You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I've been using seqtk sample to randomly subsample fastq files with about 75 M reads.
I tried to subsample 5M, 10M, 15M,..., 30M, 35M,... 70M reads but at the time the 35M reads subsampling comes, the outputs began to be empty. Does anyone know what could be the problem?
@Gil-marquez i had a look at the code, and it seems it needs to allocate RAM for N sequence structs when you want to sample N records. I suspece you might be running out of RAM.
Use the -2 option to do 2-pass mode instead.
If this works, please close this issue. Thanks!
Usage: seqtk sample [-2] [-s seed=11] <in.fa> <frac>|<number>
Options: -s INT RNG seed [11]
-2 2-pass mode: twice as slow but with much reduced memory
Activity
tseemann commentedon Oct 18, 2019
@Gil-marquez i had a look at the code, and it seems it needs to allocate RAM for
Nsequence structs when you want to sample N records. I suspece you might be running out of RAM.Use the
-2option to do 2-pass mode instead.If this works, please close this issue. Thanks!
Acribbs commentedon Feb 20, 2020
FYI I had a similar issue and @tseemann solution fixed my issue
tseemann commentedon Feb 24, 2020
@Gil-marquez please close this issue now.