sra-toolkit and fastq-dump error

Question

[chloisf]

Hello,

I am a begginner and enthusiastic to learn about bioinformatics! I am trying to learn how to use the Short Read Archive but I have a problem with fastq-dump. I am sorry to ask as I have found this error on the internet but even with other people comments I can't manage to fix the error. I would be very grateful if someone could help me understand how I can solve this. When I request for any file using fastq-dump I get this error:

2019-11-14T06:23:10 fastq-dump.2.5.7 err: name incorrect while evaluating path within network system module - Scheme is 'https'
2019-11-14T06:23:10 fastq-dump.2.5.7 err: item not found while constructing within virtual database module - the path 'SRR390728' cannot be opened as database or table

I have come to understand it is related to the fact 2.5.7 is an old version. So I have tried deleting it using this command:

sudo apt-get purge --auto-remove sra-toolkit

However if I try to use fastq-dump after removing sra-toolkit, I still get a slightly different error, while I expect to get "command not found" as I deleted the package:

2019-11-14T06:29:12 fastq-dump.2.5.7 err: error unexpected while resolving tree within virtual file system module - failed to resolve accession 'SRR390728' - Obsolete software. See https://github.com/ncbi/sra-tools/wiki/Obsolete-software ( 406 )
2019-11-14T06:29:13 fastq-dump.2.5.7 err: name incorrect while evaluating path within network system module - Scheme is 'https'
2019-11-14T06:29:13 fastq-dump.2.5.7 err: item not found while constructing within virtual database module - the path 'SRR390728' cannot be opened as database or table

So even after I tried installing the new version, the 2.5.7 still appears to be here...

Thank you in advance for your attention and time!

[lakhujanivijay]

Did you try sra-explorer : find SRA and FastQ download URLs in a couple of clicks

[chloisf]

Hi lakhujanivijay and ATpoint,

Thank you two for your answers!

I didn't know about sra-explorer, thank you two for the introduction. I have tried downloading directly from there it does seem easier and faster. I have however tried to update the package and I can see I already have a newer version than the error's when I type this:

sudo apt-get --only-upgrade install sra-toolkit
Reading package lists... Done
Building dependency tree
Reading state information... Done
sra-toolkit is already the newest version (2.8.2-5+dfsg-1).
0 upgraded, 0 newly installed, 0 to remove and 119 not upgraded.

However I still get the same error when trying to use fastq-dump without dowloading anything before, and I also get it with prefetch...

(bioinfo) chloisf@MAJOR-TOM:~/edu$ prefetch SRR1553607
Maximum file size download limit is 20,971,520KB

2019-11-15T09:51:07 prefetch.2.5.7 err: name incorrect while evaluating path within network system module - Scheme is 'https'
2019-11-15T09:51:07 prefetch.2.5.7 err: path not found while resolving tree within virtual file system module - 'SRR1553607' cannot be found.

I don't understand why it uses an older version when I have a newer one. Also why doesn't it upgrade to 2.10 ?

Thank you again for your time and fast answers!

[ATpoint]

I assume because the old one is somewhere in your PATH while the new one isn't. Check which fastq-dump to see where it is.

[chloisf]

Hi!

I checked as you suggested and found fastq-dump as well as the prefetch file in a directory. There were the fastq-dump 2.5.7 and the newer one. I deleted the 2.5.7 version and now it seems to work fine! Same for prefetch. Thank you so much for your help, I'm sure your advices will turn out useful again sometime.

Answer 1

[ATpoint]

First of all, you should upgrade to the most recent version of the toolkit as 2.5.7 is very old and obsolete as the rror message Obsolete software clearly states. Install the most recent one. Then use prefetch to download the SRA files and then run fastq-dump locally to get fastq or (preferred) simply download from the ENA directly as fastq, see Fast download of FASTQ files from the European Nucleotide Archive (ENA)

By the way, sra-explorer which was suggested above by lakhujanivijay can create download links for ENA which are based on the download strategy from the above tutorial plus links to download fastq files via FTP from NCBI, check it out.