Haruo Suzuki

----- (Page 181) You access access R’s built-in documentation *should be* You access R’s built-in documentation ----- (Page 181) apropos(norm) *printed "Error: is.character(what) is not TRUE", and thus should be*...

Errata for Bioinformatics Data Skills

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# Errata for Bioinformatics Data Skills [Confirmed Errata | O'Reilly Media](http://www.oreilly.com/catalog/errata.csp?isbn=9781449367374) ---------- ## Computer environment I’ve run examples in this book on Mac OS X 10.9.5 in which I installed...

----- (Page 131) i() { (head -n 2; tail -n 2) < "$1" | column -t} *should be* i() { (head -n 2; tail -n 2) < "$1" | column...

----- **Page 346** ``` library(BiocInstaller) biocLite('qrqc') ``` *should be* ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("qrqc") ``` https://www.bioconductor.org/packages/release/bioc/html/qrqc.html ----- **Page 350-351** counts.update(seq.upper()) The `Counter.update()` method *should be* The `counts.update()`...

README.md options

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I have questions about options in https://github.com/SionBayliss/PIRATE/blob/master/README.md ## Usage ### Basic examples - `-a|--align` - `-r|--rplots` Running PIRATE with the options `-a -r` generated the **core_alignment.fasta** and **pangenome_alignment.fasta** files, and...

Fatal Error: not enough memory, please set -M option greater than 2330

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Dear Robert: I encountered an error while using `bactopia tools pirate - 1.6.5`. ``` bactopia tools pirate --only_completed --assembly "${assembly}" --assembly_pattern *.fna --outdir ./ --cpus $(getconf _NPROCESSORS_ONLN) --steps "50,60,70,80,90,95,98" --cd_low...

PIRATE.pangenome_summary.txt

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I ran PIRATE with 322 genomes (gff files) as input, but the file indicates 321 genomes. Is there any way to investigate why the count decreased from 322 to 321?...

Error in R code

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I have got the following Error messages: ``` > ddF

I was wondering if pre-compiled binaries are available. At https://github.com/ablab/mgra/blob/master/docs/INSTALL.md#binary-distribution clicking the link https://github.com/ablab/mgra/releases moved to the page stating that "There aren’t any releases here".