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Snippy fails with genbank file

Open mesti90 opened this issue 5 months ago • 3 comments

I tried to run snippy with the following genbank file: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/632/635/GCF_008632635.1_ASM863263v1/GCF_008632635.1_ASM863263v1_genomic.gbff.gz However, the pipeline failed for me when snpEff started. My snpEff version is SnpEff 5.2a (build 2023-10-24 14:24)

The I command called was: snippy --cpus 60 --outdir outdir --ref GCF_008632635.1_ASM863263v1_genomic.gbff --R1 forward.fastq.gz --R2 reverse.fastq.gz

I also tried replacing gbff with gbk, but unsuccessfully. I'd appreciate your help

mesti90 avatar Jan 29 '24 15:01 mesti90