Question: Fastq-dump does not work
gravatar for obuhovadarina
10 weeks ago by
obuhovadarina0 wrote:

I am trying to use fastq-dump function which is the part of SRA Toolkit. However, all the time I am getting this mistake

Can't locate XML/ in @INC (you may need to install the XML::LibXML module) (@INC contains: /Users/darinaobukhova/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level /Users/darinaobukhova/anaconda3/lib/site_perl/5.26.2 /Users/darinaobukhova/anaconda3/lib/5.26.2/darwin-thread-multi-2level /Users/darinaobukhova/anaconda3/lib/5.26.2 .) at /Users/darinaobukhova/anaconda3/bin/fastq-dump line 13. BEGIN failed--compilation aborted at /Users/darinaobukhova/anaconda3/bin/fastq-dump line 13.

I have installed requested XML::LibXML module. However, this keeps on coming. Does anyone have a similar problem and can recommend a solution?

I am desperately looking forward to it!

ADD COMMENTlink written 10 weeks ago by obuhovadarina0

Please can you add the command you try to execute ?

ADD REPLYlink written 10 weeks ago by anicet.ebou160

I was trying to execute ./fastq-dump, fastq-dump and fastq-dump -X 100 -Z SRR1553607 | head (example from Biostars book)

ADD REPLYlink written 10 weeks ago by obuhovadarina0

How did you install the XML::LibXML module? Did you use something like this?

ADD REPLYlink written 10 weeks ago by genomax76k

You can simply download fastq from ENA: Fast download of FASTQ files from the European Nucleotide Archive (ENA)

ADD REPLYlink written 9 weeks ago by ATpoint28k
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