DIAMOND --all option not working

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

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!