Difficulties getting the pipeline run about viralrecon HOT 2 CLOSED

Hi @ktrns ! Hope you are and your loved ones are keeping well :)

The minia assembler was just added to the pipeline a couple of days ago so we havent really stress tested it much. By default, the pipeline will run all assembly tools so maybe you can try re-running with --assemblers spades,metaspades,unicycler -resume.

Command looks great other than the fact that the pipeline isnt using AWS iGenomes so you can remove the --igenomes_ignore flag.

I would like to know why minia is failing though. Can you cd into the work directory for the process that failed and send me the output of ls -la please? May be easier to discuss this in real-time on the #viralrecon channel on nf-core Slack.

from viralrecon.

This was partly fixed by using the human Kraken2 database as made available here and not a Kraken2 database built using the --standard flag as this will filter out most of the reads including the viral ones that we are interested in. Other issues have been reported on Slack but these relate to not enough viral reads being available to go through some of the assembly steps.

from viralrecon.