Benedek Dankó

The same problem here on Ubuntu 20.04 LTS. Still, the best solution is cloning the repo and using that way.

> > The same problem here on Ubuntu 20.04 LTS. > > Still, the best solution is cloning the repo and using that way. > > What does that mean...

Even if I use `--sample-prefix=$base` the generated .somalier files have the name from the bam files' read group tag. Output files: [somalier.samples.tsv.gz](https://github.com/brentp/somalier/files/5183871/somalier.samples.tsv.gz) [somalier.html.gz](https://github.com/brentp/somalier/files/5183872/somalier.html.gz)

> yes, you would change `--sample-prefix` to be unique for each sample, not to a shared $base. OK, I will try that, thank you!

Now the generated .tsv files look OK, but the html file is still blank. Output files: [somalier.samples.tsv.gz](https://github.com/brentp/somalier/files/5185127/somalier.samples.tsv.gz) [somalier.html.gz](https://github.com/brentp/somalier/files/5185128/somalier.html.gz)

Thank you very much! Yes, all samples are included, some of which have quite bad/lower quality.

For me this helped: Changing the `def authorization_url(self)` function in the linkedin.py file: ```python def authorization_url(self): qd = {'response_type': 'code', 'client_id': self.key, 'scope': (' '.join(self.permissions)).strip(), 'state': self.state or self._make_new_state(), 'redirect_uri':...

Thanks for the quick reply!

> > Hello, > > I generated the Whippet index file: > > ``` > > julia bin/whippet-index.jl --fasta data/genomes/fasta/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz --gtf data/transcriptomes/gencode/gencode.v34/gencode.v34.annotation.gtf.gz --index data/whippet_index > > ``` > > >...

> > > > Hello, > > > > I generated the Whippet index file: > > > > ``` > > > > julia bin/whippet-index.jl --fasta data/genomes/fasta/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz --gtf data/transcriptomes/gencode/gencode.v34/gencode.v34.annotation.gtf.gz...