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Old 12-10-2016, 02:25 AM   #1
rafaykhan
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Location: Karachi, Pakistan

Join Date: Dec 2016
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Question MaSuRCA Assembler runCA Error

Successfuly install MaSuRCA

HTML Code:
tar xfz MaSuRCA-3.2.1.tar.gz
HTML Code:
cd MaSuRCA-3.2.1
HTML Code:
sudo ./install.sh
Configure and run config.txt

Code:
MaSuRCA-3.2.1/bin/masurca MaSuRCA-3.2.1/bin/config.txt
Verifying PATHS...
jellyfish OK
Error: runCA not found or failed to run
Help me to get through this error.
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Old 12-14-2016, 10:57 AM   #2
sklages
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Location: Berlin, DE

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Please do not crosspost to Biostars if you want help here ..

jellyfish is in your PATH, runCA is not.

You could either use --path /PATH/TO/runCA with masurca or add the corresponding path to your PATH variable.

There is a bin folder in masurca installation directory which holds the common binaries. runCA and other programs are in one of the "neighbor" folders, in CA/bin or CA8/bin.

best,
Sven
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Old 12-14-2016, 09:20 PM   #3
rafaykhan
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Thank you Sven, its work

PATH=~/tools/MaSuRCA-3.2.1_12062016/CA/Linux-i686/bin:$PATH
PATH=$PATH:~/tools/MaSuRCA-3.2.1_12062016/CA/Linux-i686/bin

sudo env "PATH=$PATH" ~/tools/MaSuRCA-3.2.1_12062016/bin/masurca ~/tools/MaSuRCA-3.2.1_12062016/bin/config.txt
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Old 02-23-2017, 06:11 PM   #4
drunk_coder
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Location: china

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I also have a runCA issue, I installed MaSuRCA-3.2.1_01202017 successfully. I use CA8/bin in my PATH. During Assembly, MsSuRCA threw a runCA error:
"ERROR: the runCA option ovlHashBlockSize is not recognized.
This runCA functionality changed in CABOG version 7.
Try using ovlHashBlockLength instead."

I found masurca generated "assemble.sh" based on runCA6 command, but installed runCA version is 8.2. So how to fix this issue ?

best,
mjx
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