MaSuRCA Assembler runCA Error

rafaykhan · 12-10-2016, 02:25 AM

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.

sklages · 12-14-2016, 10:57 AM

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

rafaykhan · 12-14-2016, 09:20 PM

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

drunk_coder · 02-23-2017, 06:11 PM

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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12-10-2016, 02:25 AM	#1
rafaykhan Junior Member Location: Karachi, Pakistan Join Date: Dec 2016 Posts: 3	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.

12-14-2016, 10:57 AM	#2
sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 620	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

12-14-2016, 09:20 PM	#3
rafaykhan Junior Member Location: Karachi, Pakistan Join Date: Dec 2016 Posts: 3	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

02-23-2017, 06:11 PM	#4
drunk_coder Junior Member Location: china Join Date: Dec 2011 Posts: 9	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