When running CD-HIT-EST through the tr2aacds.pl pipeline (http://arthropods.eugenes.org/genes2/about/EvidentialGene_trassembly_pipe.html), it returns the following error message in a log file :

================================================================
Program: CD-HIT, V4.5.4 (+OpenMP), Apr 11 2014, 11:06:45
Command: /module/apps/cd-hit/4.5.4/cd-hit-est -c 1.00 -M 1000
-l 89 -d 0 -i ./Trinity-SOAP-TAnr.cds -o
./Trinity-SOAP-TAnrcd1.cds

Started: Fri Apr 11 12:25:06 2014
================================================================
Output
----------------------------------------------------------------
total seq: 1631766
longest and shortest : 50232 and 90
Total letters: 384949449
Sequences have been sorted

Fatal Error:
not enough memory, please set -M option greater than -140463122

Program halted !!


Approximated minimal memory consumption:
Sequence : 590M
Buffer : 1 X -140463832M = -140463832M
Table : 1 X 42M = 42M
Miscellaneous : 26M
Total : -140463172M

Even when giving a lot of memory to cd-hit-est through the -M option, this error occurs and it seems that the buffer requires a negative amount of memory...
I have read on an other bug report that memory consumption errors could be caused by a bad compilation ; e.g : a 32-bit installation on a 64-bit platform... However the installation does not give the choice between 32 and 64 bit.

Thank you for the time you may accept to spend on this issue.