circlator

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Hi! Would it be possible to include the option to use a nucleotide fasta that should be searched for explicitly rather than translated with promer for the organisms that does...

thorellk

fixstart: no suitable promer matches found (due to deletion in dnaA sequence of assembler output)

2

I've hit what's probably a rare corner case. Circularization completed successfully, but the start position of the chromosome was not set properly. I checked the logs for fixstart and this...

0xaf1f

I am getting an error when using the latest Docker image (sangerpathogens/circlator:latest). I am trying to run fixstart. I get no errors when using a conda installation. ``` The following...

erinyoung

[seqdump (1).txt](https://github.com/sanger-pathogens/circlator/files/10421833/seqdump.1.txt)

HieuVoDL

Dear developer, I am planning to try minimus2 from circlator package. In order to run this, [AMOS](http://sourceforge.net/projects/amos/) must be installed. Hence, I tried installing AMOS using `conda install -c bioconda...

ChongLC

Changed dnaa.py to match new uniprot format.

matt-plumb

The option `gnuplotTested=true` is no longer valid on latest versions of canu, as noted by @ilnamkang

ramongallego

circlator stuck

1

My circlator (Circlator version: 1.5.5) run with the following command was running for 3 days and then stopped and never continued. Here is the last part of the log file:...

jpinus

Could you please tell me where there is a parameter to set the number of threads? I haven't been able to find it so far.

xubiy

I am trying to use circlator but encounter the following error when running the command: circlator all --threads 4 --verbose canu_outdir/canu.contigs.fasta canu_outdir/canu.correctedReads.fasta.gz circlator_outdir --debug Steps to Reproduce: Create a new...

AymanMkhalifa