Question: erros in dowloading SRA data
0
gravatar for annaA
12 weeks ago by
annaA10
annaA10 wrote:

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

sra • 107 views
ADD COMMENTlink modified 12 weeks ago by ATpoint38k • written 12 weeks ago by annaA10
0
gravatar for ATpoint
12 weeks ago by
ATpoint38k
Germany
ATpoint38k wrote:

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.

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by ATpoint38k

Thanks for the recommendation I will check it right away!

ADD REPLYlink written 12 weeks ago by annaA10
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