Closed charlenelawdes closed 2 months ago
Thanks for reporting this. There have been several bug fixes in the latest MarkDups release (v1.1.7). Would you be able to first see whether this data works with that release?
To do that I'd recommend navigating to the MarkDups work directory from your oncoanalyser analysis then download and run MarkDups 1.1.7, something like the following should work:
cd /PPT45/oncoanalyser_test/scripts/work/d0/6d687313e1fcffb2700d85157ebf1f/
wget https://github.com/hartwigmedical/hmftools/releases/download/mark-dups-v1.1.7/mark-dups_v1.1.7.jar
java -Xmx36721970381 -jar mark-dups_v1.1.7.jar \
-samtools $(which samtools) \
-sambamba $(which sambamba) \
-sample SIGN1048 \
-input_bam SIGN1048_aligned_sorted_RG.bam \
-form_consensus \
-unmap_regions unmap_regions.38.tsv \
-ref_genome GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
-ref_genome_version 38 \
-write_stats \
-threads 6 \
-output_bam SIGN1048.markdups.bam
I'll close this issue for now - if you'd like to continue discussing/debugging, please reopen!
Description of the bug
I have Nanopore reads aligned to the GRCh38_hmf reference using minimap2, as it's the recommended tool to use for Nanopore reads. I get an error message at the process NFCORE_ONCOANALYSER:WGTS:READ_PROCESSING:MARKDUPS
Command used and terminal output
Relevant files
System information
Nextflow version : 23.10.0 Hardware: HPC Executor: slurm Container engine: Apptainer OS: CentOS nf-core/oncoanalyser version: 0.4.6