Todd J Treangen

hi itsvetkova, Thank you for your interest in Harvest/parsnp. To help troubleshoot, two questions: 1. How much available RAM do you have on the laptop/workstation/server running parsnp for this 1000...

hi Zam, > Ping! apologies for the delay! > Is that something Harvest can generate?? This is something that could be generated but is not currently available as Harvest output....

hi Zam, thanks for the ping & my apologies for the delay in getting back. I hope to have something ready relatively soon (by early September), and an official release...

thanks for the ping/reminder Zam, still working on finalizing new release with prelim support for this, hope to have something for you soon, stay tuned!

Hello, > I have three issues when I ran Parsnp. ok, happy to clarify, please see below: > the step of "determining repetitive regions..." did not show up in my...

Glen, > Is there a way to create an alignment with parsnp/harvesttools that includes the unaligned sequences in >addition to the core sequences? Good question, while creating an output file...

hi aldertzomer, > I'm assuming this is some sort of bug in the code that excludes the reference sequence from being >selected as a query genome. thanks for opening this...

Hello, This error is most likely due to an empty or malformatted fasta file. Removing all such files from your genome directory should resolve the error. This should be fixed...

hi Casey, sorry for jumping in late here to help, my responses below (which mostly echo Serge's recent email): > Where does the frozen binary attempt to create the temporary...

Hello, This is by design; Prokka is used if you are running in isolate (-I) mode or running iMetAMOS ( initPipeline -W imetamos), but not on a metagenome. Given that...