Not enough memory when running cd-hit-est

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What steps will reproduce the problem?
1. cd-hit-est -i all-contigs.fa -o all-contigs.fa.cdhit.out -M 2000 -c 0.99

What is the expected output? What do you see instead?

It turns out fine on at least half of our datasets, still there are a couple of 
input datasets will create this kind of errors.

What version of the product are you using? On what operating system?

CD-HIT 4.5.8 on Linux 2.6.18-274.12.1.el5 #1 SMP x86_64 GNU/Linux

Please provide any additional information below.

cd-hit-est -i all-contigs.fa -o all-contigs.fa.cdhit.out -M 2000 -c 0.99
================================================================
Program: CD-HIT, V4.5.8 (+OpenMP), Apr 06 2012, 00:18:06
Command: cd-hit-est -i all-contigs.fa -o
         all-contigs.fa.cdhit.out -M 2000 -c 0.99

Started: Tue Apr 24 12:08:35 2012
================================================================
                            Output
----------------------------------------------------------------
total seq: 57483
longest and shortest : 60345 and 200
Total letters: 52094767
Sequences have been sorted

Approximated minimal memory consumption:
Sequence        : 58M
Buffer          : 1 X 18446744071796M = 18446744071796M
Table           : 1 X 17M = 17M
Miscellaneous   : 4M
Total           : 18446744071877M

Fatal Error:
not enough memory, please set -M option greater than 18446744071927

Program halted !!

Original issue reported on code.google.com by wche...@gmail.com on 24 Apr 2012 at 4:21

[GoogleCodeExporter]

Fixed in revision b40f8151b845, and release V4.6.

Original comment by phooli...@gmail.com on 26 Apr 2012 at 5:31

• Changed state: Fixed

[GoogleCodeExporter]

Thank you very much~!

Original comment by wche...@gmail.com on 26 Apr 2012 at 5:43

[GoogleCodeExporter]

[deleted comment]

[GoogleCodeExporter]

I'm getting the same error with the latest version. 

Approximated minimal memory consumption:
Sequence        : 1049M
Buffer          : 30 X -140464579M = -140521638M
Table           : 2 X 51M = 103M
Miscellaneous   : 31M
Total           : -140520454M

Original comment by summerra...@gmail.com on 23 Oct 2014 at 2:55