fastp 线程数目对质控速度的影响

 

001、fastp 线程数目对质控速度的影响

 

a、4线程

fastp -i sample_name_1.fastq.gz -I sample_name_2.fastq.gz -o sample_name_qc_1P.fastq.gz -O sample_name_qc_2P.fastq.gz --thread 4 -g -q 20 -u 30 -l 75 -h sample_name_fastp.html -j sample_name_fastp.json 2> sample_name_fastp.txt && echo sample_name done || echo sample_name fail

 

b、8线程

fastp -i sample_name_1.fastq.gz -I sample_name_2.fastq.gz -o sample_name_qc_1P.fastq.gz -O sample_name_qc_2P.fastq.gz --thread 8 -g -q 20 -u 30 -l 75 -h sample_name_fastp.html -j sample_name_fastp.json 2> sample_name_fastp.txt && echo sample_name done || echo sample_name fail

 

c、16线程

fastp -i sample_name_1.fastq.gz -I sample_name_2.fastq.gz -o sample_name_qc_1P.fastq.gz -O sample_name_qc_2P.fastq.gz --thread 16 -g -q 20 -u 30 -l 75 -h sample_name_fastp.html -j sample_name_fastp.json 2> sample_name_fastp.txt && echo sample_name done || echo sample_name fail

 

d、32线程

fastp -i sample_name_1.fastq.gz -I sample_name_2.fastq.gz -o sample_name_qc_1P.fastq.gz -O sample_name_qc_2P.fastq.gz --thread 32 -g -q 20 -u 30 -l 75 -h sample_name_fastp.html -j sample_name_fastp.json 2> sample_name_fastp.txt && echo sample_name done || echo sample_name fail

 

002、时间对比

(base) [b20223040323@admin1 test2]$ find ./ -name "*time.txt" | xargs grep "min" | sort -V
./01_t4/SRR18286720_t4_time.txt:SRR18286720 6.08333min
./02_t8/SRR18286720_t8_time.txt:SRR18286720 4.53333min
./03_t16/SRR18286720_t16_time.txt:SRR18286720 7.05min
./04_t32/SRR18286720_t32_time.txt:SRR18286720 5.98333min

 

8线程速度最快。

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