# Help me with the error on mem bwa **URL:** \ **Category:** Resources\ **Tags:** gtn-tutorial, troubleshooting, bwa-mem, tool-help\ **Created:** [October 15, 2024, 6:37am UTC](https://help.galaxyproject.org/t/help-me-with-the-error-on-mem-bwa/13675 "2024-10-15T06:37:09Z")\ **Posts on this page:** 1\ **Showing post:** 2
**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:** [October 15, 2024, 7:17pm UTC](https://help.galaxyproject.org/t/help-me-with-the-error-on-mem-bwa/13675/2 "2024-10-15T19:17:49Z")
Welcome, @krupa_natrajan For an error like yours > [@krupa\_natrajan](#): > > [mem\_sam\_pe] paired reads have different names: “LH00271:14:22CCGHLT3:4:1101:27028:1080”, “LH00271:14:22CCGHLT3:4:1101:25308:1080” The tool is reporting that the two datasets input as a “pair” do not have _intact pairs_. Sometimes one end of a pair is removed during the quality assurance steps. You can adjust your quality assurance parameter settings to remove these extra _singleton_ reads, or you can remove them after. This message is from the tool directly, not from Galaxy, so the tool would work the same wherever you ran it with your data. We have another question about this that includes many more details if you are interested: [Can use BWA-MEM to concatenated files - #2 by jennaj](https://help.galaxyproject.org/t/can-use-bwa-mem-to-concatenated-files/10097/2) * * * **What to do** Not all mapping tools will expect intact pairs, and not all settings will trigger that check. But when this comes up, filtering the pairs before mapping is the usual solution. But double check your upstream quality assurance steps to make sure that how it was done is what you wanted to do. Losing one end of a pair can be a valid result! You can either adjust the settings with your trimming steps. Or, you can use tools like these to correct the pairs after: **Fastq interlacer** , then **Fastq de-interlacer**. This removes any “singletons” that are no longer paired after quality assurance. More about how to interpret fastq data is here → [Hands-on: NGS data logistics / NGS data logistics / Introduction to Galaxy Analyses](https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html) More about quality assurance and mapping is here → [Sequence analysis / Tutorial List](https://training.galaxyproject.org/training-material/topics/sequence-analysis/) We just completed a training event, and while that is now over, the materials are still published online. Slack help is not available for this, but you can use the GTN chat, and this forum instead. → [Galaxy Training Academy 2024](https://training.galaxyproject.org/training-material/events/galaxy-academy-2024.html#program) Please give that a try, and if you need more help, you can share more details. How to share your work is in the banner of this forum, or please see here directly. > [@How to get faster help with your question](https://help.galaxyproject.org/docs?topic=11469): > > How to get faster help with your question We can’t help without details! scientist Consider [Sharing your History](https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html) or posting screenshots of your [Job Information Details](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) page. Confirm the [Server URL](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting_reporting.html) (your web browser at the top!) and any [Tutorial](https://training.galaxyproject.org/) links involved. * * * Hope this helps, but we can certainly follow up more! Please let us know how this works out! 🙂 --- _[View the full topic](https://help.galaxyproject.org/t/help-me-with-the-error-on-mem-bwa/13675)._