I’ve inherited a legacy galaxy (version 16.07) installed on local Ubuntu (18.04) server, with a lot of installed tools. However, when I try to do data analysis I get the error ‘Fatal error: Exit code 1 ()’. Here is the bug report for simple fastqc (Note: I got the same/similar error message for other tools I’ve tried too).
Fatal error: Exit code 1 ()
/bin/sh: 1: fastqc: not found
Traceback (most recent call last):
File “/home/posavi/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/3a458e268066/fastqc/rgFastQC.py”, line 166, in
File “/home/posavi/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/3a458e268066/fastqc/rgFastQC.py”, line 139, in run_fastqc
File “/usr/lib/python2.7/subprocess.py”, line 190, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ‘fastqc --outdir /home/posavi/galaxy/database/jobs_directory/017/17999/dataset_35883_files --quiet --extract -f fastq tenM.fastq’ returned non-zero exit status 127
Also, most of the installed tools have either red arrow or red triangle flag (see the image)
I am also not able to either update/reinstall any of installed tools neither to install any new tools.
Please let me know if there is the way to fix this problem, except to upgrade ubuntu and galaxy.