I’m pretty new to Galaxy, so I can’t tell if this error is my fault or not. I am working through the tutorial Identification of somatic and germline variants from tumor and normal sample pairs on usegalaxy. org (The help tool is not letting me post links). I am trying to trim and filter the exome sequencing reads with trimmomatic using the setting given in the tutorial, but I get an error every time. These are the job messages:
Job Message 1:
desc: Fatal error: Exit code 1 ()
error_level: 3
type: exit_code
exit_code: 1
Job Message 2:
desc: Fatal error:
error_level: 3
type: regex
stream: stdout
match: Exception:
I imagine this is a mistake on my end, but I can’t see where I’ve diverged from the tutorial. Any help would be greatly appreciated.
I’ve adjusted your account. Would you like to try to post back a share link to your history now? → FAQ: Sharing your History
For troubleshooting in general with this tool, reviewing the log message output is where to start. How to find the logs. → FAQ: Troubleshooting errors
One of the most common issues is some problem with the input fastq data. Running FastQC can help to confirm a truncated file (possibly from a failed Upload step). The usual solution is to load the read data again. If you ask the AI assistant in Galaxy to read the log for you, this is likely what it would also suggest.
Thank you. I started fresh and reuploaded the data and everything worked much better. I appreciate the links; I’m sure I will need them in the near future.
