Hi all, I’m running nf-core/aMeta with full NCBI NT (Jan 2021) to build the MALT database, and the MALT build step has been running for more than 2 months now It’s not throwing any error, not crashing, not stopping — just continuously running. System is Ubuntu 20.04.1 (kernel 5.15.0-139-generic), Nextflow 25.04.6, using

-profile conda

. We’ve allocated high RAM (KrakenUniq chunk size 600GB), and there’s no obvious memory or disk error. Is it normal for MALT build with full NT to take this long? Or does this suggest some I/O bottleneck or resource misconfiguration? Would appreciate any suggestions on what to check to confirm whether it’s actually progressing or just stuck.

This channel is about the nf-core/tools package, not pipeline specific tools

https://github.com/NBISweden/nf-core-ameta is not an official nf-core pipeline, it just uses the template

The project is still going. I've only recently got the go ahead to keep working since they ran out of support hours a while ago. Make an issue on the repo though so I can take a look at it. Either way though the Snakemake version is the official one, so use that over this. This is simply a port that will be merged into Eager and then is likely to be archived when Eager takes it over and tests are in place to maintain parity.

We have tried to use snakemake now but i am confused what to do if have paired end data what kind of sample sheet we are supposed to give as a input kindly help on this matter.

I'm not the main developer of that version. You should make an issue on the Snakemake version and they should get back to you.