Haruo Suzuki

Thank you. Yes, I found the following information. https://grunwaldlab.github.io/metacoder_documentation/publication--08--voting.html Graphing voting geography https://grunwaldlab.github.io/metacoder_documentation/publication--09--gene_expression.html Human gene expression

Dear @rpetit3. Here are additional suggestions: - bactopia can use annotation tools such as DFAST - DDBJ Fast Annotation and Submission Tool (https://github.com/nigyta/dfast_core) as well as Prokka"? - bactopia can...

Dear @rpetit3: - bactopia can use mafft with varying options? https://mafft.cbrc.jp/alignment/software/manual/manual.html - bactopia can run PIRATE using the exactly same options as PIRATE? For example, using `-z` instead of `--keep_all_files`...

Dear @rpetit3: bactopia can generate a core genome phylogeny using FastTree as well as IQ-TREE? A tree (.nwk) can be generated by FastTree from `core_alignment.fasta.gz` as well as `binary_presence_absence.fasta.gz`? Supplying...

Dear @rpetit3: bactopia can use pan‐ and core-genome analysis tools such as GET_HOMOLOGUES/GET_PHYLOMARKERS (https://pubmed.ncbi.nlm.nih.gov/29765358/) as well as Roary/PIRATE?

Dear @rpetit3: I wonder if bactopia can modify Prokka annotations (gene and product names) and/or PIRATE annotations (in `bactopia-tools/pirate/core-genome/pirate/PIRATE.gene_families.tsv`)? For example, annotations with databases (e.g. MEGARes, VFDB, eggNOG) can be...

I noticed that the documentation "pirate - Bactopia" (https://bactopia.github.io/bactopia-tools/pirate/) has changed a lot. Is there an archive of the documentation for the Bactopia version 1.X.X?

Here are messages: ``` ==> ena-single-sample/SRX4563634/logs/fastq_status/fastq_status.err

My environment is as follows: ``` $python -V Python 3.7.9 $cat /etc/redhat-release CentOS Linux release 7.4.1708 (Core) $uname -a Linux bias5-login 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018...

Output is as follows: ``` $conda activate bactopia $/usr/bin/env python3 -V Python 3.7.10 $which python3 ~/miniconda3/envs/bactopia/bin/python3 ```