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?
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?
