Hey all, I'm receiving an error when I am running the pipeline that i'm not quite sure what to make of it. Here is my command: nextflow run nf-core/rnaseq -r 3.20.0 -profile docker --input /home/stefanie/Biggie/JF10_HIV_r4/sample_sheet.csv --outdir /home/stefanie/Biggie/nf_output --gtf /home/shared/GRCh38/gencode.v43.primary_assembly.annotation.gtf --fasta /home/shared/GRCh38/GRCh38.primary_assembly.genome.fa here is the error: Execution cancelled -- Finishing pending tasks before exit ERROR ~ Error executing process > 'NFCORE_RNASEQRNASEQFASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (HIV_RAL_6h)' Caused by: Process

NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (HIV_RAL_6h)

terminated with an error exit status (1) Command executed: fq lint \ --disable-validator P001 \ HIV_RAL_6h_trimmed_1_val_1.fq.gz HIV_RAL_6h_trimmed_2_val_2.fq.gz > HIV_RAL_6h.fq_lint.txt cat <<-END_VERSIONS > versions.yml "NFCORE_RNASEQRNASEQFASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING": fq: $(echo $(fq lint --version | sed 's/fq-lint //g')) END_VERSIONS Command exit status: 1 Command output: (empty) Command error: Error: I/O error Caused by: corrupt deflate stream Work dir: /mnt/biggie/Signaling_Systems_Drive/Users/Stefanie_Brizuela/JF10_HIV_r4/work/79/1330069ee4f77da8d17dcebf782816 Container: quay.io/biocontainers/fq:0.12.0--h9ee0642_0 Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named

.command.sh

-- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details

Command error:
 Error: I/O error
 Caused by:
   corrupt deflate stream

This looks suspiciously like corrupt data files. Probably there was an issue when you copied the files over from another computer or drive. Specifically the sample

HIV_RAL_6h_trimmed_1_val_1.fq.gz HIV_RAL_6h_trimmed_2_val_2.fq.gz

seems to be affected.