# Frequently asked questions
This section addresses common questions and issues you might encounter while using SwarmGenomics. It’s designed to help you get started quickly, troubleshoot common problems, and better understand how to use the different modules. If you don’t find your question here, please open an issue on the GitHub repository or check the documentation for the specific tool.

### Can I use the pipeline for [X] species?

SwarmGenomics is currently optimized for diploid species. While it may run on polyploid organisms, this can lead to inaccurate results due to incorrect assumptions about genome structure and heterozygosity. 

### What input files do I need?

Running through whole SwarmGenomics requires a reference genome and raw sequencing reads as SRA file or FASTQ. Most modules require a BAM, VCF, or FASTQ file, depending on the analysis step. Each module’s documentation specifies the required input.

### Can I use my own BAM/VCF/FASTQ files?

Yes. You can use files you’ve generated previously, as long as they are formatted correctly. Alternatively, you can follow the SwarmGenomics pipeline to generate them.

### Is there a recommended sequencing depth or genome size limit for using the pipeline effectively?

SwarmGenomics works best with sequencing coverage around 20–30× for the diploid individual to ensure reliable results. It can be run on lower coverage data, but results may be less accurate and less reliable. There is no strict genome size limit, though larger genomes will require more computational resources.

### I don’t have access to a powerful computer. Can I still run this?

Yes. You can run the pipeline on the de.NBI Cloud or other HPC clusters. Instructions are provided for connecting via terminal (Linux/Mac) or using PuTTY/FileZilla (Windows).

### Can I run only one part of the pipeline?

Yes. Each module is independent and can be run separately if you already have the required input files.

### My Bash script isn’t running, what should I do?

If your script doesn’t execute, it might not have the proper permissions or could have Windows-style line endings. You can fix this by:
```
# Make the script executable
chmod +x script_name.sh

# Convert Windows line endings to Unix
dos2unix script_name.sh
```
### How do I edit a file on the command line?

You can use a text editor in the terminal. Two common options are:

**nano (simple, beginner-friendly)**
```
nano filename.txt
```
- Use the arrow keys to navigate.
- Press Ctrl + O to save and Ctrl + X to exit.

**vim (more advanced)**
```
vim filename.txt
```
- Press i to enter insert mode and edit the file.
- Press Esc, then type :wq to save and quit.

### Which parameters do I need to change in params.txt before running the pipeline?
Most users only need to modify a small subset of parameters in params.txt before running SwarmGenomics. These typically include:
- Computational resources:
  - ```THREADS``` — set this according to the number of CPU cores available on your system.
- Working and software directories (required):
  - ```WORKING_DIR```, ```TOOL_DIR```, and ```SCRIPTS``` — update these to match where SwarmGenomics project, required software, and scripts are located on your system.
- Input data paths:
  - Paths to input FASTQ, BAM, or reference files are automatically constructed using ```WORKING_DIR``` and ```SPECIES```, but users should ensure their data are placed in the expected directories.

### What if I want to change a parameter and then redo a step?
Simply edit the relevant value in params.txt (for example, scaffold size or allele frequency thresholds) and run the script again. The updated parameters will be applied automatically, and the pipeline will regenerate outputs accordingly. In some cases, such as for **Genome Visualisation**, rerunning the script will only replot the existing results, and if you wish to redo for example heterozygsoity estimate, you will need to remove the previous files.

### "No such file or directory" error

This usually means the software cannot find the file at the path you provided. Double-check that the file exists, that you’re in the correct working directory, and that the file name matches exactly (case-sensitive on Linux/Mac). If your file is in another folder, be sure to include the full path.

### PSMC isn’t working or gives me an error when I run it. What should I do?

One common issue is using a fragmented or low-coverage genome, which can lead to poor consensus sequences and unreliable demographic estimates. This typically leads to a large .psmcfa file (>200 MB). Another common pitfall is incorrect input formatting (e.g., problems when converting VCF to FASTQ), so double-check your preprocessing steps.

### SRA file doesn't download properly

Large SRA files can take a long time to download, and connections may occasionally drop or timeout. To prevent interruptions, you can use a small Bash script with nohup so the download continues even if you close your terminal:
```
#!/bin/bash
# download_sra.sh
prefetch SRRXXXXXXX
```
Then run it with:
```
# make executable:
chmod +x download_sra.sh

# run:
nohup bash download_sra.sh &
```