erros in dowloading SRA data
Hello,
I am downloading a data set from SRA with the following code ;
# filename= 'SRR_Acc_List_snRNA.txt'
while read line;do
echo "Line No. $n : $line"
fastq-dump --split-files --gzip $line -O /data/scratch/anna9230/Khrameeva_data /snRNA_data/
done < SRR_Acc_List_snRNA.txt
after the first file which is downloaded successfully I am receiving the following error
timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed )
Any help will be appreciated , A
1 answer
I would not download data via fastq-dump, too unstable.
Either download fastq directly via sra-explorer.info or as described here Fast download of FASTQ files from the European Nucleotide Archive (ENA) or use prefetch to get the SRA files and then fastq-dump for the conversion locally.
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