Torsten Seemann

FYI: `--opts "careful"` is not correct, as it will pass `careful` to Spades, rather than `--careful`. It would be instructive to use the `--report` option of Snippy to look at...

You have a good point! I think I should also be using trimmed reads (if it was enabled) because I use `samclip` in the alignment filter and if there was...

It sounds like this is a bug in ParSNP ? Why would it see the `-` hyphen in the sequence _description_ and think the file is aligned FASTA? Maybe @treangen...

Yes I run `fixmate` in the Snippy pipeline for which samclip was developed but i don't do it here....

Perhaps `--fast` could be alias for `--assembler skesa --noreadcorr --nocorr` ? It does its own read correction, and doesn't seem to cause SNPs. Overlapping pairs still helps.

What does `java -version` say for you? Can you please upgrade to Shovill 1.1.0 ?

@marchoeppner I think an assembly stats output in a machine readable form is a good idea. @darwinbandoy I won't be adding an "aggregate report" option though; that is best done...

Is it possible it ran successfully and that there are *no* genes matching your query? Is the result affected by ` -c FLOAT percentage of isolates a gene must be...

Run your command with ONE gene and see what happens. Then paste the full exact command you ran here if it doesn't work.

I note the front page says this: