DIAMOND --all option not working

usegalaxy.eu support
1

DIAMOND option for outputting aligned reads (–al) not working, it just creates only result file without additional file with aligned reads.

2

Hi @vebaev

Odd. I’ve started up a test that outputs both the aligned and unaligned reads to see if I can reproduce this. I’m testing at UseGalaxy.eu with the most current version of the tool and with the tool test data. If you are working at a different server, please let me know the URL since sometimes that matters with weird errors.

Test history → https://usegalaxy.eu/u/jenj/h/test-diamond

The job is queued, and I wait like everyone else, so more feedback soon. I would suggest one rerun if you haven’t done that already. Let us know if you solve this, thanks!

3

I think when you select both unaligned and aligned all fine as in your case, but try selecting only aligned :slight_smile: In my case it did not output the additional file.

4

Hi @vebaev

Thanks for the followup. I can reproduce that and another small issue, plus a typo.

I’ve reported this to the developers here if you’d like to follow along or add anything else. Diamond: optional outputs produced do not respect tool form settings · Issue #6170 · galaxyproject/tools-iuc · GitHub

Thanks again! :slight_smile: