Question: FastQC Fatal Error: Exit code 1 ()
gravatar for sasha.atmadjaja
10 months ago by
sasha.atmadjaja0 wrote:


I'm new to Galaxy and have minimal experience with Linux. I have installed Galaxy on a local computer and installed FastQC 0.11.2 (Galaxy Version 0.67). The FastQC showed up as successfully installed in the installed tool manager, but when I tried to run it, it gave me Dataset Generation Errors with the following error message:

Fatal error: Exit code 1 ()

/bin/sh: 1: fastqc: not found

Traceback (most recent call last):

File "/home/genomics/shed_tools/", line 165, in <module> fastqc_runner.run_fastqc()

File "/home/genomics/shed_tools/", line 137, in run_fastqc subprocess.check_call(self.command_line, shell=True)

File "/usr/lib/python2.7/", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'fastqc --outdir /home/genomics/galaxy/database/jobs_directory/000/11/dataset_16_files --quiet --extract -f fastq NG-9686_CLOS3_6h_lib150881_5052_3_1.fastq' returned non-zero exit status 127

Could anyone help me fix this issue, please?


software error fastqc • 471 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson23k • written 10 months ago by sasha.atmadjaja0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson23k wrote:


In a default Galaxy release 17.01 local, this tool installs and executes correctly. My guess is that the tool installation failed to complete correctly. Try uninstalling and reinstalling.

If that does not work, please share more details. What version of Galaxy are you running? Are you using Conda? Is this a new instance or one that you have been using/updating? Do other tools work? Have they always worked/still work or is the first/only tool you have tried so far?

Thanks, Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson23k
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