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s-andrews / FastQC

A quality control analysis tool for high throughput sequencing data
GNU General Public License v3.0
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crash command #92

Closed estelabruxel closed 2 years ago

estelabruxel commented 2 years ago

Hello! I am with a trouble with fastqc command: estela@bioinf1:~/FastQC$ fastqc --help Sorry, command-not-found has crashed! Please file a bug report at: https://bugs.launchpad.net/command-not-found/+filebug Please include the following information with the report:

command-not-found version: 0.3 Python version: 3.8.10 final 0 Distributor ID: Ubuntu Description: Ubuntu 20.04.2 LTS Release: 20.04 Codename: focal Exception information:

file is not a database Traceback (most recent call last): File "/usr/lib/python3/dist-packages/CommandNotFound/util.py", line 23, in crash_guard callback() File "/usr/lib/command-not-found", line 95, in main if not cnf.advise(args[0], options.ignore_installed) and not options.no_failure_msg: File "/usr/lib/python3/dist-packages/CommandNotFound/CommandNotFound.py", line 363, in advise packages = self.get_packages(command) File "/usr/lib/python3/dist-packages/CommandNotFound/CommandNotFound.py", line 97, in get_packages return self.db.lookup(command) File "/usr/lib/python3/dist-packages/CommandNotFound/db/db.py", line 19, in lookup for row in self.con.execute( sqlite3.DatabaseError: file is not a database

Could you help me??

s-andrews commented 2 years ago

The error you're getting isn't coming from fastqc, but from another program you have installed which tries to make sensible suggestions if you try to run a program which can't be located on your system.

The FastQC problem in this is that fastqc isn't being found on your system, so either it's not installed at all, or it's installed somewhere but hasn't been added to your PATH variable which says where the system will look for programs when they're specified by name.

If you've not installed it at all then go to:

https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc

..to grab a copy and follow the install instructions.

Assuming that you've already done this and that fastqc is installed in your home directory (/home/estela/FastQC) then you have a couple of choices:

  1. You can just call fastqc explicitly rather than by using the PATH, this would mean that instead of running fastqc you'd run /home/estla/FastQC/fastqc so the system doesn't have to search for it.
  2. You could add a link to fastqc to a folder which is already in your PATH, such as /usr/local/bin, to do that you'd run sudo ln -s /home/estela/FastQC/fastqc /usr/local/bin/fastqc.
  3. You modify your PATH to add the FastQC folder to the list of locations to search. To do this you'd edit the .bashrc file in your home directory and would add a line which said export PATH=/home/estela/FastQC/fastqc:$PATH

Either of 2 or 3 would mean that you could now run FastQC from anywhere by just running fastqc. Please also note that installing FastQC involves making the launch script executable (this is in the install instructions) which in your case would, just once, mean running chmod 755 /home/estela/FastQC/fastqc

Hopefully this should get you up and running.