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"busco" step failing due to publishing issues #289

@ESapenaVentura

Description

@ESapenaVentura

Description of the bug

When running bacass for the assembly of some salmonella samples, I ran into the following error:

ERROR ~ Failed to publish file: <path_to_analysis_cwd>/work/c3/9ccb1c4f4690004eb6f2aeed6f5f71/busco_downloads/lineages/bacteria_odb10; to: <path_to_analysis_cwd>/busco/busco_downloads/lineages/bacteria_odb10 [copy] -- See log file for details

On the busco step.

Command used and terminal output

nextflow run <path_to_pipeline>/nf-core-bacass/nf-core-bacass-2.5.0/main.nf \
        -c ../../DOC/hpc_slurm_assembly.config \
        -profile singularity \
        --input samplesheet.csv \
        --outdir ./ \
        --assembly_type short \
        --assembler unicycler \
        --skip_polish true \
        --save_trimmed false \
        --fastp_args '--qualified_quality_phred 20 --cut_mean_quality 20' \
        --skip_kraken2 true \
        --skip_kmerfinder false \
        --kmerfinderdb /data/ucct/bi/references/kmerfinder/latest/bacteria \
        --ncbi_assembly_metadata <our_own_reference_path>/references/bacteria/20240626/assembly_summary_refseq.txt \
        --prokka_args '--gram -' \
        -resume

Relevant files

No response

System information

HPC - Slurm - Singularity - Redhat

NextFlow v25.04
Bacass 2.5.0

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