mwykes

Update on this - I just used an alternative tool to decode variants from prefix.hap1.bam to vcf and the resulting vcf looks fine (no Ns) and consistent with the alignments...

Hi @BCArg, seqkit should be installed as part of pomoxis. If you were able to start the basecall_guppy rule, you must have a functional pomoxis venv, as the venv/bin/activation script...

Hi @morien, what version of virtualenv are you using? You can check by running `virtualenv --version` . I just installed the latest version 20.0.7 (`pip install --upgrade virtualenv --user`) and...

Hi @Sham397243, I just tried installing katuali on a new ubuntu16.04 docker image and it worked fine. Could try installing again and save all the error messages to a file:...

Hi @Sham397243, I can't see the file - could you try attaching the file (or copying it's contents) directly on github?

Hi @Sham397243, The log file suggests that the error is occuring when pysam is being installed. For some reason, pip is trying to compile pysam from source, and then complains...

It looks like you are using the i686 32bit version of Ubuntu. As there are no i686 wheels for Pysam, pip resorts to building from source. We have never installed...

Hi @Sham397243, It looks like virtualenv is not installed. Could you run the commands you previously ran on 32-bit ubuntu to install virtualenv in your new 64-bit Ubuntu installation before...

Hi @Sham397243, Apologies for the slow reply. It looks like there have been some [issues recently with virtualenv](https://github.com/pypa/virtualenv/issues/1963). Though the github virtualenv issue suggested that this was specific to python3.4,...

Hi @ccbruels, Illegal instruction messages typically occur when racon is compiled on a CPU which supports a certain instruction set and then used on another (typically older) CPU which does...