Docs / Usage
Hopefully MultiQC will be easy to use and run without any hitches. If you have any problems, please do get in touch with the developer (Phil Ewels) by e-mail or by submitting an issue on github. Before that, here are a few things previously encountered that may help…
Not enough samples found
In this scenario, MultiQC finds some logs for the bioinformatics tool in question, but not all of your samples appear in the report. This is the most common question I get regarding MultiQC operation.
Usually, this happens because sample names collide. This happens innocently
a lot - MultiQC overwrites previous results of the same name and you get
the last one seen in the report. You can see warnings about this by running
MultiQC in verbose mode with the
-v flag, or looking at the generated log
multiqc_data/multiqc.log. If you are unsure about what log file
ended up in the report, look at
lists each source file used.
To solve this, try running MultiQC with the
The Clashing sample names
section of the docs explains this in more detail.
Big log files
Another reason that log files can be skipped is if the log filesize is very
large. For example, this could happen with very long concatenated standard out
files. By default, MultiQC skips any file that is larger than 10MB to keep
execution fast. The verbose log output (
show you if files are being skipped with messages such as these:
[DEBUG ] Ignoring file as too large: filename.txt
You can configure the threshold and parse your files by changing the
log_filesize_limit config option. For example, to parse files up to 2GB in
size, add the following to your MultiQC config file:
No logs found for a tool
In this case, you have run a bioinformatics tool and have some log files in a directory. When you run MultiQC with that directory, it finds nothing for the tool in question.
There are a couple of things you can check here:
- Is the tool definitely supported by MultiQC? If not, why not open an issue to request it!
- Did your bioinformatics tool definitely run properly? I’ve spent quite a bit of time debugging MultiQC modules only to realise that the output files from the tool were empty or incomplete. If your data is missing, take a look and the raw files and make sure that there’s something to see!
If everything looks fine, then MultiQC probably needs extending to support your data. Tools have different versions, different parameters and different output formats that can confuse the parsing code. Please open an issue with your log files and we can get it fixed.
Error messages about mkl trial mode / licences
In this case you run MultiQC and get something like this:
$ multiqc . Vendor: Continuum Analytics, Inc. Package: mkl Message: trial mode EXPIRED 2 days ago You cannot run mkl without a license any longer. A license can be purchased it at: http://continuum.io We are sorry for any inconveniences. SHUTTING DOWN PYTHON INTERPRETER
mkl library provides optimisations for
numpy, a requirement of
MatPlotLib. Recent versions of Conda have a bundled version which should
come with a licence and remove the warning. See
for more info. If you already have Conda installed you can get the updated
version by running:
conda remove mkl-rt conda install -f mkl
Another way around it is to uninstall
mkl. It seems that
without it fine:
conda remove --features mkl
Problem solved! See more here and here.
If you’re not using Conda, try installing MultiQC with that instead. You can find instructions here.
Locale Error Messages
Two MultiQC dependencies have been known to throw errors due to problems with the Python locale settings, or rather the lack of those settings.
MatPlotLib can complain that some strings (such as
en_SE) aren’t allowed.
Running MultiQC gives the following error:
# ..long traceback.. # File "/sw/comp/python/2.7.6_milou/lib/python2.7/locale.py", line 443, in _parse_localename raise ValueError, 'unknown locale: %s' % localename ValueError: unknown locale: UTF-8
Click can have a similar problem if the locale isn’t set when using Python 3. That generates an error that looks like this:
# ..truncated traceback.. # File "click/_unicodefun.py", line 118, in _verify_python3_env 'for mitigation steps.' + extra) RuntimeError: Click will abort further execution because Python 3 was configured to use ASCII as encoding for the environment. Consult http://click.pocoo.org/python3/for mitigation steps.
You can fix both of these problems by changing your system locale
to something that will be recognised. One way to do this is by adding
these lines to your
.bashrc in your home directory (or
export LC_ALL=en_US.UTF-8 export LANG=en_US.UTF-8
Other locale strings are also fine, as long as the variables are set and valid.
No space left on device
If you’re running with very large datasets or have an unusually small temporary file storage location, you may run in to the following error:
File "/usr/local/lib/python3.8/site-packages/multiqc/utils/util_functions.py", line 71, in write_data_file print( jsonstr.encode('utf-8', 'ignore').decode('utf-8'), file=f) OSError: [Errno 28] No space left on device
This happens because MultiQC writes all output files to a temporary directory before moving them to their final location (depending on configuration, MultiQC can change its output filenames based on the data that it parses).
To solve this problem you can manually set the temp folder to another folder that has more space.
This is best done with an environment variable which is understood by the base Python installation,
Note that you will have to do this in each session where you run MultiQC. To automatically apply
it at every login, add the above line to your
Be aware that setting this could have unforeseen consequences as it could affect the behaviour of other tools.