user29589776
user29589776

Reputation: 1

Sorting, merging, and deduplicating large txt files on HPC?

I am looking for some advice

I am currently creating a kmer database and looking to merge/sort and take uniq lines from 47 sample.txt.gz which are 16gb each, What would be the fastest way to do this.

i currently running this:

zcat *.merged.kmers.txt.gz | sort --parallel=48 --buffer-size= 1400G | uniq | gzip > all_unique_kmers.txt.gz

i have been running it a slurm but I wanted to know what parameters and what would someone else do, its been running 4 days!!!!

47 samples, 16gb compressed, 80gb uncompressed,

merge, sort, deduplicate

please someone help me...

Upvotes: 0

Views: 30

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