GATK4 Mutect2 Syntax Error

usegalaxy.org support
1

I have been using the Mutect2 tumor_only analysis on BAM files aligned using Bowtie2. Up until yesterday, I haven’t had any problems with running the tool. Recently, however, it has been erroring out after only about a minute of runtime and returning this error code:

Fatal error: Exit code 1 ()

  File "/usr/local/bin/gatk", line 150
gatkArgs += ["--spark-master", sparkMaster]
          ^

SyntaxError: invalid syntax

I’m not sure how this problem would have occurred as it doesn’t seem to be related to any parameters I might have changed. Even when I went back to old histories and reran instances that had previously worked, the same error code came up. Has anyone else encountered this issue?

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2

Hi @tmccarty

This looks like an issue with an older version of the tool wrapper. What happens if you try a different version? FAQ: Changing the tool version

If that is not enough, you are welcome to share the history with one of these jobs. We can help to confirm that at least one of the versions of this tool are installed correctly on that particular server (actually UseGalaxy.org? Or somewhere else) or to report an issue to the administrators. Or, maybe the container this tool is running in needs a correction. We’ll just need an example to get started with.

If this was happening at (your own?) local server instead – is is hard to guess, but you can clarify that and we can help to troubleshoot if you share some details.. Maybe some recent change or update for another part of the server impacted this tool? Possibly how or where the jobs are running?

Let’s start there! :slight_smile:

3

Thank you so much! I’m very new to using Galaxy, so you might have to bear with me.

I checked the version I used for the previous successful runs and it was the same version that’s failing to run now. I also tried using older versions and I ran into the same problem. However, the error code I’ve been getting today has been different than yesterday:

Fatal error: Exit code 134 ()
bash: loadlocale.c:130: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))’ failed.

I’m pretty sure I’m on the UseGalaxy.org server, and when I looked at the support page, it said the current web client was built Tuesday Jul 15th 3:40:26 2025 GMT-5, which seems to be roughly the time I started having problems. Could that maybe be part of the issue?

Here is a link to a history with an example of what’s happening: Galaxy

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4

HI @tmccarty

Yes, I can confirm the issue now. We will be looking at it at UseGalaxy.org. We will get back to you about this, possibly by tomorrow.

Meanwhile, you can try at a different public Galaxy server since this is likely isolated. The UseGalaxy.eu and UseGalaxy.org.au servers are both good options. Having an account at each is a good idea anyway, and you can easily move data between them.

Which server you are working at is in the https address at top of your browser window. Each server will be different and your account at each is distinct.

Thanks for reporting the issue and more feedback soon! :slight_smile:

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5

@tmccarty please try again. The environment that this tool runs in on usegalaxy.org has been updated and should now allow jobs to succeed again.

Thanks for your patience and for reporting the issue!

2 Likes
6

It’s working perfectly! Thank you all for your help!

1 Like