Amanda Warr

Hi Marie, would you be able to check how much coverage amplicon 51 has? If it has coverage below the threshold that would suggest that the pipeline is failing because...

Could you have a try with the attached version of Lilo and let me know if it gets past that point? [LILO_issue_1.txt](https://github.com/amandawarr/Lilo/files/8087965/LILO_issue_1.txt) It shouldn't be necessary, I have it running...

I have just tested your input files on my data and they work perfectly, so it isn't that. Are you using the version of snakemake from the conda environment? The...

Can you check what happens when you run the command that it says failed? i.e.: > bedtools intersect -F 0.9 -wa -wb -bed -abam FAR95540_pass_unclassified_7f618209_73/alignments/reads_to_ref.bam -b amplicons.bed | grep amplicon51...

Hi Elisabeth, Yes I am afraid this is an error caused entirely by my own laziness and I apologise for not having fixed it yet. For a quick fix outside...