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
Description of the bug
When running bacass for the assembly of some salmonella samples, I ran into the following error:
On the busco step.
Command used and terminal output
Relevant files
No response
System information
HPC - Slurm - Singularity - Redhat
NextFlow v25.04
Bacass 2.5.0