cannot execute binary file: Exec format error
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11 months ago
applepie ▴ 10

Hi everyone.

I was trying to download and install the SRA Toolkit based on the instructions of the following website: https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit and https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit

However, after installation, I could't successfully leverage the SRA Toolkit to download scRNA seq data, and instead, an error message was observed:

"-bash: /home/billychan509/SRA/sratoolkit.3.0.6-mac64/bin/fastq-dump: cannot execute binary file: Exec format error"

May I know what's wrong with it ?

linux • 1.8k views
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This is the script I used to download and install the SRA Toolkit:

**1. Downloading the SRA Toolkit for MacOs (Done on linux terminal)

wget "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.6/sratoolkit.3.0.6-mac64.tar.gz"

tar -vxzf sratoolkit.3.0.6-mac64.tar.gz

2. installation of SRA Toolkit:

curl --output sratoolkit.tar.gz https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-mac64.tar.gz

tar -vxzf sratoolkit.tar.gz

export PATH=$PATH:$PWD/sratoolkit.3.0.6-mac64/bin

which fastq-dump

**3. Downloading data:

fastq-dump --stdout -X 2 SRR390728

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Downloading the SRA Toolkit for MacOs (Done on linux terminal)

You can't use macOS binaries on linux and vice varsa. They are not compatible. If you are using linux they download the linux binary.

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What operating system are you using? Some Linux flavour or MacOS?

Also, the wget "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.6/sratoolkit.3.0.6-mac64.tar.gz" and the curl --output sratoolkit.tar.gz https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-mac64.tar.gz are essentially redundant.

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May I ask why?

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Because both download the software. The first one exactly version 3.0.6, the other one the most current one - which happens to be version 3.0.6 for now. This may change of course in a couple of weeks.

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Based on this post you maybe be trying to use a 64bit binary on a 32 bit architecture. It isn't a SRA-toolkit specific error anyway so you may find more relevant information on a general purpose forum.

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You are trying to use the MacOS binary under some kind of Linux. To determine the proper installation method, pls answer the following questions:

  • what is the output of uname -a?
  • are you allowed to run commands via sudo? check sudo apt or sudo yum to find out if you can install software system wide.
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