I downloaded 330 SRA files by prefetch and tried to extract fastq files using for loop + fasterq-dump When I run this very simple bash script, error messages pop up #!/bin/bash for i in $(cat accession.txt) # It contains SRA accession do...
time fasterq-dump --split-3 SRR5318040.sra -e 20 -o SRR5318040 # 582.70s user 121.06s system 1130% cpu 1:02.25 total 同样的如果上面的fastqer-dump运行报错,请把 SRR5318040.sra 改成 ./SRR5318040. 从用户模式(user mode)来看, 两者的总CPU使用时间都差不多是560秒,从内核模式来看(Kernel Mode...
Hi All, I am trying to use fasterq-dump to extract fasta files for this accession SRR16235266 Anytime I use it fastq files are rather generated. Below is the command I use fasterq-dump --fasta 60 SRR16235266 Please advice.
Your second command "fasterq-dump ERR695638" does not use the accession you downloaded via prefetch. By specifying a bare accession the tool always goes out over the internet and fetches the data again - in other words - it ignores your prefetched data. The right way to specify a local co...
I am trying to download files from project GEO series GSE132044. From what I can tell, most (if not all) of the associated runs are paired-end with multiple fastq files deposited, but I only get a single fastq file every single time. For...
A (faster) wrapper for NCBI's fastq-dump with some convenience functions - fasterq_dump/fasterq_dump at main · glarue/fasterq_dump