These are chat archives for dereneaton/ipyrad

Dec 2018
tracy burkhard
Dec 18 2018 15:50
Hi! I am having a problem getting ipyrad to work on a HPC at my university. I am trying to run the first step, and what is happening is that ipyrad is getting stuck during the sorting step ( [ ] 0% sorting reads #indefinitely). I have been talking with the staff who run our uni's supercomputer, and it appears to be an issue with how ipyrad is using the ipcluster random port range, although they are uncertain on how they could limit or assign the application to specific ports. Any help with this issue would be greatly appreciated. I can forward the chain of emails as well. Thanks! Tracy
Seth Hamby
Dec 18 2018 20:20
I am trying to filter the output vcf file from iPyrad in vcfTools, but the file is not recognized. I was told that there are some formatting differences between the iPyrad output vcf and the dDocent output vcf, but I am unsure how to correct the problem. When I filter SNP's with the dDocent vcf file, it works fine, but with the iPyrad output vcf, it filters out all samples and tells me I have no more data left to analyze! When I look at the logfile, it says that the file cannot be recognized. Please advise. Thank you.