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thackl / minidot

Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2
MIT License
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Error upon Running Minidot #10

Closed Jome0169 closed 6 years ago

Jome0169 commented 6 years ago

Hello, I recently discovered minidot, and it seems like a very useful program. I am snagging an issue however. Whenever I run it I get the following error.

Loading required package: proto
[12:43:19] /home/pabster212/data/Programs/minimap2/minimap2 .. ok
[12:43:19] samtools .. ok
[12:43:19] prepping .. done
[12:45:00] mode: fast (2242694751 bp) "-L 500 -c 15"
[12:45:00] mapping .. failed
[ERROR] failed to open file '500'
[ERROR] failed to open file '500'

Any idea what this error could be? The command executed was ~/data/Programs/minidot/bin/minidot -M ~/data/Programs/minimap2/minimap2 -o test222.pdf A10.spades.contigs.fa ref.fa .

iimog commented 6 years ago

Hi @Jome0169 I came across a similar problem. I see that you are using minimap2 (not minimap - which is no longer developed). However, the default parameters added to the call to minimap by minidot internally (-L 500 -c 15) do not make sense for minimap2, -L has a totally different meaning now and does not take an argument. That is why minimap2 considers the 500 as a file name. So I see two possible solutions:

  1. Use minimap
  2. Use the -m option to provide parameters that work with minimap2
thackl commented 6 years ago

@iimog is right. minidot works with minimap, not minimap2. I haven't had the time yet to port it... It should however, be possible to use the -m parameter to manually specify your minimap2 optionsand overwrite minidot's defaults, which don't make sense with minimap2 ...