wrpearson
commented
1 year ago The message "cannot allocate buffer ..." is coming from a failed attempt to allocate a buffer of that size. It is a limitation of your computer/operating system.
To avoid this message, you should ask to allocate less memory, not more. This number can be decreased with the -XM option.
The karlin lambda message indicates a problem with your scoring matrix. You need to make negative values more negative.
Bill Pearson
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From: ZLoo @.**@.>>
Subject: Re: [wrpearson/fasta36] Cannot allocate buffer 3000002 (Issue #49)
Date: January 18, 2023 at 6:15:15 AM EST
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Hi. How to increase the buffer? Base size ~400mb
FASTA searches a protein or DNA sequence data bank version 36.3.8i Nov, 2022 Please cite: W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
(karlin lambda) non-negative expected score: 0.75 *** ERROR [comp_lib9.c:2155]: cannot allocate buffer 3000002
extended options -XM=MySize ?
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Hi. How to increase the buffer? Base size ~400mb
FASTA searches a protein or DNA sequence data bank version 36.3.8i Nov, 2022 Please cite: W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
(karlin lambda) non-negative expected score: 0.75 *** ERROR [comp_lib9.c:2155]: cannot allocate buffer 3000002
extended options -XM=MySize ?