Chandini

This is my dockerfile: ``` FROM ubuntu:22.04 ENV DEBIAN_FRONTEND=noninteractive RUN apt-get update && apt-get install -y \ wget \ curl \ bzip2 \ ca-certificates \ libglib2.0-0 \ libxext6 \ libsm6...

@jodyphelan Seems I was running it outside tbdb, not inside the folder. Thank you, but I am facing a different error. I had built a custom db using my amplicons...

Seems the bed file gt_tbdb.bed is empty ``` (base) root@ee5e30768c4b:/data/MTB/3-12-MTB_Analysis/TB-PROFILER# head /tbdb/who.bed Chromosome 1 1524 Rv0001 dnaA isoniazid Chromosome 4933 7267 Rv0005 gyrB levofloxacin,moxifloxacin Chromosome 7068 9818 Rv0006 gyrA levofloxacin,moxifloxacin...

> The primers file that you supply is not actually a bed file but should be a three column, tab separated, text file with > > 1. the amplicon name...

The .bed created inside the tbdb folder is still empty ``` (base) root@22a11c22bb98:/data/MTB/MTB_RUN2/VARIANTS# head -n5 /tbdb/tbdb.bed NC_000962.3 1 1524 Rv0001 dnaA isoniazid NC_000962.3 4933 7267 Rv0005 gyrB levofloxacin,moxifloxacin NC_000962.3 7068...

@jodyphelan It's giving no stdout or output file ``` (base) root@1a873959019b:/tbdb# rm gt.bed (base) root@1a873959019b:/tbdb# seqkit amplicon gt.fasta -p /primers.tsv --bed [INFO] 46 primer pair loaded (base) root@1a873959019b:/tbdb# ``` But...

@jodyphelan Nope, the primers have exact matches against the ref. ``` query id s. start s. end query id s. start s. end atpEFP 1460795 1460814 atpERP 1461567 1461586 ethAFP1...