run a small number of contigs (10contigs) using core 1 and max_cores 1 …
-
Hi @jtamames,
While running the pipeline, I encountered a recurring issue at the chemM.batch.pl step, as indicated by the log file. Specifically, the file 17.human_metagenome.checkM was not generat…