Hi I recently used the featureCount to quantitate aligned reads from STAR. And, I have faced this similar error code. According to AI, it seems to be suggesting that this might be due to its incompability of the current software version. I would like to know if there is a way to fix this? Thank you!
Hi @kitchia96,
Do you see any messages pointing on error in the standard output and standard error log files? Expand black boxes by clicking at double arrow icon on the right end.
If you share your history and post link in reply, people can check the log files and job setup. History sharing: click at History options (three horizontal bars icon) in the top right corner, in the menu select Share and Manage Access, in the middle window change Make history accessible switch, copy the URL and paste it into reply.
Kind regards,
Igor
Hi @kitchia96,
I see a completed featureCounts job in your history. It seems you figured out the cause of the error.
If you click at Error icon, you’ll see:
featureCounts: unrecognized option ‘–checkFragLength’
When you kept “Check paired-end distance” option in default No, the tool works. Maybe do not activate this option to get the data.
I have not investigated, why the tool failed with “Check paired-end distance” set to Yes. You can try an older version of tool.
Kind regards,
Igor
Hello @kitchia96
There is a known bug in FeatureCounts that has been around for a while but it was just recently clarified. The correction has already been made to the code, but this is not published to the UseGalaxy servers yet.
This will likely happen over the next week or so.
For now, please follow the advice from @igor and avoid that option for now. Or, you can try to go back to a much earlier version, although you might run into other bugs, so this is exploratory advice! If you are running through a tutorial, it won’t matter too much, but if this is for a research project, you’ll want to wait if you really need the option.
Hope this helps! 