Hello, Im trying to run the pipeline to assemble environmental samples, this is my code:

#!/bin/bash
#
#SBATCH -o logs/MAG.log_%J.out
#SBATCH -e logs/MAG.log_%J.err
#SBATCH --mail-type END
#SBATCH --cpus-per-task 36
#SBATCH --mem 150GB
#SBATCH -p long

cd /shared/projects/metat_margo/vidy/nf-core-MAG

module purge
module load nextflow
module load singularity
module load openjdk

nextflow run nf-core/mag \
	-profile ifb_core \
	-r 5.3.0 \
	--input /shared/projects/metat_margo/vidy/samplesheet.csv \
	--outdir /shared/projects/metat_margo/vidy/output/nf_core_mag \
	--spadeshybrid_fix_cpus 36 \
	--fastp_trim_polyg \
	--gtdb_db /shared/bank/gtdbtk/release226/ \
	--gtdbtk_pplacer_cpus 4 \
	--skip_metaeuk \
	--run_checkm2 \
	--checkm2_db /shared/bank/checkM2/version_3/CheckM2_database/uniref100.KO.1.dmnd \
	--refine_bin_dastool \
	--postbinning_input both \
	-resume

And the job its failing because there is a problem with the nf-amazon pluging. This is the line of the .nextflow.log: Jan-22 155241.575 [main] DEBUG nextflow.Session - Session aborted -- Cause: The following invalid input values have been detected: * --igenomes_base (s3://ngi-igenomes/igenomes/): could not validate file format of 's3://ngi-igenomes/igenomes/': Missing plugin 'nf-amazon' required to read file: s3://ngi-igenomes/igenomes/ * --checkm_download_url (https://zenodo.org/records/7401545/files/checkm_data_2015_01_16.tar.gz): the file or directory 'https://zenodo.org/records/7401545/files/checkm_data_2015_01_16.tar.gz' does not exist I've read somethings about ajusting the config file but Im not sure if is a problem of my config or if there is an issue with the cluster profile. Can someone help me?

Hi Carla The

--checkm_download

thing is an annoying sporadic thing that we are thinking about how to fix - basically Zenodo is sometimes(!) blocking downloads so fails validation by a plugin in the pipeline. Just running it again should fix it (or download the database yourself and supply it the pipeline, even if you don't use CheckM itself) For the

--igenomes-base

error, that is a bit odd. The

nf-amazon

plugin should be downloaded by nextflow by default 🤔 . To get around it you could try specifying

--igenomes_base false

Awesome thanks, Ill try those things!