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Cannot allocate memory error despite small hash size #141

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joshua-theisen opened this issue Mar 10, 2020 · 0 comments
Open

Cannot allocate memory error despite small hash size #141

joshua-theisen opened this issue Mar 10, 2020 · 0 comments

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@joshua-theisen
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I am trying to build the bacterial library on a cluster with 512GB of RAM using the following code:

kraken-build --download-taxonomy --threads 8 --db bactarch
kraken-build --download-library bacteria --threads 8 --db bactarch
kraken-build --build --threads 8 --jellyfish-hash-size 128M --db bactarch

This generates a large number of files similar to these

-rw-rw-r-- 1 user user 1.2G Mar  8 16:37 database_96
-rw-rw-r-- 1 user user 1.2G Mar  8 16:38 database_97
-rw-rw-r-- 1 user user 1.1G Mar  8 16:38 database_98
-rw-rw-r-- 1 user user 1.2G Mar  8 16:38 database_99

and eventually generates a .jdb file

-rw-rw-r-- 1 joshua.theisen joshua.theisen 233G Mar  8 22:42 database.jdb

that gets bigger and bigger until is crashes with the error

db_sort: unable to mmap database.jdb: Cannot allocate memory

I've been experimenting with making the hash size smaller and smaller, to no avail. Is this error because of the hash size? Would the --work-on-disk switch help my situation? Thanks.

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