Issue

[Sid1507711]

Hello, @tseemann my friends tried to make a loop on output that we got from running bbduk on snippy code example provided by you but it won't work the output file does not contain anything. any suggestions #!/bin/bash source /opt/asn/etc/asn-bash-profiles-special/modules.sh module load snippy #input fastq.gz files mkdir SNP_output for fq1 in ./*.clean_trim1.fq do echo "working with file $fq1" base=$(basename $fq1 .clean_trim1.fq) echo "base name is $base" fq1=./${base}.clean_trim1.fq fq2=./${base}.clean_trim2.fq snippy --outdir SNP_output --ref GCF_000022165.1_ASM2216v1_genomic.gbk --R1 ${base}.clean_trim1.fq --R2 ${base}.clean_trim2.fq done