# Troubleshooting

Software > On Instrument Analysis Software > Troubleshooting

* [Creating a custom DRAGEN reference genome for NextSeq1000/2000 analysis](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000007055)
* [Generate FASTQ from an incomplete run in Local Run Manager](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000001807)
* [How to remove a BCL file from analysis in MiSeq Reporter or Local Run Manager](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000002415)
* [Troubleshooting demultiplexing issues using Local Run Manager](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000002862)
* [Troubleshooting demultiplexing issues using MiSeq Reporter](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000002227)
* [Troubleshooting demultiplexing issues using onboard DRAGEN on the NextSeq 1000/2000](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000003817)
* [Unlocking an account or resetting the password on Local Run Manager version 4](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000009008)