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Allow increasing cd-hit-est memory allocation #255

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simonrharris opened this issue Mar 1, 2019 · 2 comments
Closed

Allow increasing cd-hit-est memory allocation #255

simonrharris opened this issue Mar 1, 2019 · 2 comments

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@simonrharris
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When running prepareref on a large input fasta file I get the following error from cd-hit-est

Fatal Error:
not enough memory, please set -M option greater than 1212

Program halted !!

Currently it appears it is not possible to increase this cd-hit-est option via the prepareref options. Could an option be added to allow this to be increased when necessary?
kpepper added a commit to kpepper/ariba that referenced this issue Mar 13, 2019
@kpepper
Added ability to set CD-HIT memory limit on the command line - Issue s…
70c82f5 
…anger-pathogens#255
kpepper added a commit that referenced this issue Mar 15, 2019
@kpepper
Merge pull request #256 from kpepper/issue255_cd_hit_est_memory_feature
f40cc15 
Allow increasing cd-hit-est memory allocation #255
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kpepper commented Mar 15, 2019

This option has now been added in release v2.13.4 of Ariba. Use the --cdhit_max_memory command line argument to specify the cdhit memory in MB.

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kpepper commented Mar 27, 2019

Now available in pypi.

@kpepper kpepper closed this as completed Mar 27, 2019
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@simonrharris @kpepper