# SortMeRNA have some problem with paired samples **URL:** \ **Category:** usegalaxy.org support\ **Tags:** troubleshooting, tool-help, bg\_sortmerna\ **Created:** [September 16, 2022, 5:33pm UTC](https://help.galaxyproject.org/t/sortmerna-have-some-problem-with-paired-samples/8676 "2022-09-16T17:33:15Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Pinhki](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/pinhki/32/3654_2.png) [@Pinhki](https://help.galaxyproject.org/u/Pinhki)\ **Post date:** [September 16, 2022, 5:33pm UTC](https://help.galaxyproject.org/t/sortmerna-have-some-problem-with-paired-samples/8676/1 "2022-09-16T17:33:15Z")
Hello, We have occurred some problems when using the SortMeRNA with paired end samples. We suspect our RNA seq reads have ribosomal RNA contamination and try to filter them out. However, SortMeRNA reported an error (still green but the output file is 0kb) as shown below. We were wondering which part could be wrong. All parameters are default, and we tried the non-paired option which works perfectly, but the results cannot be used for further analysis like STAR. Thank you so much for your time! ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/328121bbbd4a13e0aae27dea211b60d048c0651b.jpeg) ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [September 16, 2022, 8:17pm UTC](https://help.galaxyproject.org/t/sortmerna-have-some-problem-with-paired-samples/8676/2 "2022-09-16T20:17:42Z")
Hi @Pinhki We discussed this over email but maybe this summary helps 🙂 1. The reference needs to be input to the tool (required). It was empty last time I checked, and the `stderr` in your screenshot has that same error message. Another error I reviewed included a reference but it was in the wrong format. 2. ~~[UseGalaxy.org](http://UseGalaxy.org) does not have any references for this tool natively indexed at this time.~~ **Update April 24 2024 – References are available!** 3. **For a successful run** , you’ll need to provide a properly formatted reference yourself from the history, or consider using the tool at [UseGalaxy.eu](http://UseGalaxy.eu) (has some indexes). ---
**Author:** ![Pinhki](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/pinhki/32/3654_2.png) [@Pinhki](https://help.galaxyproject.org/u/Pinhki)\ **Post date:** [September 16, 2022, 8:38pm UTC](https://help.galaxyproject.org/t/sortmerna-have-some-problem-with-paired-samples/8676/3 "2022-09-16T20:38:45Z")
Thank you for your help and previous email! However, this is another problem I met, and I indeed inputted the reference into the tool. Actually, I downloaded all the references provided and upload them to the Galaxy. I have successfully run samples with the non-paired option, so I think the problem should be something about the paired function. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [September 16, 2022, 9:08pm UTC](https://help.galaxyproject.org/t/sortmerna-have-some-problem-with-paired-samples/8676/4 "2022-09-16T21:08:59Z")
> [@Pinhki](#): > > so I think the problem should be something about the paired function. Oh, sorry, I forgot that you asked about that. I’ll review. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [November 15, 2022, 11:42pm UTC](https://help.galaxyproject.org/t/sortmerna-have-some-problem-with-paired-samples/8676/6 "2022-11-15T23:42:54Z")