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Mohamedema / NGS_Group_project

RNA-Seq analysis
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Download Raw sequence data #4

Open nofal-50404 opened 4 years ago

nofal-50404 commented 4 years ago

I tried to use prefetch from SRA Toolkit to extract raw sequence data in fastq format from SRA

prefetch -v SRR10509508

prefetch SRR10509508

########### But Prefetch was giving the following error:

2020-02-24T14:13:42 prefetch.2.10.1 int: timeout exhausted while reading file within network system module - Cannot KStreamRead: https://sra-download.ncbi.nlm.nih.gov/traces/sra68/SRR/010263/SRR10509509 2020-02-24T14:13:42 prefetch.2.10.1: https download failed 2020-02-24T14:13:42 prefetch.2.10.1: 1) failed to download SRR10509509

2020-02-24T12:52:39 prefetch.2.10.1 int: transfer incomplete while reading file within network system module - Cannot KStreamRead: https://sra-download.ncbi.nlm.nih.gov/traces/sra73/SRR/010263/SRR10509508 2020-02-24T12:52:39 prefetch.2.10.1: https download failed 2020-02-24T12:52:39 prefetch.2.10.1: 1) failed to download SRR10509508

nofal-50404 commented 4 years ago

I found the solution for this problem (timeout exhausted while reading file within network system module - Cannot KStreamRead) I just ignored that warning and didn't get any problem using those files then apply the next command to convert SRA file to fastq file

fastq-dump SRR10509508.sra

nofal-50404 commented 4 years ago

Another solution nano Data_set.txt #this file contains all links of samples wget -i Data_set.txt