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Old 03-17-2014, 12:58 AM   #1
JonB
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Default unknown option -shortPaired3 in velveth

Hi,

I am trying to assemble three paired-end libraries, but get an error with the option -shortPaired3. Anyone know if I can assemble more than two libraries?

Heres the command:

Code:
velveth assembly-kmer-67 67 -shortPaired -fastq -separate ~/lib1_1.fastq ~/lib1_2.fastq -shortPaired2 -fastq -separate ~/lib2_1.fastq ~/lib2_2.fastq -shortPaired3 -fastq -separate ~/lib3_1.fastq ~/lib3_2.fastq
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Old 03-17-2014, 02:53 AM   #2
mastal
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Default

I haven't tried, but I think it should be possible.

How many CATEGORIES is your version of velvet compiled with?
You need to have CATEGGORIES=3 if you are going to use 3 different libraries.
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Old 03-17-2014, 04:36 AM   #3
JonB
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Thanks for the tip, I didn't know that. I have to ask the guys who run our cluster, but that seems to be what's causing the problem.
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