Ben J Woodcroft

icon indicating a website link https://research.qut.edu.au/cmr/team/ben-woodcroft icon indicating an email [email protected]

icon company Queensland University of Technology icon location Brisbane, Australia icon location Assoc. prof. of microbial informatics at the Centre for Microbiome Research (CMR)

Results 187 comments of Ben J Woodcroft

What is the meaning about "--min-read-percent-identity "

Hi, It seems I forgot to respond here - it is the percent identity of the read and the reference are calculated, and any mappings that do not pass the...

Regarding galah output

Hi Shail, Thanks for kind words. This can happen when no genomes are clustered together. Did you look towards the end of the file too? A bit odd that the...

Regarding galah output

Hmm, this is a little odd. Is it hard to transfer these bins to me somehow? Obviously will only look at them in the context of this bug. Thanks.

Regarding galah output

Hi again, Lots of MAGs you have there.. nice. Sorry, between attempting to read this issue on my phone's small screen and not having used this format in a while,...

Switch genome name lookup to hashmap

Maybe just use string from

Switch genome name lookup to hashmap

Something along these lines? https://stackoverflow.com/questions/65549983/trait-borrowstring-is-not-implemented-for-str

Dashing failed

Hi, I think this is likely due to a compilation issue with dashing - does running it outside of galah work?

bam_generator] Failed to correctly find or parse BAM file at "/tmp/coverm_fifo.wyqhN9T2ujOl/foo.pipe"

Hi Holly, Thanks for including the command you used. I think this might already be fixed in the code in the repo, but just not released. Are you able to...

Request: Foreign function interface

Hi, Thanks for your interest. This sounds like a good idea, though I would probably like to concentrate my efforts on some other things first. Without asking you to delve...

Too many open files error!

Hi, Thanks for the kind words. That's a new one. Likely what is happening is due to their being many many samples, which means many mappings, which means too many...