[phylocom-user] phylomatic: error trying to match large taxa file against R20100701 megatree.

Gustavo Carvalho gustavo.bio at gmail.com
Mon Sep 5 07:42:12 PDT 2011


Dear all,

I have been trying to match a very large (> 90 000 lines) taxa file
against the latest megatree (R20100701), but without success so far.
The error I get is this:

Numerical Recipes run-time error...
allocation failure 2 in cmatrix()
...now exiting to system...

This happens right after phylomatic prints the taxa that couldn't be
matched (about 70 lines), so it looks like the problem occurs when
phylomatic calls Fy2newRec().

I tried compiling phylomatic in 64-bit mode, but it didn't help.
Splitting the taxa file into smaller (10 000 lines) bits works. I'm
running this on a Linux box with 8 gb of ram:

[gustavo at desktop src]$ uname -a
Linux desktop 3.0-ARCH #1 SMP PREEMPT Wed Aug 17 21:55:57 CEST 2011
x86_64 Intel(R) Core(TM) i5-2500 CPU @ 3.30GHz GenuineIntel GNU/Linux

gcc 4.6.1

I'm calling phylomatic with the following arguments:

./phylomatic -t taxa -f R20100701.new -l > test.new

Is there anything that can be done?

Thank you very much,

Gustavo.



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