nullarbor
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tseemann
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
Hi Torsten! I've made a custom database for abricate and was wondering if it is possible to point to that particular database when running nullarbor? Those results would be great...
Installing from conda (as of 2020-03-10) is resulting in some software version incompatibilities. Install commands: ``` . ~/bin/.miniconda3/etc/profile.d/conda.sh conda create -n Nullarbor-2.0.20191013 conda activate Nullarbor-2.0.20191013 conda install -c conda-forge -c...
Hi, 1) Is it possible to start the pipeline with assembled genomes? (if not, that would be a nice addition) 2) Can you add cgMLST to the analysis? (using PubMLST...
Hi Torsten, Recently I have sequenced 95 S.a aureus isolates using the NextSeq. I have concatenated the 4 reads using the attached command tab. For example Isolate 3 cat WA3-r69_S13_L001_R1_001.fastq.gz...
Hi, I'm trying to install Nullarbor in a new environment but when I do --check it says it cannot find database.idx Can anyone help? Cheers, P (Nullarbor) [peflanag@login3 ~]$ mkdir...
Hello everyone, I am running a Nullarbor analysis on S. Agalctiae fastq files, was able to get to this [14:02:51] Hello dn927558 [14:02:51] This is nullarbor.pl 2.0.20191013 [14:02:51] Send complaints...
Hi Need some assistance . I do not get any reports and roary after few runs. It didn't give any error log but it sems it didnt complete the run....
When I install miniconda3, i get the message: UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: - nullarbor -> python[version='2.7.*|3.5.*|3.6.*|=3.6,=2.7,=3.5,
I am getting the below error Memory provided is insufficient to do runs in 10 cycles for the read coverage. We find that 16 Gb for 20x coverage of a...
Hi, i am trying to run nullarbor, but it fails on the first step with the following error: ERROR: Could not determine shovill version using '--version': when i try shovill...
