Failed samples

[gdauria]

Dear Sir/Mrs, first of all I would like to thank you for your efforts in these scripts. I tried it on a bunch of minion samples in which some of them failed giving a very low reads files. Everything works fine until there are enough reads for carrying out the pipeline but in case the bam comes out empty, the pipeline stops with this last error:

Command failed:longshot -P 0 -F -A --no_haps --bam test_barcode96.primertrimmed.rg.sorted.bam --ref primer-schemes/nCoV-2019/V3/nCoV-2019.reference.fasta --out test_barcode96.longshot.vcf --potential_variants test_barcode96.merged.vcf.gz

Please can you help me in figuring out how I can go over this?
Thank you in advance

Giuseppe