limengfdu

Missing parentheses in call to 'print'

1

Dear all, I run the code "snippy --outdir 'SJ_2016_1531' --R1 '/home/ND140/lm/cgMLST_test/SJ_2016_1531_R1.fastq.gz' --R2 '/home/ND140/lm/cgMLST_test/SJ_2016_1531_R2.fastq.gz' --ref /home/edwin/template/bwa/tb_h37rv.fasta --cpus 16", it showed "Error running command, check SJ_2016_1531/snps.log". ### samtools faidx reference/ref.fa ### bwa...

ValueError: Cant find programs: trimmomatic

3

Hi Jody, I used "mamba create -n tb-profiler tb-profiler" to install tb-profiler v4.3.0. I ran "tb-profiler profile -1 SJ_2012_0029_R1.fastq.gz -2 SJ_2012_0029_R2.fastq.gz -p SJ_2012_0029", and I got Traceback (most recent call...