Problem when downloading Fastq files from ENA Database automatically with accession number

Problem when downloading Fastq files from ENA Database automatically with accession number

0

Hi all! I’m trying to download the FASTQ files from different experiments stored in ENA Database in a automatized way just having the SRR codes of the sample.

I’m using ENA File Downloader Command Lines Tool and I’m able to download almost all the FASTQ that I want in a automaticed way. But, when I try to uncompressed it with gunzip I obtained the following problem:

gunzip: /direction_to_file/file.fastq.gz: invalid compressed data–format violated.

I have downloaded the same fastq in a manual way from the webpage and I can uncompressed it without any problem. I have compared the sizes of the 2 fastq files. And I see that they have mostly the same size but a little bit different:

size manually way downloaded: 550306224 Bytes
size autommatically downloaded: 550314301 Bytes.

Do you know what could happened here?
I have tried different samples and I obtained the same error.

I am using linux and the command line that I have used to download the sample automatically was the following:

java -jar path_to_ena_file_downloader/ena-file-downloader.jar –accessions=SRR6435746 –format=READS_FASTQ –location=path_to_Fastq_downloaded_folder –protocol=FTP –email=NONE

Thank you very much in advance.


ENA


Fastq


download


Command


Downloader

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