Support #7599
closed
arv-copy pipeline template copy added non-ASCII character in file
Description
This happened in a couple of my crunch_scripts when copying over from tb05z. I'm pretty sure this is not my doing. I also cannot find that character when I search in the file, so I end up just deleting the entire line and rewriting. IIRC, it was near the '-Xmx20g' part in the line number that the log specified.
https://cloud.curoverse.com/pipeline_instances/qr1hi-d1hrv-p90izy6k8su0tz4#Log
https://cloud.curoverse.com/pipeline_instances/qr1hi-d1hrv-43eougs69ebntog#Log
2015-10-16_21:02:55 qr1hi-8i9sb-a8hqdn5mjkfvsob 51626 0 stderr File "/tmp/crunch-job/src/crunch_scripts/reorderbam.py", line 30
2015-10-16_21:02:55 qr1hi-8i9sb-a8hqdn5mjkfvsob 51626 0 stderr SyntaxError: Non-ASCII character '\xe2' in file /tmp/crunch-job/src/crunch_scripts/reorderbam.py on line 30, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details
2015-10-16_21:03:03 qr1hi-8i9sb-a8hqdn5mjkfvsob 51626 0 stderr srun: error: compute7: task 0: Exited with exit code 1
2015-10-16_21:03:03 qr1hi-8i9sb-a8hqdn5mjkfvsob 51626 0 child 52164 on compute7.1 exit 1 success=false
Updated by Brett Smith over 10 years ago
Need to look at the Crunch script to see if it includes non-ASCII characters. It's possible that the issue here is that the cluster upgrade means that Python is being stricter about the encoding of source files.
Updated by Tom Clegg over 10 years ago
That looks like an en-dash instead of a hyphen in a command line flag in reorderbam.py.
(Perhaps your text editor was Helping you make better dashes? Or that particular bit was copied & pasted from a web page that was Helping by automatically using fancier typography?)
Updated by Brett Smith over 10 years ago
- Tracker changed from Bug to Support
- Status changed from New to Resolved
The git log confirms that the script had this en-dash when it was first added to the original repository in qr1hi, in c2d5290896a940cdfb508ff70141493debf1ebbb.
I don't doubt something funky happened here, but right now there's no reason to believe that any Arvados tool created this en-dash. I agree with Tom it looks like something added by a fancy text editor, or copied-and-pasted from a Web site.