Hi, I’m trying to run annotatemyid on my featurecounts table. I put as input ID type Entrez, but a error occurs .
Fatal error: Exit code 1 ()
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 2 did not have 8 elements
Calls: read.table → scan
Can anyone help me?
Thanks
Hi - On the annotateMyIds tool form, try setting the option “File has header?” to “Yes”.
Ok, thanks for trying that. I ran a few tests, at different servers and using different versions of the tool – all fail in a similar way. I’m not sure why so will reply again once known.
To use the tool now, first run the tool Remove beginning of a file to remove the first line (header), then run the tool annotateMyIds. That worked in my tests, across servers and tool versions.
Appreciate the follow up – this was unexpected!
Update 11/16/2022
The indexes are restored at UseGalaxy.org. Prior failed runs should now complete successfully.
Thanks to all who reported the issue for their patience!
Update: This was a bug. I opened a ticket for the correction here if interested: annotateMyIDs (several versions) is not really ignoring header line when option set · Issue #2319 · galaxyproject/tools-iuc · GitHub
Until that is completed, continue to remove header lines from any inputs to this tool, no matter which server or tool version you may be using.
Thank you very much!
