Torsten Seemann comments

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                                            Torsten Seemann

Names for forwards and reverse reads does not match. Cannot continue

Thanks once again @aunderwo

Names for forwards and reverse reads does not match. Cannot continue

Argh. Our other system is to use `SAMPLE/{R1,R2}.fq.gz` but that fails too. `Names for forwards and reverse reads does not match. Cannot continue` :(

Names for forwards and reverse reads does not match. Cannot continue

I don't feel I should have to rename my files for a tool to work :(

After kmc, error "Stopping! Signal received: 13"

I get `pred.tsv` but `detailed_serogroup_info.txt ` is missing :(

No detailed output file

Is the problem related to this? https://github.com/sanger-pathogens/seroba/issues/43

Can't build DB? False | ariba prepare_ref | no such file

Thanks Ant! @aunderwo

pkg_resources.ResolutionError: No script named 'seroba'

Why do I need `ariba` ? And what is this magic `MPLBACKED="agg"` ?

Snippy-multi issue

`snippy-multi` takes a 3-column (or 2-column) TSV file (with Unix line endings) as input. To check the input is in the correct format `cat -vet samples.tsv` You will see `^I`...

Snippy-multi issue

@arunprasanna83 oh... you have uncovered a bug in my script! it seems i ignore lines with comments `#` but I don;t skip blank lines! I have tagged this as a...

There is something wrong with your reference file. Valid file types are .fasta, .gbk, .fasta.gz, .gbk.gz. Please check your inputs and try again.

@Vikash84 did you get it working in the end? If you think any2fasta is the problem, file an issue here: https://github.com/tseemann/any2fasta