atlas: atlas metatranscriptome data - MissingOutputException in rule run_spades

Hi,

I am running atlas (version 2.16.2) on metatranscriptome data. I started a new project for this with atlas init specifying --data-type metatranscriptome and changed the assembler to rnaSPAdes. When running the assembly I got the following error:

MissingOutputException in rule run_spades in file /home/jill/mambaforge/envs/atlasenv/lib/python3.10/site-packages/atlas/workflow/rules/assemble.smk, line 419: Job 1124 completed successfully, but some output files are missing. Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait: T231/assembly/scaffolds.fasta

On the forum here I found a similar issue explaining this is due to different naming of output files with rnaSPAdes. Following the solution proposed in this issue I modified the file assemble.smk with the code given there, which seemed to work for the author of the issue. However, when I restart atlas I still get the same error message.

I also saw this discussion where you suggest to make symbolic links to the according files. But I am not sure on how to do this, do I make this adjustment in the config file or also in the assemble.smk file?

What modification would I have to make to adapt the naming according with the naming atlas needs?

Thank you for any help you can give.

Best, Jill