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Originally (late 2018, early 2019), I wanted AMRFinder+ databases to be apart of `bactopia datasets`. I think since (https://github.com/ncbi/amr/issues/16) is now resolved, it might be worth revisitin…
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Dear Robert,
First of all many thanks for providing us with such an amazing pipeline :). I have installed bactopia using conda to my MacOS Big Sur. It looks like it has installed everything properl…
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When I run Bactopia on multiple samples using a FOFN file, BLAST against the PLSDB fails. I haven't had that issue when using Bactopia one sample at a time. Here is the call that has been causing thi…
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**When I ran the following command:**
`bactopia --sample fk --R1 ./FK2159/2_HQData/FK2159.SOAP_cor_R1.fq.gz --R2 ./FK2159/2_HQData/FK2159.SOAP_cor_R2.fq.gz --cpus 6`
**It promted some errors:**
…
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Hi,
When I run the command:
bactopia --R1 /home/sam/Downloads/BAGEP/fastq/018_R1.fastq.gz --R2 /home/sam/Downloads/BAGEP/fastq/018_R2.fastq.gz --sample 018 --datasets /home/sam/Downloads/datase…
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First, thanks for describing your experience [using AWS Batch to process 67,000 genomes with Bactopia](https://read-lab-confederation.github.io/blog/posts/bactopia-aws-and-67000-genomes/) in such deta…
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This can be the same file at https://github.com/waldronlab/bugphyzz/issues/14, but I'm creating this issue separately as a high-urgency issue to enable a unit test that all the attributes are expected…
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```To this end, several freely available bioinformatics resources were identified to find the antimicrobial resistance genes in nucleotide as well as amino acid sequence data [@hendriksen2019using]. S…
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A number of programs like BBDUK, mentaLIST etc are not installed. After I installed bactopia in conda evironment, I am gettting the following. I am doing unset PYTHONPATH
unset PERL5LIB
conda activa…
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**Description**
I am new to bactopia and following the posted tutorials. In an early step to install bactopia datasets, I did the following:
conda create -y -n bactopia -c conda-forge -c bioconda …