run_clair3.sh fails in WSL when windows username has a space in it, not clear where exactly this is entering but it seems likely it's a fieldbioinformatics issue!
Running: samtools index PHL013.unmatched.primertrimmed.rg.sorted.bam
Running: run_clair3.sh --enable_long_indel --chunk_size=10000 --haploid_sensitive --no_phasing_for_fa --bam_fn='PHL013.unmatched.primertrimmed.rg.sorted.bam' --ref_fn='data/amplicon-nf/primer-schemes/artic-training-lhf/600/v1.0.0/reference.fasta' --output='PHL013_rg_unmatched' --threads='2' --platform='ont' --model_path='data/amplicon-nf/clair3-models//r1041_e82_400bps_hac_v520' --include_all_ctgs --enable_variant_calling_at_sequence_head_and_tail
Unexpected command failure: run_clair3.sh --enable_long_indel --chunk_size=10000 --haploid_sensitive --no_phasing_for_fa --bam_fn='PHL013.unmatched.primertrimmed.rg.sorted.bam' --ref_fn='data/amplicon-nf/primer-schemes/artic-training-lhf/600/v1.0.0/reference.fasta' --output='PHL013_rg_unmatched' --threads='2' --platform='ont' --model_path='data/amplicon-nf/clair3-models//r1041_e82_400bps_hac_v520' --include_all_ctgs --enable_variant_calling_at_sequence_head_and_tail
Command stderr: /opt/conda/bin/run_clair3.sh: line 230: [: too many arguments
mkdir: cannot create directory ‘/mnt/c/Users/LENOVO’: Permission denied
run_clair3.sh fails in WSL when windows username has a space in it, not clear where exactly this is entering but it seems likely it's a fieldbioinformatics issue!