> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list.md).

# Troubleshooting

Software > General > Troubleshooting

* [Creating custom reference genomes (non human) to use with DRAGEN apps on BaseSpace Sequence Hub](/software/general/software-general-troubleshooting-list/000007488.md)
* [DRAGEN reference differences for on instrument and standalone analysis](/software/general/software-general-troubleshooting-list/000009589.md)
* [How to demultiplex an incomplete run using bcl2fastq2 and BCL Convert](/software/general/software-general-troubleshooting-list/000003577.md)
* [How to generate FASTQs from an incomplete run in Local Run Manager](/software/general/software-general-troubleshooting-list/000001807.md)
* [How to troubleshoot a "None of the specified endpoints were reachable" error in Local Run Manager](/software/general/software-general-troubleshooting-list/000001217.md)
* [How to troubleshoot barcode collision and not enough hamming distance errors when demultiplexing runs with BCL Convert and bcl2fastq2](/software/general/software-general-troubleshooting-list/000002326.md)
* [Illumina Connected Analytics (ICA) kernel cannot connect in a Bench Workspaces](/software/general/software-general-troubleshooting-list/000007769.md)
* [Options for demultiplexing libraries with different index lengths in the same sequencing run](/software/general/software-general-troubleshooting-list/000005982.md)
* [Sample specific nucleotide error bias estimation filter and systematic noise filter in DRAGEN](/software/general/software-general-troubleshooting-list/000006989.md)
* [Troubleshooting demultiplexing issues for local DRAGEN analysis onboard the NextSeq 1000/2000](/software/general/software-general-troubleshooting-list/000003817.md)
* [Troubleshooting demultiplexing issues using BaseSpace Sequence Hub and bcl2fastq2 v2.17+](/software/general/software-general-troubleshooting-list/000002875.md)
* [Troubleshooting demultiplexing issues using Local Run Manager](/software/general/software-general-troubleshooting-list/000002862.md)
* [Troubleshooting demultiplexing issues using MiSeq Reporter](/software/general/software-general-troubleshooting-list/000002227.md)
* [Unlocking an account or resetting the password on Local Run Manager version 4](/software/general/software-general-troubleshooting-list/000009008.md)


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