hallamlab / FAST

FAST Aligner
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no output using large query file (fastq 32GB) #2

Open xushaolin opened 6 years ago

xushaolin commented 6 years ago

I'm using fastal recently, it's really easy to use and fast

however, there are many times when I use large fastq query file, such as 32 GB. At the beginning, I have to wait 40 min until multi-thread start to be functional, then for the next 2 hours, it looks all good. But after the process ended, no output was given, so wired

Sometimes this happen, sometimes don't, so frustrating. So I have to split my query into small file, then all is fine

by the way: I make the database using a fastq file, and there are 24 cores on my server.

here is my code: ./fastal -o split_K3_2P_aa.id -P 22 -K 1 -E 1e-05 -X temp_dir -Q 1 ../fast_Fq_DB/ALL_need_MG_FQ_DB split_K3_2P_aa.fq

all the best