I am using 5.3.0/5 in oflline mode as: export PATH=/z/bio/biotools/apptainer_1.2.5-1.el7/bin:$PATH export NXF_SINGULARITY_CACHEDIR="/z/datasets/ds_mr_metagenome/nfcore_pipelines/nf-core-mag/nf-core-mag_5.3.0/singularity-images" export NXF_ENABLE_FS_SYNC=false export NXF_OFFLINE='true' nextflow run /z/datasets/ds_mr_metagenome/nfcore_pipelines/nf-core-mag/nf-core-mag_5.3.0/5_3_0/ --run_checkm2 --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 --checkm2_db /z/datasets/ds_mr_metagenome/nfcore_pipelines/data/checkm2_database.tar.gz -profile sge,singularity 1>out 2>error But I get the error below. The mode if offline and the checkm2_database is specified so why this error ? The following invalid input values have been detected: * --igenomes_base (s3://ngi-igenomes/igenomes/): could not validate file format of 's3://ngi-igenomes/igenomes/': Unable to execute HTTP request: Connect to ngi-igenomes.s3.us-east-1.amazonaws.com:443 [ngi-igenomes.s3.us-east-1.amazonaws.com/52.217.228.194, ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.207.169, ngi-igenomes.s3.us-east-1.amazonaws.com/54.231.138.210, ngi-igenomes.s3.us-east-1.amazonaws.com/3.5.20.128, ngi-igenomes.s3.us-east-1.amazonaws.com/52.216.220.170, ngi-igenomes.s3.us-east-1.amazonaws.com/16.182.72.146, ngi-igenomes.s3.us-east-1.amazonaws.com/52.216.218.114, ngi-igenomes.s3.us-east-1.amazonaws.com/16.15.181.82] failed: Connect timed out (SDK Attempt Count: 6) * --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 -- Check script '/z/datasets/ds_mr_metagenome/nfcore_pipelines/nf-core-mag/nf-core-mag_5.3.0/5_3_0/subworkflows/nf-core/utils_nfschema_plugin/main.nf' at line: 68 or see '.nextflow.log' file for more details

Can you try giving to your command

--checkm_download_url false --igenomes_base false

?

Thanks i added this and the error disappeared but now i get [nf-core/mag] ERROR: Both --skip_binqc and --run_<bin_qc_tool_name> are specified! Invalid combination, please specify either --skip_binqc or --run_<bin_qc_tool_name>. Strange: Is this a bug ?

REforamtting to make it more readable

nextflow run /z/datasets/ds_mr_metagenome/nfcore_pipelines/nf-core-mag/nf-core-mag_5.3.0/5_3_0/ --run_checkm2  --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 --checkm2_db /z/datasets/ds_mr_metagenome/nfcore_pipelines/data/checkm2_database.tar.gz   -profile sge,singularity   1>out 2>error

Thanks for the continued help ! Unfortutely I overwrote the output. What I am after is a working command in 5.3.0 in oflline mode where I only use flye as the assembler only comebin as the binner and only qualty check of the bins with checkm2. I have the checkm2 and gtdb databases locally.

Hrmmm, it should work what you have above. I can try and see if I can replicate what you want on Monday...