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Old 02-01-2016, 06:04 PM   #1
Junior Member
Location: Toronto

Join Date: Feb 2016
Posts: 1
Default Velveth help

I ran ~/mypath/velveth Assem 21 -shortPaired -fastq -separate clean_1.fq clean_2.fq

and got:

velveth: Can't malloc 181 chars: Cannot allocate memory
Aborted (core dumped)

I clearly have RAM and 1.2TB of space available.

What can I do? Thanks in advance

UPDATE: it worked by itself after awhile

however when I tried velvetg for the first time, I got seg fault (core dumped)

UPDATE: now I'm getting killed

Last edited by Naina; 02-02-2016 at 03:25 PM.
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Old 02-03-2016, 06:34 PM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

You may be running out of memory. How much do you have, and how much is the program using (you can see this with the command 'top' while it is running).
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assembly, memory limits, velvet

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