Haruo Suzuki
Haruo Suzuki
I wonder if it is possible to make results reproducible using abricate. Different results were sometimes produced when the same command was run several times. ``` abricate --threads 80 --db...
abricate failed to extract a plasmidfinder database accession as follows: https://github.com/tseemann/abricate/blob/master/db/plasmidfinder/sequences#L3779 ``` >plasmidfinder~~~rep29_2_EFAU085p4001(Aus0085p4)_Aus0085~~~~~~ rep29_2_EFAU085p4001(Aus0085p4)_Aus0085 ```
I wonder if the code to reproduce Fig 6 (geographic location data) and Fig 7 (gene ontology) in the manuscript is available. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340466/ Data Availability Statement A manual with documentation...
Dear developers: [2021-07-31.zip](https://github.com/Cibiv/IQ-TREE/files/6911321/2021-07-31.zip) contains *** Log file: core_aa_loci.log *** Alignment files: ALN_DIR=core_aa I got the following ERROR messages: ``` ERROR: phylotree.cpp:5689: void PhyloTree::convertToRooted(): Assertion `dad_len >= 0.0' failed. ERROR: STACK...
I run bactopia tools pirate - 1.6.5 with local assemblies (*.fna of completed genomes) using: ``` bactopia tools pirate --only_completed --assembly ./data/fna/ --assembly_pattern *.fna --skip_clonalframe ``` I would be grateful...
https://bactopia.github.io/tutorial/ I'm working through the tutorial. ``` # https://bactopia.github.io/tutorial/#build-datasets bactopia datasets --ariba "vfdb_core,card" --species "Staphylococcus aureus" --include_genus --cpus $(getconf _NPROCESSORS_ONLN) # https://bactopia.github.io/tutorial/#acquire-staphopia-datasets git clone -b staphopia-v1 https://github.com/bactopia/bactopia-datasets.git cp -r bactopia-datasets/species-specific/...
Thank you for suggesting `--skip_clonalframe` in https://github.com/bactopia/bactopia/issues/100 In [Bactopia Tools - pirate](https://bactopia.github.io/bactopia-tools/pirate/), [Input for ClonalFrameML](https://github.com/xavierdidelot/clonalframeml/wiki#input) `alignment.fa` is a copy of `core_alignment.fasta` produced by PIRATE? ``` $cat work/pirate/bf/566e5ea3ffc4aef61d5beb4e3d4eb7/.command.sh #!/bin/bash -ue mkdir...
Is there an option equivalent to "Logo Range:" in WebLogo? https://weblogo.berkeley.edu/logo.cgi WebLogo - Create Sequence Logos https://weblogo.berkeley.edu/info.html#range Logo Range
https://github.com/ropensci/rentrez/blob/master/README.md#web_history-and-big-queries While it is stated that 'When I wrote this that was a little over 200 000 SNPs', I have got the following messages: ``` > snp_search snp_search Entrez search...
I failed to install gubbins using Conda and Homebrew as follows. Any comments would be greatly appreciated. ### Conda ``` $conda install gubbins Solving environment: failed UnsatisfiableError: The following specifications...