am trying to install Jalview 2.11.5.1 on my Mac with M1 chip (2020), but the installation consistently fails. The following error appears:
“We were unable to download the necessary files after five attempts”
I have tried multiple times, but the issue persists. Could you please advise how to resolve this?
Thank you
hi ! This sounds like the Jalview app is failing to download updates - but it should still launch if you have created a fresh installation.
Could you try launching the Jalview application directly from the DMG image downloaded from here ? https://www.jalview.org/downloads/installers/release/Jalview-2_11_5_1-macos-aarch64-java_8.dmg - just double click on the Jalview application icon directly rather than the ‘Install Jalview’ app.
Thank you so much for your aswer. It is happening with the DMG image by just clicking the Jalview icon, not sure why.
@ben_soares may be able to help here, but we’ve not seen this problem ourselves. If you can, check with a colleague with a similar M1 macbook to see if they are also having problems.
One issue that could be happening is that Jalview is failing to create a local ‘cache’ of the application - these are kept under ~/Library/Application\ Support/Jalview-Desktop/Jalview/, which you should be able to read and write to without any issues. To test this, try opening a Terminal window and typing these two lines, if they both work without any error or other messages, then all is well:
touch ~/Library/Application\ Support/Jalview-Desktop/Jalview/test_file
rm ~/Library/Application\ Support/Jalview-Desktop/Jalview/test_file
If there are problems with either command it could be that somehow you have wrong permissions for the directory under ~/Library/Application\ Support/Jalview-Desktop - in that case, try the following:
sudo rm -Rf ~/Library/Application\ Support/Jalview-Desktop
Then after that, try launching the Jalview app from the DMG again. This time it should start correctly but warn you that you are running it from the dmg.
After trying the above advice, you should have a hidden file .jalview.log in your home directory which will probably have some errors in it towards the end of the file.
The file will contain some information like your home directory path so I would advise not to post the whole of it into this thread. If you can copy and paste the “Exception” errors, or better still, send it to Jim and/or me in a direct message as an attachment (use the Upload icon 
in the message to attach a file).
It’s possible you might have to rename the file to e.g. jalview.log without the dot for your browser to see it. You can use the command
mv ~/.jalview.log ~/jalview.log
to do that.
Either way, let us know how you get on!
Ben
Thank you so much for your help! Here you can find part of the exception errors I get (see below). I tried updating the Java version to the latest one, but it did not help:
LAUNCHER: Failed to find ‘/channel.props’ file at ‘null’. Using class defaultProps.
LAUNCHER: Failed to load channel image logo.16=/default_images/jalview_logo-16.png
LAUNCHER: Failed to load channel image logo.32=/default_images/jalview_logo-32.png
LAUNCHER: Failed to load channel image logo.48=/default_images/jalview_logo-48.png
LAUNCHER: Failed to load channel image logo.64=/default_images/jalview_logo-64.png
LAUNCHER: Failed to load channel image logo.128=/default_images/jalview_logo-128.png
LAUNCHER: Failed to load channel image logo.256=/default_images/jalview_logo-256.png
LAUNCHER: Failed to load channel image logo.512=/default_images/jalview_logo-512.png
2026/04/16 21:29:20:282 INFO Checking whether we need to use a proxy…
2026/04/16 21:29:20:695 INFO Keep on top set to [keep_on_top=true]
2026/04/16 21:29:20:756 INFO Displaying instant background image
2026/04/16 21:29:20:765 WARNING Tried to invokeAndWait but couldn’t. Going to invokeLater instead [Exception=null]
2026/04/16 21:29:20:869 INFO Downloading 0 resources [totalBytes=0, maxConcurrent=10]
2026/04/16 21:29:20:872 INFO Testing whether proxy is needed
2026/04/16 21:29:22:364 INFO Failed to establish connection: javax.net.ssl.SSLException: Couldn’t kickstart handshaking
2026/04/16 21:29:22:364 INFO We probably need a proxy, but auto-detection failed.
2026/04/16 21:29:22:368 INFO Able to lock for updates: true
2026/04/16 21:29:22:368 INFO Verifying application
2026/04/16 21:29:22:368 INFO Version: -1
2026/04/16 21:29:22:368 INFO Class: jalview.bin.Jalview
2026/04/16 21:29:22:380 INFO Attempting to refetch digest file
2026/04/16 21:29:22:448 WARNING Failed to refresh digest: Couldn’t kickstart handshaking. Proceeding…
2026/04/16 21:29:22:455 INFO Resource failed digest check [missing file: flatlaf-3.5.4.jar]
2026/04/16 21:29:22:457 INFO Resource failed digest check [missing file: libquaqua64-8.0.jnilib.jar]
2026/04/16 21:29:22:457 INFO Resource failed digest check [missing file: libquaqua-8.0.jnilib.jar]
2026/04/16 21:29:22:468 INFO Verified resources [count=100]
2026/04/16 21:29:22:468 INFO 3 of 100 resources require update
2026/04/16 21:29:22:596 WARNING Download failed due to SSL handshake error
javax.net.ssl.SSLException: Couldn’t kickstart handshaking
Caused by: java.net.SocketException: Broken pipe (Write failed)
Hi Carolina,
Thanks for that snippet from the .jalview.log file.
It looks like there is a failure with the SSL/TLS certificate handshake. We’ve seen a similar problem when Jalview is launched from within an intranet that intercepts all HTTP and HTTPS traffic, with its own certificates. These intranet certificates are probably inserted automatically into browsers, but the Java binary bundled with Jalview will not have access to them, and so can’t check the HTTPS connection its trying to make.
If this is the case, then there are some workarounds. Most of them are quite technical, and we explored some of them in an issue you can read about here:
https://issues.jalview.org/browse/JAL-4491
It might just be that some http proxy settings need to be made.
However, possibly the easiest workaround is to run Jalview from the command line, which by-passes the automatic update that is causing the launch problem, although ultimately you will probably have problems accessing external services such as PFAM or 3D-Beacons without further work. At least this will get things started.
To run Jalview from the command line, open a Terminal window and (if you installed Jalview in /Applications, [“For all users”] the default option) then run the command
jalview
but if this doesn’t work (with a “command not found” error), try
/Applications/Jalview.app/Contents/MacOS/jalview
If you installed it just for your user, use the command
~/Applications/Jalview.app/Contents/MacOS/jalview
If you think you are on an intranet that checks HTTPS traffic, then we can discuss the workarounds further, and also let us know if the above command line launch works.
Ben
Thank you for your answer. This code worked to run jalview from the command line, but I don’t have access to MSAs (or anything related to external services, as you indicated). I am working from home (WiFi connection), so I don’t think I am on an intranet that checks HTTPS traffic.
Thanks for confirming the command line result.
That’s an odd situation, if you are using a work-managed computer, it’s possible the WiFi is still going through a VPN. If so, would you be able to check with your IT people to see if the laptop/computer might be using a VPN when you’re working from home and if that, or another reason, might cause a certificate problem with a standard Java Runtime?
Other than that I’m at a bit of a loss as to why Jalview’s bundled Java (the Apple Silicon bundled Java is a standard Azul Zulu Java 8 distribution) can’t perform a TLS handshake.
If you want to try something different as well, try installing the macOS Intel DMG (https://www.jalview.org/download/macos/) and see if that works (most M1 macs have Rosetta pre-installed so it should still run, but it’s possible it just won’t). That has a bundled Adoptium Java 8 runtime, which just might work better (I can’t find a “clutching-at-straws” emoji)!
After that, if you try installing our development version, Jalview Develop, from https://www.jalview.org/development/jalview_develop/ that uses an Adoptium Java 11 runtime, which is different again.
I am not at all sure any of these will help, but it’s what I might try next (after asking local IT support).
Sorry not to have a definitive solution.
Ben
In the end, I realized that with the latest computer update, an antivirus extension was activated that was affecting HTTPS traffic. After disabling it, everything works perfectly! Thank you so much for your help!
Good to hear that you found a solution. If you can share the name of the antivirus system you are using and the platform you are on then it might help others who see this problem in the future.
Many thanks,
Geoff Barton FRSE FRSB | Professor of Bioinformatics | Head of Computational Biology
Faculty of Life Sciences | University of Dundee | Scotland, UK | email: gjbarton@dundee.ac.uk
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