# nf-core/rnafusion: Troubleshooting

## Input files not found

If only no file, only one input file , or only read one and not read two is picked up then something is wrong with your input file declaration

1. The path must be enclosed in quotes (`'` or `"`)
2. The path must have at least one `*` wildcard character. This is even if you are only running one paired end sample.
3. When using the pipeline with paired end data, the path must use `{1,2}` or `{R1,R2}` notation to specify read pairs.
4. If you are running Single end data make sure to specify `--singleEnd`

If the pipeline can't find your files then you will get the following error

```bash
ERROR ~ Cannot find any reads matching: *{1,2}.fastq.gz
```

Note that if your sample name is "messy" then you have to be very particular with your glob specification. A file name like `L1-1-D-2h_S1_L002_R1_001.fastq.gz` can be difficult enough for a human to read. Specifying `*{1,2}*.gz` wont work give you what you want Whilst `*{R1,R2}*.gz` will.

## Data organization

The pipeline can't take a list of multiple input files - it takes a glob expression. If your input files are scattered in different paths then we recommend that you generate a directory with symlinked files. If running in paired end mode please make sure that your files are sensibly named so that they can be properly paired. See the previous point.

## Strange errors from tools

Make sure you are using the **recommended** amount of RAM. Some tools will fail because of this and will break the pipeline throwing strange error messages and codes. Some of the tools are not maintained any more and require small hacking as can be seen in some `Dockerfiles` defined in `tools/` folder.

## Extra resources and getting help

If you still have an issue with running the pipeline then feel free to contact us.
Have a look at the [pipeline website](https://github.com/nf-core/rnafusion) to find out how.

If you have problems that are related to Nextflow and not our pipeline then check out the [Nextflow gitter channel](https://gitter.im/nextflow-io/nextflow) or the [google group](https://groups.google.com/forum/#!forum/nextflow).
