Many thanks for the help so far! I have been running nf-core/mag 5.2.0 in offline mode using 4 ONT reds from http://www.inbirg.com/hlrmdb/ as a test. Using extflow run nf-core/mag --skip_metabinner --run_busco false --input samplesheet.csv --outdir mag_out --gtdb_db /z/datasets/ds_mr_metagenome/nfcore_pipelines/data/gtdbtk_r226_data.tar.gz -profile sge,singularity In NFCORE_MAG🔍GTDBTK:GTDBTK_SUMMARY I now get an error when executing "summary_gtdbtk.py --extension fa --out gtdbtk_summary.tsv”. I have attached stdout (outlog.txt)

moreinfo

To help we'd love a few more details please: 1. The Nextflow command you used to launch the pipeline 2. Any custom Nextflow config files 3. The full error message 4. The corresponding

.nextflow.log

file, where you are running the analysis. Remember to use triple backslashes on their own lines for code blocks. Also take a look at https://nf-co.re/usage/troubleshooting for more information on debugging failed pipelines. Thanks!

If you could send nr 4 (it's a hidden file, so you need to use

ls -a

to see it

nextflow.log.1

That still works...

nextflow.log

I'm a bit confused... somehow GTDBTK_SUMMARY is executing before GTDBTK_CLASSIFYWF has even started... We do have a completeness/contamination filter, to remove low quality MAGs, but that should give a warning that I don't see in the log...

No problem . Thanks for all your help !

Hi @Peter Bjarke Olsen, I see you disabled BUSCO, so no Bin QC is run, and because of that the Nextflow resolves that GTDBTK_SUMMARY is ready to run, and fails

Thanks Diego. I disabled BUSCO because it failed https://nfcore.slack.com/archives/CE9MS66BS/p1764578174712409

Yes, we have a fix for that already, it will be in 5.3.0. For the meantime, you can try with CheckM2?

Thanks Diego. My current run is : nextflow run nf-core/mag --skip_metabinner --run_busco false --input samplesheet.csv --outdir mag_out --gtdb_db /z/datasets/ds_mr_metagenome/nfcore_pipelines/data/gtdbtk_r226_data.tar.gz -profile sge,singularity . What should I change here ? I am not sure. Both --skip_metabinner and --run_busco false are added to avoid errors.

To that add

--run_checkm2

and that's it

Thanks Diego !