Error while downloading the data using SRA Tools
This is the command:
esearch -db sra -query PRJNA714081 efetch -format runinfo | cut -d "," -f1 | grep SRR | xargs fastq-dump -X 10000 --skip-technical --readids --read-filter pass -dumpbase --split-3 --gzip
The error that appears for me:
2022-12-24T17:30:25 fastq-dump.2.8.0 err: param empty while validating argument list - expected accession
Could anyone please help me to fix this error as soon as possible because I have a deadline to submit it thanks.
1 answer
Get the fastq download URL's from https://sra-explorer.info
How to use --> sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Here is a partial list for PRJNA714081 :
https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR139/093/SRR13953393/SRR13953393.fastq.gz
https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR139/096/SRR13953396/SRR13953396.fastq.gz
https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR139/091/SRR13953391/SRR13953391.fastq.gz
https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR139/095/SRR13953395/SRR13953395.fastq.gz
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Where I can download the data using this accession number PRJNA714081 or PRJNA732831? Is there a website that can help me to download the data without this command line or I should use the command line?