nextflow run nf-core/mag \ -r 5.4.0 \ -profile singularity \ --input samplesheet.csv \ --outdir results \ --skip_spades \ --skip_spadeshybrid \ --skip_shortread_qc \ --skip_concoct \ --skip_comebin \ --skip_metabinner \ --binning_map_mode own \ --bin_domain_classification \ --run_checkm2 \ --refine_bins_dastool \ --postbinning_input refined_bins_only \ --gtdb_db /path/to/gtdbtk/release226/ [1:42 PM] Issue 1: BUSCO publish error BUSCO runs by default (

run_busco = true

). Without explicitly setting

--run_busco false

, the pipeline failed with:

ERROR ~ Failed to publish file: BCD0846-auto-busco to: GenomeBinning/QC/BUSCO/MEGAHIT-DASTool-BCD0846/BCD0846-auto-busco [copy]

Issue 2:

--postbinning_input refined_bins_only

does not pass refined bins to CheckM2 and GTDB-Tk DASTool produced 396 refined bins across 24 samples. However CheckM2 and GTDB-Tk only processed unbinned contigs from one sample. The pipeline completed with this warning:

No contigs passed GTDB-TK min. completeness filters. GTDB-TK summary will execute but results will be empty!

Hi @Brad Zhang, Issue 1 should be fixed in 5.4.2 (https://github.com/nf-core/mag/pull/1002) Issue 2 has a fix too, but not released yet (https://github.com/nf-core/mag/pull/1011). You can use dev branch (

-r dev

) for the meantime.

Thank you so much! Brad