Sam Lipworth

segmentation fault

5

Hi, When mapping sequences (from nanopore reads) to a graph (~ 5.2M) I get no output an segmentation fault. Works OK when I run the test - is there a...

not enough memory

4

Hi - I am getting a memory error which I don't understand - as you can see I'm using a cluster with ~ 2TB of RAM and so I don't...

failed while running raxml internal sequence reconstruction gubbins

2

I get the following error, the sequences are all of decent quality, I'm running gubbins installed through conda. What is the issue?

pre-2015 data?

1

Is it possible to get data pre-2015 from anywhere?

Plot intersection size on a log scale

10

Is this possible?

problem with expand_no

4

My understanding of expan_no in panatoo-gene-neighbourhood is that it should give N genes up and downstream of the target gene X. In my version of panaroo (from conda - version...

?! doesn't work

3

Trying to code a custom scheme (diabetes complication severity) - trying to use ?! as not followed by - the visualise command recognises this correctly but then I get an...

easier input of fasta

1

Hi, looks useful - I want to run it on thousands of assemblies - might be useful to modify so that I can feed it a text file rather than...

e.g. if I want particular virulence genes annotated as well as the standard plascad output?

pyhmmer not found

6

Hello, Installed via conda, ERROR: Pyhmmer could not be executed! Please make sure Pyhmmer is installed and executable or skip requiring workflow steps via via '--skip-cds --skip-sorf'. mamba install pyhmmer...