Could not allocate enough memory for 90576558080 sequences

lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats

MIT License

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Could not allocate enough memory for 90576558080 sequences #140

Open Antony-1996 opened 5 years ago

Antony-1996 commented 5 years ago

Dear author I encountered a problem when I use seqtk to downsample fastq file ，the result look like this： Is there any way that I can do to solve this ? thank you so much

tseemann commented 4 years ago

Please use the two-pass mode: seqtk sample -2

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

If that works, please close this issue. Thanks!

fidibidi commented 1 year ago

This helped me thanks!