Bryce Kille

@valeriaR89 Thanks for running that. Looking at the output its not immediately clear what's causing the issue. Would you mind running `ls -lh /storage/snp/output` ? I'd like to see which...

Hi, It looks like the `parsnp.ggr` file is missing, which is causing the `.mblocks` file to be empty resulting in a failed RAxML run. If your intermediate files are still...

Yup :disappointed: I'm new to autotools and have been putting this on the backburner. I'll see if I can take care of this.

Hi @chrisgulvik! Thanks for opening an issue regarding this feature request. We have plans to support this functionality at some point in the future, but as of right now there...

Hi @Archaea810! Parsnp alignments are allowed to contain indels, and in the VCF file the record will have the `INDEL` filter set. That being said, it is possible that Parsnp...

Thanks for opening an issue! Could you * Provide the output of the command with the `--verbose` flag * Provide the contents of the `parsnpAligner.log` file With those, I hopefully...

Does the reference and/or any of the inputs have multiple contigs? Unfortunately, I don't work on the Gingr repo, but I do know that the header information of multi-contig inputs...

Hmm, I'm not sure who maintains that repository now. Would you mind pasting the output of the `parsnpAligner.ini` file here? If parsnp truly isn't aligning that region, then it should...

Hi @thierrygrange, sorry for the delayed response. I've made a fix that will make sure the pyspoa module is not imported if you run with `--no-partition`. It will be in...

Hi @AceM1188, thanks for opening an issue and attaching the files! I am able to run parsnp on these files with no issue. Due to the error message you received...