Hi! I am having an issue with the pipeline finding duplicate names for the sample files. I am not sure why, I have cleared singularity and the nextflow cache and deleted the files anywhere but the folder I told the pipeline they are in. This is the error output: Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred FixedFiles27_L1_R1.fastq.gz835708011: [S007] DuplicateNameValidator: duplicate name: '@AV250604148Run3 08 26 2026 SEQ WANG253251457611010200360031'

Hi! The S007 error points to duplicate read IDs within the FASTQ data, so clearing the container or Nextflow cache wouldn’t resolve that. Disabling P001 addresses a different check—matching names between paired reads. Were these FASTQs merged from multiple files, or were their read headers modified? It would also help to check whether the same input file appears more than once in the samplesheet. Those could help narrow down where the duplicated IDs came from.