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kamimrcht / REINDEER

REINDEER REad Index for abuNDancE quERy
GNU Affero General Public License v3.0
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error setting rlimit when --index #8

Open Krannich479 opened 4 years ago

Krannich479 commented 4 years ago

Hi, I get an error

#Monotigs and index constuction...
error setting rlimit to 1035

no matter if I run Reindeer with reads or pre-computed unitigs.

The calls are ./Reindeer --index -f <path-to-my>/fof.txt --nocount --bcalm or ./Reindeer --index -f <path-to-my>/fof_unitigs.txt --nocount respectively.

Both input files contain a single line in the style of /absolute/path/to/my/sequenes.fasta

Any ideas whats going on here?

kamimrcht commented 4 years ago

Hi @Krannich479 REINDEER needs to open numerous files, and it seems you are restricted to a certain number on the machine you're using. You should be able to modify the open file limit with ulimit -n (which resets the limit only for your current shell). Best. C