[Typo] "Removing short conting" + [bug?] error when running with max RAM about shovill HOT 9 CLOSED

1. I've fixed the typo - thank you!

2. I am also getting Error 256 on trimmomatic and pilon now too. I am investigating it. It's probably due to the _JAVA_OPTIONS I set, which were to ensure it didn't get killed on clusters where you have to know how much RAM you will be using. I'm working on it. Thank for letting me know it is not just me.

Q1. how much RAM does your computer have?
Q2. What does java -version say?
Q3. What does cat $(which pilon) say?

from shovill.

Misery and problems love company! I first switched everything to the Linuxbrew installation (some dependencies were already in usr/bin), but that did not help, only not including --ram 20.00 did.

A1) 32 Gb RAM, it is a virtualbox Ubuntu computer in a Windows 7 host with 64 Gb RAM (I wanted it dual boot, IT said no). The computer has been bought for the Minion sequencer, but can double up as Linux analysis computer, otherwise I have to use dual core, 8 Gb terminal only virtual computers.

A2) java version "1.8.0_144", Java(TM) SE Runtime Environment (build 1.8.0_144-b01), Java HotSpot(TM) 64-Bit Server VM (build 25.144-b01, mixed mode)

A3) exec java -mx1000m -ms20m -jar /home/linuxbrew/.linuxbrew/Cellar/pilon/1.22/pilon-1.22.jar "$@"

from shovill.

Does it really say -mx1000m and not -Xmx1000m ?

I'm thinking the -ms20m might be too small... can you change it to -Xms100m ?

from shovill.

Yes, it says "exec java -mx1000m -ms20m", not Xmx1000m.

Where do I change this?

from shovill.

Turns out that pilon memory line is my work from long ago. Looks like I messed it up. I will try and fix.

from shovill.

Can you try brew install brewsci/bio/pilon (or reinstall) ?

from shovill.

With reinstall I now get "-Xmx1000m -Xms20m" (the rest stays the same).

When brew first updated (hadn't used it for a while), it also complains about perl being deprecated:

Warning: Calling 'depends_on ... => :perl' is deprecated!
There is no replacement.
/home/linuxbrew/.linuxbrew/Homebrew/Library/Taps/tseemann/homebrew-bioinformatics-linux/Formula/shovill.rb:12:in `class:Shovill'
Please report this to the tseemann/bioinformatics-linux tap!

from shovill.

Do this:

brew untap homebrew/science
brew tap brewsci/science
brew tap brewsci/bio
brew update
brew upgrade
brew install brewsci/bio/shovill

from shovill.

I assume you fixed it.

from shovill.