fastq-dump ... ERROR

[PC2021]

Hi there! I have been following the Step-by-Step installation and got two errors as you can see below. Could anyone help me?

$ ~/bin/doctor.py

Doctor! Doctor! Give me the news.

Checking symptoms ...

bwa ... OK

datamash ... OK

fastqc -h ... OK

hisat2 ... OK

seqret -h ... OK

featureCounts ... OK

efetch ... OK

esearch ... OK

samtools ... OK

fastq-dump ... ERROR

bowtie2 ... OK

bcftools ... OK

seqtk ... OK

seqkit ... OK

bio ... OK

fastq-dump -X 1 -Z SRR1553591 ... ERROR

Your system shows 2 errors!

I tried to fix, and I got the following error message.

$ fastq-dump --stdout -X 2 SRR390728
Can't locate XML/LibXML.pm in @inc (you may need to install the XML::LibXML module) (@inc contains: /home/pdc/miniconda3/envs/bioinfo/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/pdc/miniconda3/envs/bioinfo/lib/site_perl/5.26.2 /home/pdc/miniconda3/envs/bioinfo/lib/5.26.2/x86_64-linux-thread-multi /home/pdc/miniconda3/envs/bioinfo/lib/5.26.2 .) at /home/pdc/miniconda3/envs/bioinfo/bin/fastq-dump line 13.
BEGIN failed--compilation aborted at /home/pdc/miniconda3/envs/bioinfo/bin/fastq-dump line 13.

[ialbert]

the step by step instruction has an alternative sratools install,

follow that

[PC2021]

Thanks for your prompt reply.

I followed "The step-by-step instructions too" and I got the same message errors.

I installed the XML::LibXML module again and I got the same error message.

Do you have any further instructions to solve this problem?

[ialbert]

no something is not right, you should not be getting any error of such sort,

fastq-dump is not a Perl script, you should not be getting this error at all, there is no reason to start installing Perl modules

check where is fastq-dump running from

which fastq-dump

what does it print?

[ialbert]

I was explicitly referring to look for the fastq-dump section not the rest of it

have yo installed the latest tools as described there? have you restarted the terminal because that tool does not require perl,

[PC2021]

I restarted the terminal when I was installing the tools.

I ran the command "which fastq-dump" and I got the following path:

/home/pdc/miniconda3/envs/bioinfo/bin/fastq-dump

[ialbert]

yes you seem to still have the wrong fastqdum

have you done the step as indicated in the How to fix fastq-dump errors

  curl http://data.biostarhandbook.com/sratools.sh | bash

you don't have to do the other steps, just that one.

[PC2021]

pdc@PDC ~
$ curl http://data.biostarhandbook.com/sratools.sh | bash
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 898 100 898 0 0 2217 0 --:--:-- --:--:-- --:--:-- 2217
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 81.8M 100 81.8M 0 0 12.2M 0 0:00:06 0:00:06 --:--:-- 17.7M

Installation complete

Close and reopen the terminal.

In the new terminal activate the bioinfo environment.

pdc@PDC ~
$ grep BIOSTAR_HANDBOOK_START ~/.bashrc

>>> BIOSTAR_HANDBOOK_START

>>> BIOSTAR_HANDBOOK_START

[PC2021]

Hi again!

I uninstalled and installed it three times. I tried installing it in a new directory but got the same error message. There seems to be a problem on line 13 as you can see in the error message: "...BEGIN failed--compilation aborted at /home/pdc/miniconda3/envs/bioinfo/bin/fastq-dump line 13..."

[PC2021]

Hi again!

I uninstalled and installed it three times. I tried installing it in a new directory but got the same error message. There seems to be a problem on line 13 as you can see in the error message: "...BEGIN failed--compilation aborted at /home/pdc/miniconda3/envs/bioinfo/bin/fastq-dump line 13

[ialbert]

I don't understand your problem, something else is going badly

fastq-dump is not a Perl script, there is no reason for Perl to run at all!

the second point is that the other fastq-dump should be found first, it should be located in

~/bin/sratoolkit.3.0.0-mac64/bin/fastq-dump

on a mac, or

~/bin/sratoolkit.3.0.0-ubuntu64/bin/fastq-dump

on a Linux machine. And that path should be already activated.

Try running the command above.

Long story short, something else is wrong

[PC2021]

I ran the command below

$ ~/bin/sratoolkit.3.0.0-ubuntu64/bin/fastq-dump

This sra toolkit installation has not been configured.
Before continuing, please run: vdb-config --interactive
For more information, see https://www.ncbi.nlm.nih.gov/sra/docs/sra-cloud/

[ialbert]

what system are you running this on? the messages that you are getting are very a typical from what people experience

[ialbert]

just do what it says then, normally you would never need to that any of that

https://www.biostars.org/p/424404/

[PC2021]

I have been using:

$ cat /etc/os-release
NAME="Linux Mint"
VERSION="20.3 (Una)"
ID=linuxmint
ID_LIKE=ubuntu
PRETTY_NAME="Linux Mint 20.3"
VERSION_ID="20.3"
HOME_URL="https://www.linuxmint.com/"
SUPPORT_URL="https://forums.linuxmint.com/"
BUG_REPORT_URL="http://linuxmint-troubleshooting-guide.readthedocs.io/en/latest/"
PRIVACY_POLICY_URL="https://www.linuxmint.com/"
VERSION_CODENAME=una
UBUNTU_CODENAME=focal

[ialbert]

the Entrez Direct installation step runs the commands that are described here:

https://www.ncbi.nlm.nih.gov/books/NBK179288/

rerun them separately, perhaps - though evidently there are some other things not quite optimal with your system

[PC2021]

Should I activate conda and write these commands?

[ialbert]

these should work independently of bioconda

[PC2021]

Hi, Ialbert!
Good news! Everything is running appropriately.
The error message is coming up due to incompatibility between the python version and sratoolkit. Even using your command, bioconda was not updating to the latest version of Sratoolkit=3.0.0. I had to remove the sratoolkit=2.9.1.1 version and separately install sratoolkit=3.0.0. Additionally, I had to install one of the older versions of python, python=3.8.13. I have created other environments inside conda using the latest version of python and the newest version of sratoolkit. Also, it worked perfectly. I'm writing because this information may help other people with the same problem.

Thanks for trying to help.

Best

[ialbert]

thanks for following up, bioconda is tested only with Python 3.8 thus that explains it