velvet adjust MAXKMERLEGNTH on HPC

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2.9 years ago

rrsowmya ▴ 20

I am using velvet assembler on the HPC which comes with a default maxkerlength of 31. How should I change this to a higher value? The usual command make maxkmerlength=200 maker velveth velvetg returns - make: *** No targets specified and no makefile found. Stop. This is maybe because velvet is loaded as an environment module. Thanks for your help in advance!

velvetoptimiser Velvet HPC • 846 views

ADD COMMENT • link updated 2.9 years ago by Ram 43k • written 2.9 years ago by rrsowmya ▴ 20

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Please contact your HPC admin. They should be able to help you better, as they probably installed it in the first place.

If you're confident that you can navigate user installations on your HPC, try installing velvet in a directory under $HOME and follow the instructions from the user manual to get to a point when you can make it yourself.

ADD REPLY • link 2.9 years ago by Ram 43k

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Hi Ram, thank you. Yes I installed velvet and velvetOptimiser separately and ran using that. Just need to make a note to add that velveth to PATH. Thank you.

ADD REPLY • link 2.9 years ago by rrsowmya ▴ 20

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Unfortunately, now I get an error

Velveth failed! Response:1

Would anyone know what this error indicates? The test data from VelvetOptimiser runs fine but my data returns this error. I haven't been able to find a solution yet. I will appreciate any comments on the subject. Thanks.

ADD REPLY • link updated 2.9 years ago by Ram 43k • written 2.9 years ago by rrsowmya ▴ 20

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