Anurag Priyam

Check the contents of `run/h99_longest_transcript/lifted_cleanup.log`maybe

(and let me know too)

Do you mean it is taking too long or that the program aborts at blat step. Is it because `mygenome.fasta.out` can't be found or is it because it should have...

Very likely - because of the chunking, the coordinates specified in RepeatMasker's output no longer tally with target assembly's coordinate. I think you will need to get your hands dirty...

My bad. Since we aren't chunking `liftUp` doesn't need to happen either and thus [L174-176](https://github.com/wurmlab/flo/blob/master/Rakefile#L174-L176) should be commented out as well. Repeats mess up alignment edges, causing the resulting chains...

Works with zsh here. The error looks like the script was invoked with `sh`, which would not recognise the array on line 3. I suppose that can happen if zsh...

XML output generated by DIAMOND can now be imported and visualised in SequenceServer. I am closing this issue. Please open a new one for BWA support if you still think...

Thanks for the quick response, @mbj. Do you have any plans regarding when could one expect a solution to be in?

I could try, but only after mid-July. Before that I am quite swamped too. Besides, this is not urgent for me yet. I will ping you when I get time...

I will be happy to address this after I'm back (I'm home for ~2 weeks). In the meantime I would like to draw your attention to the [NOTICE.txt](https://github.com/wurmlab/afra/blob/master/NOTICE.txt) file, where...