# Troubleshooting

## Help

## Support Request

For debugging or support request, please include the files from the top level of the analysis output folder, the work directory and the errors directory content, in addition to the MetricsOutput.tsv from the Results folder.

### Stopping Analysis

Pressing Ctrl+C during a DRAGEN step stops the currently running analysis and might cause an FPGA error. To recover from an FPGA error, shut down and restart the server.

### Using a Non-root User

CAUTION: Do not run analyses as the root user as it can lead to permissions issues when managing data generated by the software.

### Using ssh

When running the analysis software using SSH, Illumina recommends using additional software to prevent unexpected termination of analysis. Illumina recommends `screen` and `tmux`.

### Using DAM

The Heme pipeline depends on the DRAGEN Application Manager (DAM). For issues related to the DRAGEN Application Manager installation, refer to the [DRAGEN Application Manager Installation Guide](/reference/dragen-application-manager.md).

* Ensure DRAGEN App Manager is running properly.

### Using docker

* Ensure Docker is running properly. For docker configuration help, please check the DRAGEN Application Manager installation guide and [docker.org documentation](https://docs.docker.com/reference/cli/dockerd/).

## Limitations

### CIFS Support

* In CIFS (SMB 1.0), the mounted volume may have a permission check issue and cause the Nextflow workflow to exit prematurely when a non-root user account is used for analysis, unless the filesystem permission check is disabled. The workaround is to use newer SMB protocols and configure Windows Active Directory for analysis with non-root users.

### Using multiple FASTQ files for increased coverage (top-off)

* To increase the coverage of a sample using multiple FASTQ files, the FASTQ files must follow the [Illumina naming convention](https://help.basespace.illumina.com/files-used-by-basespace/fastq-files). The current limit is up to 16 FASTQ files from 8 lanes based on available flow cell types.
* If there are more than 16 FASTQ files, then use `cat` or other command line utility to concatenate the FASTQ files as a single FASTQ file to get around the file number restriction.


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